Re: [Jmol-users] Remove Jmol Watermark
David, You make a good point. I don't remember having looked at your suggestion. Here is another possibility. Just having the word Jmol at the bottom right doesn't clue people in to the fact that it is a menu, as you said. Putting at the top left and putting a "bar" across the top - just a slightly different color or lighter shade - would lead people to think it was a menu, which it is. Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Oct 19, 2009, at 12:57 PM, David Leader wrote: Graeme wrote: Sorry if this is another silly question but is it possible to remove the bottom right "Jmol" water mark? Usually these things can?t be removed but I haven't seen an open source application do this before. In which case what are you hoping to achieve by adding it there because at the moment I feel it just gets in the way. and Angel told him how, but added: Ah, apart from teh advertising, the Jmol frank is good for opening the popup menu by left-click. Further, it opens a reduced menu based on the last item used (sort of a shortcut menu). I've bitched about this before, but I think this is bad interface design. Graeme clearly did not guess that clicking on Jmol brought up the menu because it just looks like a trademark. It would therefore be an improvement in usability if the Jmol 'frank' (an inkmark defacing your postage stamp, rather than a watermark you can only see if you hold it up to the light) were replaced by an icon indicating a pull- down menu. Some years ago I mocked up one (on the basis of comparison with standard user interfaces) and suggested it to this list, only to be met with a deafening silence, even though it incorporated the word Jmol. I can't find the page I mounted it on (or even a copy of my original email) but have found the graphic and could mount it again if people were interested. David ___ Dr. David P. Leader, Faculty of Biomedical & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 (0)141 330 5905 http://doolittle.ibls.gla.ac.uk/leader http://motif.gla.ac.uk/ The University of Glasgow, charity number SC004401 ___ -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Remove Jmol Watermark
Angel, I agree with you. I like to use the same background color for my Jmol applets too. To me the frank looks out of place when I do that so I turn it off. I would do the same if the frank was in a kind of menubar. I suppose the "menubar" could only extend as long as the word Jmol but then it wouldn't be so obvious that it is a menu. Like I said, I haven't seen David's suggestion. It might work fine. I do think having it in the top left is more likely to trigger one to think it is a menu. ******* Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Oct 19, 2009, at 3:39 PM, Angel Herráez wrote: > Jeff's right -- in principle. > But I do not like at all the idea of a menubar obscuring the Jmol > canvas. > As it is now, it can be made to nicely integrate in the webpage (by > using the same > background color). A menubar would break the charm. Also, a menubar > for a single entry > seems overkill. > Of course, someone could suggest having a menu with more entries, > but we already have > the popup menu which is there when you need it but does not obscure > the model when yu > don't. > > Regarding David's proposal to change the subtle frank for a clear > buttonlike menu, I have > doubts, and anyway will leave that for the programmers to comment on. > > > > -- > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Remove Jmol Watermark
David, I think you are right that your proposed solution is too obtrusive. Having something that indicates the pop-up menu when you mouse over the word Jmol is definitely unobtrusive. However, for the inexperienced user (who I think this is for) I don't see that being helpful What are the chances someone is going to just happen to mouse over that part of the applet so the pop-up menu becomes evident? I think a small circle with a triangle pointing up just to the right of Jmol would not get in the way and would signal to most users that there is a pop-up menu down there. Some mouse-over prompt as Bob suggested would be good in addition to that. Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Oct 20, 2009, at 5:23 AM, David Leader wrote: > I've mounted a mockup pic of the current Jmol frank and what I > proposed some years ago at: > > http://www.q7design.demon.co.uk/temp/JmolMockup.html. > > On reflection, although the drop down nature is made clear, my > proposal has a couple of defects: > > 1. It is more obtrusive than the current frank. > 2. The style reflects a single platform (here Mac OS X) and it might > be difficult to make it cross-platform. > > Perhaps some modern effect where the plain Jmol changes to a drop- > down menu on mouse-over, as has been suggested, might be a better > compromise, with developer switches for those who wanted to suppress > the frank completely etc. > > David > > > ___ > > Dr. David P. Leader, Faculty of Biomedical & Life Sciences, > University of Glasgow, Glasgow G12 8QQ, UK > Phone: +44 (0)141 330 5905 > http://doolittle.ibls.gla.ac.uk/leader > > The University of Glasgow, charity number SC004401 > ___ > > > > > > > -- > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Remove Jmol Watermark
I like the tool bar idea. A little triangle at the bottom in the middle would suffice to clue one in that it is there. And about the Mac interface, there's lots of help to get started either with the system help or with online tutorials. Once you get started I think you'll find lots of consistency and over time things will seem more intuitive. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Oct 20, 2009, at 11:21 AM, Robert Hanson wrote: I, too, think that menu-frank looks way too "in my face". The frank is supposed to be a subtle reminder of what this is; we added a little functionality to it just to enable right-mouse-less operation, I'm pretty sure. I think you have to remember that there are LOTS of unobvious things about every interface. I've recently started using a Mac, and it frustrates me no end that the designers somehow assume I know everything about the interface -- or that it is somehow "intuitive." It is not. In Jmol we have all sorts of control/alt key/mouse combinations, for example, that are equally unobvious. Generally to take care of this you need a full toolbar or menu. Before we go changing the look of Jmol, though, I suggest thinking more about what else we could do to make the interface more obvious without detracting too much from it. Maybe everything doesn't need to be in the pop-up menu only. Perhaps, for example, when you hover near the baseline of the applet a toolbar pops up that has a suite of options (including help!). Bob On Tue, Oct 20, 2009 at 7:10 AM, Jeff Hansen wrote: David, I think you are right that your proposed solution is too obtrusive. Having something that indicates the pop-up menu when you mouse over the word Jmol is definitely unobtrusive. However, for the inexperienced user (who I think this is for) I don't see that being helpful What are the chances someone is going to just happen to mouse over that part of the applet so the pop-up menu becomes evident? I think a small circle with a triangle pointing up just to the right of Jmol would not get in the way and would signal to most users that there is a pop-up menu down there. Some mouse-over prompt as Bob suggested would be good in addition to that. Jeff ******* Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Oct 20, 2009, at 5:23 AM, David Leader wrote: > I've mounted a mockup pic of the current Jmol frank and what I > proposed some years ago at: > > http://www.q7design.demon.co.uk/temp/JmolMockup.html. > > On reflection, although the drop down nature is made clear, my > proposal has a couple of defects: > > 1. It is more obtrusive than the current frank. > 2. The style reflects a single platform (here Mac OS X) and it might > be difficult to make it cross-platform. > > Perhaps some modern effect where the plain Jmol changes to a drop- > down menu on mouse-over, as has been suggested, might be a better > compromise, with developer switches for those who wanted to suppress > the frank completely etc. > > David > > > ___ > > Dr. David P. Leader, Faculty of Biomedical & Life Sciences, > University of Glasgow, Glasgow G12 8QQ, UK > Phone: +44 (0)141 330 5905 > http://doolittle.ibls.gla.ac.uk/leader > > The University of Glasgow, charity number SC004401 > ___ > > > > > > > -- > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___
Re: [Jmol-users] Remove Jmol Watermark
On Oct 20, 2009, at 12:08 PM, Robert Hanson wrote: > > And about the Mac interface, there's lots of help to get started > either with the system help or with online tutorials. Once you get > started I think you'll find lots of consistency and over time things > will seem more intuitive. > > > The same is true for Jmol...;) > Yes. And organic chemistry and lots of other things that seem to not make sense at first but with a little effort (well worth it) do make sense. : ) Jeff -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] feedback appreciated
Lets just go extreme with this. Make every side of the applet available for adjusting something. I could see zoom, Z-rotation, slab, atom size. Why not just make it configurable so a little javascript or Jmol script can assign a property to a particular side and we can adjust whatever we want to adjust? Kind of a built in slider. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Nov 18, 2009, at 4:12 PM, Robert Hanson wrote: maybe the bottom 2%? 2009/11/18 Angel Herráez On 18 Nov 2009 at 13:17, Robert Hanson wrote: > OK, please take another look at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm Nice! This brings an idea: how about having also the 6% top of the applet do Z-rotation? It's often difficult to do that by shift-horizDrag without changing zoom (yes, I know there are specific ways of doing just Zrot, but I never remember or care to) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] NWChem output produces pink balls
I've seen this before too - I believe in .mol files output from Spartan. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Dec 1, 2009, at 1:48 PM, Angel Herráez wrote: > This happens at times with pdb files that have the wrong position of > atom IDs (typically, > shifted by one column position). Jmol does not identify the element, > then makes it unknown, > with is colored pink and sized as a smallish sphere. > Don't know how the NWChem specifies the element, but looks a similar > problem. The file > open parser is the likely culprit (well, it really is the file > writer). > > > -- > Join us December 9, 2009 for the Red Hat Virtual Experience, > a free event focused on virtualization and cloud computing. > Attend in-depth sessions from your desk. Your couch. Anywhere. > http://p.sf.net/sfu/redhat-sfdev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] what is Jmol for?
Jmol is modular already is it not? As it stands now only portions of Jmol are loaded initially then others as needed. Am I right about that? If so it seems these graphing features could be pulled out and packaged together. Then if Jmol needs them they can be loaded. If Sage or anyone else wants to use that portion of Jmol or any other part they ought to be able to do that without necessarily having to use all of Jmol. This could be spun off as a new SourceForge project as Bob suggested and still be used by Jmol. As Tom said, it may prove useful in unexpected ways. Starting a new SourceForge project would not preclude continuing to use it in Jmol. Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Dec 16, 2009, at 3:44 PM, Thomas Stout wrote: While the plotting functionality may not be directly molecular- centric, I don't see how it detracts from Jmol. If the program were to become "bloat-ware" then yes, of course, that's a problem. For the moment it seems to be constrained within the bounds of scientific functionalities that many of us will use and/or be interested in. I think having flexible 3D surface descriptors and routines may prove to be very useful in ways that may not be fully appreciated as yet -- I'd vote for keeping it all in one package for the time being! -Tom On Wed, Dec 16, 2009 at 12:22 PM, Robert Hanson wrote: Rich, Good point. Yes, yes. I was just thinking the same thought this morning myself. It's nice that the Sage community has caught on to how useful Jmol is for general surface display. If the Jmol community, though, feels that displaying data in graphical form is outside the bounds of the project, they should speak up, and a new SourceForge project could be started that starts with what we have in Jmol but pulls out all the molecular business and focuses on the mathematical. So far all the additions that have helped Sage have also been a benefit for general molecular surface drawing -- the ability to draw contours, better mesh drawing, consolidation in code of pmesh and isosurface. These are all modifications that have helped all. But I agree, the business with axes and tics and such is pretty far afield of the core Jmol mission. Bob On Wed, Dec 16, 2009 at 1:01 PM, wrote: As interesting as it is to plot stuff I really don't see the purpose of putting time and effort into making Jmol a generic 3D plotting program. Maybe if its abilities and interface were perfected for plotting molecules (large and small) then there might be some impetus to create Jplot (or something) to be able to plot any 3D surface with intelligent tic marks and axis selection etc. Rich -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --
Re: [Jmol-users] what is Jmol for?
So perhaps we need to brainstorm on what features related to display of small and large molecules we want to see added to Jmol. It is difficult to think of some. Jmol is so full of features now. Or maybe it is just my brain is too fuzzy from grading and this cold I've got. So what are things you can't currently do now or wish were easier to do? I find it difficult to extract data, such as energies, out of files. Probably just my neophyte javascript skills. But I wonder if when the files are read in an array could be created containing such data so it could be easily retrieved. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Dec 16, 2009, at 5:35 PM, rgb wrote: > It detracts from the time devoted to the development of Jmol more than > anything else. I don't disagree that some things might be of interest > down the road but given the limited development resources I think they > should be focused on the functionality related to the display of small > and large molecules and the user interface of that use. If others from > Sage or another environment want to build on Jmol's display capability > then that is great and could be encouraged. Jmol is pretty modular and > incorporating new functionality in some optional modules shouldn't > be a > problem. > > Rich > > Thomas Stout wrote: >> >> While the plotting functionality may not be directly >> molecular-centric, I don't see how it detracts from Jmol. If the >> program were to become "bloat-ware" then yes, of course, that's a >> problem. For the moment it seems to be constrained within the bounds >> of scientific functionalities that many of us will use and/or be >> interested in. I think having flexible 3D surface descriptors and >> routines may prove to be very useful in ways that may not be fully >> appreciated as yet -- I'd vote for keeping it all in one package for >> the time being! >> >> -Tom >> >> >> >> On Wed, Dec 16, 2009 at 12:22 PM, Robert Hanson > <mailto:hans...@stolaf.edu>> wrote: >> >>Rich, >> >>Good point. >> >>Yes, yes. I was just thinking the same thought this morning >>myself. It's nice that the Sage community has caught on to how >>useful Jmol is for general surface display. If the Jmol >>community, though, feels that displaying data in graphical form is >>outside the bounds of the project, they should speak up, and a new >>SourceForge project could be started that starts with what we have >>in Jmol but pulls out all the molecular business and focuses on >>the mathematical. >> >>So far all the additions that have helped Sage have also been a >>benefit for general molecular surface drawing -- the ability to >>draw contours, better mesh drawing, consolidation in code of pmesh >>and isosurface. These are all modifications that have helped all. >> >>But I agree, the business with axes and tics and such is pretty >>far afield of the core Jmol mission. >> >>Bob >> >> >> >>On Wed, Dec 16, 2009 at 1:01 PM, ><mailto:r...@ellerbach.com>> wrote: >> >>As interesting as it is to plot stuff I really don't see the >>purpose of >>putting time and effort into making Jmol a generic 3D plotting >>program. >>Maybe if its abilities and interface were perfected for >>plotting molecules >>(large and small) then there might be some impetus to create >>Jplot (or >>something) to be able to plot any 3D surface with intelligent >>tic marks >>and axis selection etc. >> >>Rich >> > > > -- > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] GUI javascript color picker widget for Jmol, please look at and vote on inclusion in Jmol.js...
Very nice! *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jan 2, 2010, at 4:35 PM, Jonathan Gutow wrote: > Dear Jmol Users: > > (What I did on my holiday break...:)) As part of my work on the Jmol > interface for the SAGEmath project, I have put together a color picker > box that pops up a palette of colors to choose from and then passes > the user's choice into a Jmol script which is then passed to the > applet. I don't think it would take much more effort to make this > work as part of Jmol.js. However, before I and possibly other people > put any effort towards that, I wanted to find out if the Jmol > community thinks this is something they would use. > > Please take a look at the example page showing the color picker box in > action to see what I'm talking about: > > http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Jmol%20Color%20Picker%20Test.html > > Then please vote directly to this list with a > > yes or +1 (for you would like to see it included) > > or > > no or -1 (for you can't see a use for this) > > Also comments about how it looks or functions would be useful. > > Then I and other people working on Jmol development can decide how > much more effort to put towards this. > > Thanks, > Jonathan > Dr. Jonathan H. Gutow > Chemistry Department gu...@uwosh.edu > UW-Oshkosh Office:920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/facstaff/gutow > > > > > > > -- > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] GUI javascript color picker widget for Jmol, please look at and vote on inclusion in Jmol.js...
I can see this possibly being good (I mean embedded within the applet & accessed through a pop-up.. It would somehow have to be context sensitive. In other words, coloring whatever is selected and maybe if nothing is selected coloring the background. There was some discussion a few weeks ago about having different sides of the applet activate different pop-ups when mousing to them. Perhaps the color pop-up could be activated when mousing to a particular corner? Not sure I like that better than Jonathan's original implementation. Just thought I would suggest it and see what people think. ******* Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jan 4, 2010, at 5:54 PM, Thomas Stout wrote: > > > Oh! I meant to have the whole "dealie" embedded within the Jmol applet & > accessed through a pop-up window/menu, rather than in the html portion of the > web page -- I guess that is what would happen if it were incorporated into > Jmol.js?? > > -Tom > > > > On Mon, Jan 4, 2010 at 2:43 PM, Jonathan Gutow wrote: > > On Jan 4, 2010, at 2:55 PM, jmol-users-requ...@lists.sourceforge.net > wrote: > > > Date: Mon, 4 Jan 2010 12:55:50 -0800 > > From: Thomas Stout > > Subject: Re: [Jmol-users] GUI javascript color picker widget for Jmol, > > please look at and vote on inclusion in Jmol.js... > > To: jmol-users@lists.sourceforge.net > > Message-ID: > > <75750581001041255q3c4413b8s6a3ea5b69c40e...@mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > I think this would make a very useful addition to Jmol! Is there a > > way to > > vote >+1 ?! :) > Tom, > Thanks! > > > > One thought for future implementation: I would love to utilize it as a > > pop-up color selection menu/window, so that it's there when needed > > but not > > occupying screen space other times... > Not sure what you mean here. Do you want something smaller than the > two little squares that the colorpicker pops up from? I have thought > about a more general color picker that is not specific to Jmol, is > that what you want? > > Jonathan > > Dr. Jonathan H. Gutow > Chemistry Department gu...@uwosh.edu > UW-Oshkosh Office:920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/facstaff/gutow > > > > > > > -- > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Requesting opinions on how organization for Jmol JavaScript Widgets Package...
I think a page on the wiki with a description of each individual wiki and a download link (and links for any .js supporting files) would be great. Then people could go grab whatever they needed. One stop shopping. I think part of the description should be a clear attribution of whoever contributed the widget so we could give proper credit when we use it. I think a series of widgets that pulled bits of data from files would be great. I know I've had a need to grab energies out of multiple model xyz files. I've seen posts from others asking for help on the best way to grab other bits of data (hetnam or something recently I believe). Many of these files contain a wealth of data that is certainly available but not always trivial to get at. Jmol is great at visualizing the molecules and provides the tools to get at and manipulate data. Providing some widgets to help would make it that much more useful. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jan 9, 2010, at 4:57 PM, Jonathan Gutow wrote: > Dear Jmol Community: > Starting with the minimalist pop-up color picker I've been working on > I have begun to build a package of Jmol JavaScript Widgets. My > question to the community is do you want one .js file or would it be > better to have to load separate files for each widget and possibly > separate supporting .js files as well? > For the color picker I use a bitmap generator available under the > Apache License. I just folded it into the JmolWidgets.js file I'm > building, but realized I will have to include a lot of other librarys > to make sliders and some other widgets work. > As an aside, what other widgets do people want? > > Jonathan > Dr. Jonathan H. Gutow > Chemistry Department gu...@uwosh.edu > UW-Oshkosh Office:920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/facstaff/gutow > > > > > > > -- > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol usually not displaying molecule
Here is what happened on my MacBook Pro running OS X 10.6.2 with Java 1.6.0_17. After entering the ~alert(bobFile); then clicking on Run I got the following: Marvin 12290623562D 23 26 0 0 0 0999 V2000 4.35080.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 3.63630.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 3.6363 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 4.3508 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0 0 5.0653 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 5.06530.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 5.77970.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 5.7797 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0 0 6.4942 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 6.49420.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 6.49421.72160. C 0 0 0 0 0 0 0 0 0 0 0 0 5.77971.30910. C 0 0 0 0 0 0 0 0 0 0 0 0 7.20870.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 7.20871.30910. C 0 0 0 0 0 0 0 0 0 0 0 0 6.9067 -0.64290. C 0 0 0 0 0 0 0 0 0 0 0 0 7.6212 -0.23040. C 0 0 0 0 0 0 0 0 0 0 0 0 8.4181 -0.44390. C 0 0 0 0 0 0 0 0 0 0 0 0 3.9383 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0 4.7633 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0 7.92311.72160. O 0 0 0 0 0 0 0 0 0 0 0 0 5.06530.89660. C 0 0 0 0 0 0 0 0 0 0 0 0 5.0653 -1.57850. H 0 0 0 0 0 0 0 0 0 0 0 0 5.7797 -0.34090. H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 6 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 18 1 0 0 0 0 4 19 1 0 0 0 0 6 5 1 0 0 0 0 I'm pretty sure this was not the end of the file. The window that popped up containing this seemed to extend off the bottom of the screen and I couldn't scroll down. Hitting return closed the window (normal for an alert). Next I entered the second command, ~document.getElementById(pickApplet).loadInlineString(bobFile, "", false); This loaded a new molecule. The molecule was strange in that it was completely flat with several atoms overlapping. I don't know if that is how the structure should be, but it looked very odd. Hope this helps. ******* Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jan 13, 2010, at 9:46 PM, Otis Rothenberger wrote: > Hi Again Bob, > > I don't know if this will help, but I put your latest coordinate file > string into a JavaScript variable called bobFile on the following > page: > > http://chemagic.com/web_molecules/script_page_large.aspx > > bobFile was not altered. It has the \n's. > > The page uses Jmol 11.9.9. > > There is a JavaScript Jmol Script execution field on the page. > JavaScript commands require a leading tilde. Further, the tilde must > be the first character in the field with no space between the tilde > and the JavaScript command. Click Run to see script results. On my > Windows XP platform, the following commands are instructive: > > ~alert(bobFile); > > ~document.getElementById(pickApplet).loadInlineString(bobFile, "", false); > > pickApplet is my variable for the applet name. The above command, > including the tilde, is good to go. Remember, the tilde makes my page > interpret this as JavaScript. > > On my machine, the alert, of course, shows the string, sans the \n - > i.e. Jmol is reading them as intended. The direct call of the applet > method properly loads the string. > > I should mention that I do not use jmol.js. I use a cross browser object tag. > > I do not have quick access to a Mac, so I'm interested in how a Mac > responds to this page. I hope the above information is of some use to > you. As an aside, check out Jmol's UFF fuction on your model once > (if?) it loads (UFF link). I think this relatively new addition to > Jmol is really neat. > > Otis > > -- > Otis Rothenberger > http://chemagic.org > > -- > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for Conference > attendees to learn about information security's most important issues through > interactions with peers, luminaries and emer
Re: [Jmol-users] Jmol usually not displaying molecule
Forgot to mention this was with Safari 4.0.4. Pretty much the same behavior in Firefox 3.5.6. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jan 13, 2010, at 10:24 PM, Jeff Hansen wrote: > Here is what happened on my MacBook Pro running OS X 10.6.2 with Java > 1.6.0_17. After entering the ~alert(bobFile); then clicking on Run I got the > following: > > Marvin 12290623562D > > 23 26 0 0 0 0999 V2000 >4.35080.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 >3.63630.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 >3.6363 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 >4.3508 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0 0 >5.0653 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 >5.06530.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 >5.77970.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 >5.7797 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0 0 >6.4942 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 >6.49420.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 >6.49421.72160. C 0 0 0 0 0 0 0 0 0 0 0 0 >5.77971.30910. C 0 0 0 0 0 0 0 0 0 0 0 0 >7.20870.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 >7.20871.30910. C 0 0 0 0 0 0 0 0 0 0 0 0 >6.9067 -0.64290. C 0 0 0 0 0 0 0 0 0 0 0 0 >7.6212 -0.23040. C 0 0 0 0 0 0 0 0 0 0 0 0 >8.4181 -0.44390. C 0 0 0 0 0 0 0 0 0 0 0 0 >3.9383 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0 >4.7633 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0 >7.92311.72160. O 0 0 0 0 0 0 0 0 0 0 0 0 >5.06530.89660. C 0 0 0 0 0 0 0 0 0 0 0 0 >5.0653 -1.57850. H 0 0 0 0 0 0 0 0 0 0 0 0 >5.7797 -0.34090. H 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 0 > 1 6 1 0 0 0 0 > 2 3 1 0 0 0 0 > 3 4 1 0 0 0 0 > 4 5 1 0 0 0 0 > 4 18 1 0 0 0 0 > 4 19 1 0 0 0 0 > 6 5 1 0 0 0 0 > > I'm pretty sure this was not the end of the file. The window that popped up > containing this seemed to extend off the bottom of the screen and I couldn't > scroll down. Hitting return closed the window (normal for an alert). > > Next I entered the second command, > ~document.getElementById(pickApplet).loadInlineString(bobFile, "", false); > This loaded a new molecule. The molecule was strange in that it was > completely flat with several atoms overlapping. I don't know if that is how > the structure should be, but it looked very odd. > > Hope this helps. > > > *** > Jeff Hansen > Department of Chemistry and Biochemistry > DePauw University > 602 S. College Ave. > Greencastle, IN 46135 > jhan...@depauw.edu > *** > > > On Jan 13, 2010, at 9:46 PM, Otis Rothenberger wrote: > >> Hi Again Bob, >> >> I don't know if this will help, but I put your latest coordinate file >> string into a JavaScript variable called bobFile on the following >> page: >> >> http://chemagic.com/web_molecules/script_page_large.aspx >> >> bobFile was not altered. It has the \n's. >> >> The page uses Jmol 11.9.9. >> >> There is a JavaScript Jmol Script execution field on the page. >> JavaScript commands require a leading tilde. Further, the tilde must >> be the first character in the field with no space between the tilde >> and the JavaScript command. Click Run to see script results. On my >> Windows XP platform, the following commands are instructive: >> >> ~alert(bobFile); >> >> ~document.getElementById(pickApplet).loadInlineString(bobFile, "", false); >> >> pickApplet is my variable for the applet name. The above command, >> including the tilde, is good to go. Remember, the tilde makes my page >> interpret this as JavaScript. >> >> On my machine, the alert, of course, shows the string, sans the \n - >> i.e. Jmol is reading them as intended. The direct call of the applet >> method properly loads the string. >> >> I should mention that I do not u
Re: [Jmol-users] RFC - proposal for hetero subentries in popup menu
How about selecting aromatic rings or different functional groups? *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jan 23, 2010, at 11:31 AM, Angel Herráez wrote: > You have a point, Rich, but what kind of options could we have for nonprotein > molecules? > There is select by element and by symmetry already. The list of selectable > elements could > be certainly expanded (ideally, to cover all elements present in the model, > as it is done for > amino acids). > > The whole business of residue name and chemical nature is tied to proteins > and nucleic > acids. > > The atom expressions are documented at http://wiki.jmol.org/index.php/AtomSets > > I am going to collect bits of thought and proposals at a new > http://wiki.jmol.org/index.php/AtomSets/Popup_Menu > > please, feel free to add any comments there (maybe in the Talk page if you > don't want to > insert actual content) > > > > > -- > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for Conference > attendees to learn about information security's most important issues through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Prevent applet resizing with browser zoom?
If the applet were within a div of defined size would the size of the div stay the same and thereby keep the applet the same size? Don't know but thought maybe this could be a solution? *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Mar 3, 2010, at 11:58 AM, Rolf Huehne wrote: > Hi all, > > I noticed today that the Jmol applet is resized in the main browsers > (recent versions of IE, Firefox, Chrome, Safari, Opera) with a zoom change. > Unfortunately this makes it difficult to set a defined applet size for > exporting a snapshot image. The applet size is always scaled > additionally by the zoom factor, compared to the initial size. > The applet is currently resized within our Jena3D viewer by setting the > CSS properties "width" and "height". > Does anyone know a reliable way to resize the applet without this > additional scaling factor? > (I would really like to avoid having to instruct the users to reset the > zoom level to be able to define the applet size. Or in some browsers to > set the option "zoom text only".) > > Regards, > Rolf > > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Appending frames to a trajectory
I don't think that is what he needs. How about this idea though. Rather than append points to the trajectory as you go along. Concatenate those points to the end of your trajectory file then reload the trajectory. So, when you read in the initial file and initial trajectory I assume that trajectory file has just one point. As you generate new points along the trajectory you need to add those points to the end of the trajectory file. The trajectory file is just a text file right? So write the new coordinates to the end of that text file then reload the trajectory file. This I believe would all be done outside of Jmol using javascript (to rewrite the trajectory file) then tell Jmol to reload the trajectory file. Is that what you need? *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Mar 19, 2010, at 8:34 AM, Robert Hanson wrote: > I think I understand. You have a set of models, each in a different PDB file, > which together represent a set of trajectories -- meaning there is a 1:1 > homology between atoms in one model to the next. > > The very simplest way to load these as a trajectory is to concatenate the > files into one large file, then read that file as a trajectory. You can still > select specific models from that file to load or just load the whole thing. > > Is that perhaps all you need? > > Bob > > On Fri, Mar 19, 2010 at 6:59 AM, Andrew R Turner > wrote: > > Hi Angel, > > I probably was not very clear. As I understand it, when you use: > > load TRAJECTORY file > > you get one set of atoms and 'number-of-frames' sets of coordinates > (one set of coordinates for each model/frame in the file). > > All my files will have one model in them. What I want to do is have: > > load file > > to get the initial atom set and initial coordinates. Then have a loop: > > for i=1, nframe >load file(i) > end > > that appends just the coordinates to the data that is already loaded > without creating a new atom set. (This is essentially splitting up the > "load TRAJECTORY file" command into its component parts.) > > set appendNew false > > will not help me I do not think as it will add new frames (which is > what I want to be able to animate the trajectory), it will just append > the atoms in the appended file to the current frame. > > Cheers > Andy > > Quoting Angel Herráez : > > > Hi Andy > > > > I'm not sure I understand what you mean by adding a trajectory point > > (I haven't worked with > > trajectories), but regarding the addition of atoms without > > generating new frame/model, there > > is > > > > set appendNew false > > > > Don't know if that would fix the slowness. > > > > > > > > -- > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > ___ > > Jmol-users mailing list > > Jmol-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > > == > Dr Andrew R. Turner > e: andrew.tur...@ed.ac.uk > t: +44 (0)131 651 3578 > p: EPCC, University of Edinburgh EH9 3JZ > == > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we wan
Re: [Jmol-users] Drag and drop into signed applet
All three of the links on that page worked for me on Mac OS X 10.6.3 and Safari 4.0.4. However, when I tried to drag a pdb file from a Finder window, I got a FileNotFoundException. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Apr 14, 2010, at 11:03 AM, Robert Hanson wrote: > Possibly valuable: > > Jmol 12.0.RC5 adds drag-and-drop capability for the signed applet and adds > MULTIPLE-FILE drag-and-drop for both SIGNED applet and application. Just fire > up a page such as simple.htm that uses the signed > applet and then select and drag from a directory listing into the applet as > many files as you like. They will be loaded into different frames, and > frame *;reset will be issued so that they are all displayed. If set > defaultLoadScript is defined, then that script will be executed. (For > example, a simple one might be set defaultLoadScript \'select protein or > nucleic;cartoons only\'.) Needs testing on Macs. > > Using MSIE and Firefox links to scripts or files can be dragged into the > applet. > > Using MSIE Jmol-created PNG and JPG images can be dragged into the applet. > > If someone with a Mac would try this at > > http://chemapps.stolaf.edu/jmol/docs/examples-11/drop.htm > > that would be helpful. It offers quite an interesting way to operate. > > Thanks. > > Bob > > > > > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Drag and drop into signed applet
Success!! I was able to drag and drop one or multiple files from the Finder to the applet. I was even able to drag and drop files from different folders. Question: Once the two structure are loaded, is there a simple way to select one and either translate it or rotate it while not changing the other? By simple I mean with mouse actions. I know it could be done via the console. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Apr 14, 2010, at 12:59 PM, Robert Hanson wrote: > I JUST updated again -- this time I have all functions working in MSIE > and Mozilla -- > > drop image with link, > drop image without link, > drop link > drop one file from hard drive > drop multiple files from hard drive > > So do please test that with the Mac. Be sure to close and reopen browser > > Bob > > On Wed, Apr 14, 2010 at 11:50 AM, Robert Hanson wrote: > OK, I got it working in FF. > > Jeff, can you try that again and report back what the error message is saying? > > Close and reopen your browser -- I updated all files. > > > http://chemapps.stolaf.edu/jmol/docs/examples-11/drop.htm > > On Wed, Apr 14, 2010 at 10:25 AM, Jeff Hansen wrote: > All three of the links on that page worked for me on Mac OS X 10.6.3 and > Safari 4.0.4. However, when I tried to drag a pdb file from a Finder window, > I got a FileNotFoundException. > > > *** > Jeff Hansen > Department of Chemistry and Biochemistry > DePauw University > 602 S. College Ave. > Greencastle, IN 46135 > jhan...@depauw.edu > *** > > > On Apr 14, 2010, at 11:03 AM, Robert Hanson wrote: > >> Possibly valuable: >> >> Jmol 12.0.RC5 adds drag-and-drop capability for the signed applet and adds >> MULTIPLE-FILE drag-and-drop for both SIGNED applet and application. Just >> fire up a page such as simple.htm that uses the >> signed applet and then select and drag from a directory listing into the >> applet as many files as you like. They will be loaded into different frames, >> and frame *;reset will be issued so that they are all displayed. If >> set defaultLoadScript is defined, then that script will be executed. >> (For example, a simple one might be set defaultLoadScript \'select >> protein or nucleic;cartoons only\'.) Needs testing on Macs. >> >> Using MSIE and Firefox links to scripts or files can be dragged into the >> applet. >> >> Using MSIE Jmol-created PNG and JPG images can be dragged into the applet. >> >> If someone with a Mac would try this at >> >> http://chemapps.stolaf.edu/jmol/docs/examples-11/drop.htm >> >> that would be helpful. It offers quite an interesting way to operate. >> >> Thanks. >> >> Bob >> >> >> >> >> -- >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr
Re: [Jmol-users] Drag and drop into signed applet
All worked fine for me, including drag and drop of multiple files from multiple
folders in Finder. On Firefox 3.6 and OS X 10.6.3.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 14, 2010, at 1:51 PM, Philip Bays wrote:
> Bob:
>
> On the mac I can drop either image or the link onto Jmol successfully in
> Safari. However, in Firefox I can only drop the link. I get an error
> message with either of the images. ("unrecognized file format for file
> string")
>
> Phil
>
> On Apr 14, 2010, at 12:59 PM, Robert Hanson wrote:
>
>> I JUST updated again -- this time I have all functions working in MSIE
>> and Mozilla --
>>
>> drop image with link,
>> drop image without link,
>> drop link
>> drop one file from hard drive
>> drop multiple files from hard drive
>>
>> So do please test that with the Mac. Be sure to close and reopen browser
>>
>> Bob
>>
>> On Wed, Apr 14, 2010 at 11:50 AM, Robert Hanson wrote:
>> OK, I got it working in FF.
>>
>> Jeff, can you try that again and report back what the error message is
>> saying?
>>
>> Close and reopen your browser -- I updated all files.
>>
>>
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/drop.htm
>>
>> On Wed, Apr 14, 2010 at 10:25 AM, Jeff Hansen wrote:
>> All three of the links on that page worked for me on Mac OS X 10.6.3 and
>> Safari 4.0.4. However, when I tried to drag a pdb file from a Finder
>> window, I got a FileNotFoundException.
>>
>>
>> ***
>> Jeff Hansen
>> Department of Chemistry and Biochemistry
>> DePauw University
>> 602 S. College Ave.
>> Greencastle, IN 46135
>> jhan...@depauw.edu
>> ***
>>
>>
>> On Apr 14, 2010, at 11:03 AM, Robert Hanson wrote:
>>
>>> Possibly valuable:
>>>
>>> Jmol 12.0.RC5 adds drag-and-drop capability for the signed applet and adds
>>> MULTIPLE-FILE drag-and-drop for both SIGNED applet and application. Just
>>> fire up a page such as simple.htm that uses the
>>> signed applet and then select and drag from a directory listing into the
>>> applet as many files as you like. They will be loaded into different
>>> frames, and frame *;reset will be issued so that they are all
>>> displayed. If set defaultLoadScript is defined, then that script
>>> will be executed. (For example, a simple one might be set
>>> defaultLoadScript \'select protein or nucleic;cartoons only\'.) Needs
>>> testing on Macs.
>>>
>>> Using MSIE and Firefox links to scripts or files can be dragged into the
>>> applet.
>>>
>>> Using MSIE Jmol-created PNG and JPG images can be dragged into the applet.
>>>
>>> If someone with a Mac would try this at
>>>
>>> http://chemapps.stolaf.edu/jmol/docs/examples-11/drop.htm
>>>
>>> that would be helpful. It offers quite an interesting way to operate.
>>>
>>> Thanks.
>>>
>>> Bob
>>>
>>>
>>>
>>>
>>> --
>>> Download Intel® Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>> --
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemist
Re: [Jmol-users] Want some opinions on rotation about bond before posting a feature request...
How about hovering over the bond instead of atoms, or at least a single click
on the bond instead of having to click two atoms.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 14, 2010, at 1:43 PM, Otis Rothenberger wrote:
> Hi Jonathan,
>
> I'm working on this right now. Currently, we use unbind and bind to
> allow mouse rotation and translation of separate models in a Jmol
> window. In the same application, we use the two atom click system that
> you mention for bond rotation definition. This is followed by the need
> to click a rotate button. I'm trying to use the same logic that we use
> with the independent movement of molecules via mouse movement. I think
> it's doable.
>
> While the feature (independent movement of two model) must be turned on
> and off, it's painless once it's on. A hover callback does all the
> required selection. That's the part of the code that I'm working on now
> for bond rotation. Writing an appropriate hover callback for the bond
> rotation. I will say that so far I see no way around the two atom click
> definition of the bond axis. If anyone has an idea of how a hover
> callback could define this, please send suggestions. In the case of
> using hover to define (select) one or the other model of a two model
> system, it's pretty easy. They are not connected. For a single connected
> system, hover could select the hovered atom and maybe even pick up the
> required second atom, but subsequent mouse movement could easily screw
> up these selections.
>
> Otis
>
>
>
>
>
> On 4/14/2010 1:14 PM, Jonathan Gutow wrote:
>> Dear Jmol Users,
>>
>> One of my colleagues asked for an easier way to do rotation about a
>> bond than selecting the atoms in a group and then using
>> "rotateSelected {ID of atom 1 of bond} {ID of atom 2 of bond}". They
>> would like some kind of a GUI interface that students could use. I
>> think clicking on atoms to select them is OK. It is having to use the
>> command that is a problem. Any thoughts on how this should work?
>> There is something working in a recent version of RasMol according to
>> this colleague. Avogadro and Spartan also have relatively elegant ways
>> of doing this. Once a general consensus is reached I will add it to
>> the feature request list.
>>
>> Jonathan
>> Dr. Jonathan H. Gutow
>> Chemistry Department gu...@uwosh.edu
>> UW-Oshkosh Office:920-424-1326
>> 800 Algoma Boulevard FAX:920-424-2042
>> Oshkosh, WI 54901
>> http://www.uwosh.edu/facstaff/gutow
>>
>>
>>
>>
>>
>>
>> --
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Want some opinions on rotation about bond before posting a feature request...
Otis, Unfortunately, this does not work if you don't have a wheel. On my MacBook Pro I use two-finger scrolling as an equivalent to a scroll wheel. In other words, moving two fingers up or down on the touch pad scrolls up or down (works left or write too). Is it possible to bind to control and two-finger scrolling? Even outside of using a MacBook Pro, I'm sure not everyone uses a scroll wheel. Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Apr 15, 2010, at 1:01 AM, Otis Rothenberger wrote: > Jeff and Jonathan- > > A single click on a bond would be nice, but I think only atoms (and possibly > draw objects???) can pass to a clickcallback. > > This is very tentative, so I put it on the department server rather than the > chemagic server: > > http://www.che.ilstu.edu/osrothen/web_molecules/script_page_large.aspx > > Click Display Molecular Editor. At the Bond Rotation group, clicking the set > rotation link will prompt you to click two atoms to define a bond. The first > click is the anchor atom, and the second click defines the group that moves. > > The rotate link still works, but that's going to go. The rotation about the > defined bond is now tied to mouse actions: > > CTRL-WHEEL rotates on way > CTRL-ALT-WHEEL rotates the other way > > It would be nice to use CTR-WHEEL only with forward and backward wheel going > in different directions, but I can't find a feedback for wheel direction - > just feedback for wheel action. > > I don't know if Macs have an ALT? There are other bindings that can be used, > but the wheel binding is appropriate for this kind of action. > > Jonathan, It may be that users would like this type of feature built in, and > the users group may want to encourage developers to go in that direction. As > a user, I just had this on my to do list, so your note gave me the push that > I needed to get it done. I think you were on the mark in your original note. > The ability to rotate about bonds with a fair degree of ease is important. > > Best Regards, Otis > > > On 4/14/2010 2:21 PM, Jeff Hansen wrote: >> >> How about hovering over the bond instead of atoms, or at least a single >> click on the bond instead of having to click two atoms. >> >> >> *** >> Jeff Hansen >> Department of Chemistry and Biochemistry >> DePauw University >> 602 S. College Ave. >> Greencastle, IN 46135 >> jhan...@depauw.edu >> *** >> >> > > -- > Otis Rothenberger > chemagic.com > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Want some opinions on rotation about bond before posting a feature request...
Still does not work with a trackpad.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 15, 2010, at 8:19 AM, Otis Rothenberger wrote:
> Jeff and Jonathan-
>
> Here's a Mac fix, I hope!
>
> First, I forgot. There is a WHEEL direction feedback. That allows this to be
> a bit more compact:
>
> Mac (without wheel): After defining the two atoms with the set rotation link,
> CTRL-RIGHT will rotate the moving group. Remember, the first clicked atom is
> the anchor.
>
> For a WHEEL mouse: The above will work, or you can use CTRL-WHEEL
>
> Because I can get direction feedback in both cases, both directions of
> rotation are possible with each mouse action - (WHEEL forward/backward or
> MOUSE +Y/-Y)
>
> I'm stepping on a the Jmol CTR-RIGHT for pop menu, but CTRL-LEFT also brings
> up the menu.
>
> The code for this is pretty simple. Recently, Bob posted a note on Jmol
> global variables, and understanding global variables makes this task pretty
> easy. In the load script, two global variables are defined, rot1 and rot2.
> That allows the following global binding:
>
> unbind 'CTRL-LEFT'; bind 'CTRL-LEFT' 'select WITHIN(BRANCH,{atomIndex =
> rot1}, {atomIndex = rot2});rotateSelected {atomIndex = rot1} {atomIndex =
> rot2} @{_DELTAY*1};'
>
> The select rotation link simply needs to puts atomIndex numbers into rot1 and
> rot2 prior to the rotation. There may be slicker ways to fill rot1 and rot
> prior to rotation. I'm open to suggestions.
>
> I still have not put this on chemagic. It's at:
> http://www.che.ilstu.edu/osrothen/web_molecules/script_page_large.aspx
>
> Best, Otis
>
> On 4/15/2010 2:13 AM, Jeff Hansen wrote:
>>
>> Otis,
>>
>> Unfortunately, this does not work if you don't have a wheel. On my MacBook
>> Pro I use two-finger scrolling as an equivalent to a scroll wheel. In other
>> words, moving two fingers up or down on the touch pad scrolls up or down
>> (works left or write too). Is it possible to bind to control and two-finger
>> scrolling? Even outside of using a MacBook Pro, I'm sure not everyone uses
>> a scroll wheel.
>>
>>
>> Jeff
>>
>>
>> ***
>> Jeff Hansen
>> Department of Chemistry and Biochemistry
>> DePauw University
>> 602 S. College Ave.
>> Greencastle, IN 46135
>> jhan...@depauw.edu
>> ***
>>
>>
>> On Apr 15, 2010, at 1:01 AM, Otis Rothenberger wrote:
>>
>>> Jeff and Jonathan-
>>>
>>> A single click on a bond would be nice, but I think only atoms (and
>>> possibly draw objects???) can pass to a clickcallback.
>>>
>>> This is very tentative, so I put it on the department server rather than
>>> the chemagic server:
>>>
>>> http://www.che.ilstu.edu/osrothen/web_molecules/script_page_large.aspx
>>>
>>> Click Display Molecular Editor. At the Bond Rotation group, clicking the
>>> set rotation link will prompt you to click two atoms to define a bond. The
>>> first click is the anchor atom, and the second click defines the group that
>>> moves.
>>>
>>> The rotate link still works, but that's going to go. The rotation about the
>>> defined bond is now tied to mouse actions:
>>>
>>> CTRL-WHEEL rotates on way
>>> CTRL-ALT-WHEEL rotates the other way
>>>
>>> It would be nice to use CTR-WHEEL only with forward and backward wheel
>>> going in different directions, but I can't find a feedback for wheel
>>> direction - just feedback for wheel action.
>>>
>>> I don't know if Macs have an ALT? There are other bindings that can be
>>> used, but the wheel binding is appropriate for this kind of action.
>>>
>>> Jonathan, It may be that users would like this type of feature built in,
>>> and the users group may want to encourage developers to go in that
>>> direction. As a user, I just had this on my to do list, so your note gave
>>> me the push that I needed to get it done. I think you were on the mark in
>>> your original note. The ability to rotate about bonds with a fair degree of
>>> ease is important.
>>>
>>> Best Regards, Otis
>>>
>>>
>>> On 4/14/2010 2:21 PM, Jeff Hansen wrote:
&
Re: [Jmol-users] Want some opinions on rotation about bond before posting a feature request...
Otis, On the Mac Trackpad a left mouse click and drag is achieved by either clicking (the entire pad is the button) or double tapping and dragging. Neither one causes rotation about the selected bond. I checked to make sure the bond is actually selected by using the rotate link. I'm not sure why it is not interpreting either of those actions as a left click so that it does the bind. In all other cases that I have encountered either the trackpad click or the double tap and drag work. Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Apr 15, 2010, at 9:04 AM, Otis Rothenberger wrote: > Hi Jeff- > > My notes had a synchrony problem. Did you get my correction on the CTRL? It > should be CTRL-LEFT - not CTRL-RIGHT > > I'm not familiar with the Mac track pad. Is there an equivalent of CTRL-LEFT? > At a scripting level, the only binding that is possible uses standard mouse > terminology. There is no special terminology relating directly to other input > devices. Again, at the scripting level, the terms are CTRL, ALT, SHIFT, > RIGHT, MIDDLE, LEFT, WHEEL, SINGLE, DOUBLE. A computer, Mac or PC, would have > to have an equivalent of these interface concepts. > > Otis > > > On 4/15/2010 8:46 AM, Jeff Hansen wrote: >> >> Still does not work with a trackpad. >> >> >> *** >> Jeff Hansen >> Department of Chemistry and Biochemistry >> DePauw University >> 602 S. College Ave. >> Greencastle, IN 46135 >> jhan...@depauw.edu >> *** >> >> > > -- > Otis Rothenberger > chemagic.com > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Want some opinions on rotation about bond before posting a feature request...
Otis, 'Tis a thing of beauty. Works wonderfully, either way (option double tap or option two finger tap). Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Apr 15, 2010, at 11:32 AM, Otis Rothenberger wrote: > Jeff and Jonathan- > > Tom Newton, my colleague in this project, is a Mac user, and I think we > have things worked out. I was stepping on some bindings that Mac > evidently has reserved. Here's the current status of the version that's > on the ISU server (end of email). You may need to clear cache. I have > three bindings: > > 1) Works on Windows only : CTRL-WHEEL > > 2) Works on Mac Safari and Firefox (and Windows): ALT-WHEEL > > Tom tells me that on the above, he pressed the option/ALT key only - > i.e. this is a single key on his Mac, and he did not modify with another > key press. > > 3) Works on Mac Safari and Firefox (and Windows): ALT-LEFT > > On item 3, I double checked the scar on my hand. That is a LEFT. Right > now the ALT-LEFT is up/down in the y direction only. I need to do some > experimentation make any upward motion turn one way and any downward > motion turn the other way - weighting factors. > > I think the WHEEL gives best control for bond rotation, but hopefully, > item 3 covers a wheeless mouse. > > > http://www.che.ilstu.edu/osrothen/web_molecules/script_page_large.aspx > > Otis > > -- > Otis Rothenberger > chemagic.com > > > > > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac User Query
I get a non-planar carbocation.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 25, 2010, at 10:06 PM, Otis Rothenberger wrote:
> This is a request for a Mac user test of a page. I'm trying to create
> the appearance of a JME to Jmol loading of a planar carbocation.
> Admittedly, this is a work around, but it's a work around of UFF not
> Jmol. The following works on Windows (MSIE, Firefox, and Chrome), but
> apparently there are Mac issues:
>
> On http://www.che.ilstu.edu/osrothen/web_molecules/script_page_large.aspx
>
> 1) Click Display Molecular Editor.
> 2) On the subsequent control screen click Draw.
> 3) Draw a simple carbocation - e.g. 2-propyl cation.
> 4) Click Load Model.
>
> On Windows, I consistently see a planar carbocation. On Mac, I have a
> problem report.
>
> Again, I admit that this is all smoke and mirrors, but on Windows it
> accomplishes our objective - A "carbocation" model JME --> Jmol with a
> planar geometry:
>
> jmolScript("load INLINE '" +
> document.getElementById(jme1).jmeFile().replace("C+", "B+") + "';color
> {boron and formalCharge = 1} '#909090';hover off;{boron and formalCharge
> = 1}.element='C';calculate hydrogens;{carbon and formalCharge =
> 1}.element='B';color {boron and formalCharge = 1} '#909090';", "01")
>
> The above is followed by a minimize. Are any Mac users seeing the planar
> result?
>
> Otis
>
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac User Query
Depicting the "carbocation" back to JME does reveal it to be a boron.
Reloading that back into Jmol shows it as a pretty pink boron atom. Still not
planar, even after another optimize.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 25, 2010, at 11:34 PM, Otis Rothenberger wrote:
> Thanks Jeff. I definitely have a Mac problem with this approach. In an
> attempt to track it down, maybe one more request?
>
> That cation "carbon" is (or should be) in reality a boron atom - i.e. smoke
> and mirrors. I'm now curious if Mac made the swap. Would you try one more
> test. After you load the "2-propyl cation," Depict it back to JME. Is the
> cation carbon in JME now a boron? It should be. If it is, reload it in Jmol.
> Is the resulting boron compound model planar? If the boron atom is Depicted
> back to JME, the charge will not be transferred - just a neutral BH(CH3)2.
>
> Otis
>
>
>
> On 4/25/2010 10:43 PM, Jeff Hansen wrote:
>>
>> I get a non-planar carbocation.
>>
>>
>> ***
>> Jeff Hansen
>> Department of Chemistry and Biochemistry
>> DePauw University
>> 602 S. College Ave.
>> Greencastle, IN 46135
>> jhan...@depauw.edu
>> ***
>>
>>
>> On Apr 25, 2010, at 10:06 PM, Otis Rothenberger wrote:
>>
>>> This is a request for a Mac user test of a page. I'm trying to create
>>> the appearance of a JME to Jmol loading of a planar carbocation.
>>> Admittedly, this is a work around, but it's a work around of UFF not
>>> Jmol. The following works on Windows (MSIE, Firefox, and Chrome), but
>>> apparently there are Mac issues:
>>>
>>> On http://www.che.ilstu.edu/osrothen/web_molecules/script_page_large.aspx
>>>
>>> 1) Click Display Molecular Editor.
>>> 2) On the subsequent control screen click Draw.
>>> 3) Draw a simple carbocation - e.g. 2-propyl cation.
>>> 4) Click Load Model.
>>>
>>> On Windows, I consistently see a planar carbocation. On Mac, I have a
>>> problem report.
>>>
>>> Again, I admit that this is all smoke and mirrors, but on Windows it
>>> accomplishes our objective - A "carbocation" model JME --> Jmol with a
>>> planar geometry:
>>>
>>> jmolScript("load INLINE '" +
>>> document.getElementById(jme1).jmeFile().replace("C+", "B+") + "';color
>>> {boron and formalCharge = 1} '#909090';hover off;{boron and formalCharge
>>> = 1}.element='C';calculate hydrogens;{carbon and formalCharge =
>>> 1}.element='B';color {boron and formalCharge = 1} '#909090';", "01")
>>>
>>> The above is followed by a minimize. Are any Mac users seeing the planar
>>> result?
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> chemagic.com
>>>
>>>
>>>
>>>
>>> --
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>> --
>>
>>
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
> --
> Otis Rothenberger
> chemagic.com
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac User Query
I've tried several variations now and can report the following:
t-butyl gives a flat structure. Using depict model creates a structure in JME
with a boron. Loading that structure creates a flat boron structure.
2-propyl cation does not result in a flat model. Depicting that model in JME
makes the boron structure. Loading that structures results in still not flat.
ethyl behaves same as 2-propyl.
methyl is very interesting. It is not flat. Depicting the model in JME
doesn't give a structure containing boron. Loading in back into Jmol it still
isn't flat.
Just to further explore I made a cylopentyl cation in JME and loaded it into
Jmol. Behaved like 2-propyl. When I made 1-methyl-1-cyclopentyl cation and
tried to load it into Jmol it displayed nothing. Depicting that back into JME
showed methylcyclopentane with no charge. This was weird so I reloaded the
page and started over. Now the methylcyclopentyl cation loaded into JMol fine
but flat. Depicted in JME fine (with boron). Loaded back to Jmol now flat. A
few more experiments and I determined that if I just cleared the JME and built
a new molecule it was a problem. Either it didn't display or the molecule
wasn't ever flat. If I reload the web page and build the molecule then loaded
into JMol etc. It seemed to behave better. 2-propyl cation still wasn't flat,
but now after depicting back to JME where it changes to boron then reloading
into Jmol, it now becomes flat. No matter what, though ethyl and methyl always
behaved as described above. I also tried benzyl (after reloading the page) and
the cation was definitely not flat and the hydrogens were rotated almost
perpendicular to the plane of the ring. After depicting into JME (changed to
boron) then reloading into JMol, it flattened out nicely.
*******
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Apr 26, 2010, at 9:24 PM, Philip Bays wrote:
> I see the flat structure with the t-butyl cation.
>
>
> On Apr 25, 2010, at 10:06 PM, Otis Rothenberger wrote:
>
>> This is a request for a Mac user test of a page. I'm trying to create
>> the appearance of a JME to Jmol loading of a planar carbocation.
>> Admittedly, this is a work around, but it's a work around of UFF not
>> Jmol. The following works on Windows (MSIE, Firefox, and Chrome), but
>> apparently there are Mac issues:
>>
>> On http://www.che.ilstu.edu/osrothen/web_molecules/script_page_large.aspx
>>
>> 1) Click Display Molecular Editor.
>> 2) On the subsequent control screen click Draw.
>> 3) Draw a simple carbocation - e.g. 2-propyl cation.
>> 4) Click Load Model.
>>
>> On Windows, I consistently see a planar carbocation. On Mac, I have a
>> problem report.
>>
>> Again, I admit that this is all smoke and mirrors, but on Windows it
>> accomplishes our objective - A "carbocation" model JME --> Jmol with a
>> planar geometry:
>>
>> jmolScript("load INLINE '" +
>> document.getElementById(jme1).jmeFile().replace("C+", "B+") + "';color
>> {boron and formalCharge = 1} '#909090';hover off;{boron and formalCharge
>> = 1}.element='C';calculate hydrogens;{carbon and formalCharge =
>> 1}.element='B';color {boron and formalCharge = 1} '#909090';", "01")
>>
>> The above is followed by a minimize. Are any Mac users seeing the planar
>> result?
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> chemagic.com
>>
>>
>>
>>
>> --
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> J. Philip Bays
> Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> (574) 284-4663
> pb...@saintmarys.edu
>
>
>
>
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac User Query
Otis, I think you are right about my reloading coinciding with you updating your server. Today I'm not needing to reload the page. Ethyl still not flat. 2-propyl is now flat. Cyclopentyl and cyclohexyl are not flat, even after depicting into JME then reloading into Jmol. Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Apr 27, 2010, at 1:32 AM, Otis Rothenberger wrote: > Jeff, > > Your notes were a big help - thanks. By coincidence, I think your page > reloading coincided with changes that I was making on the server! > > I think the problem involved a Java vs JavaScript string issue that Firefox > on Mac ignored but Safari did not. I think I have that fixed. On the other > points: > > 1) C+ - I caused this problem by the way I handle single atom loads from JME. > I can fix this. > 2) CC+ - I see the same thing. I think this is also fixable. > 3) Charges - Unfortunately, the charges are not passed back to JME. This is > caused by the fact that I'm passing the extracted molfiles back (not the JME > files). The molfiles do not have the charge information. > > There are some cases where UFF does not produce a flat BX3. In the cases > where it does, I think we are getting a flat "carbocation." > > Thanks for the help. > > Otis > > > On 4/26/2010 11:54 PM, Jeff Hansen wrote: >> >> I've tried several variations now and can report the following: >> >> t-butyl gives a flat structure. Using depict model creates a structure in >> JME with a boron. Loading that structure creates a flat boron structure. >> 2-propyl cation does not result in a flat model. Depicting that model in >> JME makes the boron structure. Loading that structures results in still not >> flat. >> ethyl behaves same as 2-propyl. >> methyl is very interesting. It is not flat. Depicting the model in JME >> doesn't give a structure containing boron. Loading in back into Jmol it >> still isn't flat. >> >> Just to further explore I made a cylopentyl cation in JME and loaded it into >> Jmol. Behaved like 2-propyl. When I made 1-methyl-1-cyclopentyl cation and >> tried to load it into Jmol it displayed nothing. Depicting that back into >> JME showed methylcyclopentane with no charge. This was weird so I reloaded >> the page and started over. Now the methylcyclopentyl cation loaded into >> JMol fine but flat. Depicted in JME fine (with boron). Loaded back to Jmol >> now flat. A few more experiments and I determined that if I just cleared >> the JME and built a new molecule it was a problem. Either it didn't display >> or the molecule wasn't ever flat. If I reload the web page and build the >> molecule then loaded into JMol etc. It seemed to behave better. 2-propyl >> cation still wasn't flat, but now after depicting back to JME where it >> changes to boron then reloading into Jmol, it now becomes flat. No matter >> what, though ethyl and methyl always behaved as described above. I also >> tried benzyl (after reloading the page) and the cation was definitely not >> flat and the hydrogens were rotated almost perpendicular to the plane of the >> ring. After depicting into JME (changed to boron) then reloading into JMol, >> it flattened out nicely. >> >> >> *** >> Jeff Hansen >> Department of Chemistry and Biochemistry >> DePauw University >> 602 S. College Ave. >> Greencastle, IN 46135 >> jhan...@depauw.edu >> * > -- > Otis Rothenberger > chemagic.com > -- > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] ah, this is very, ah, WEIRD
Very cool. I could switch between equatorial and axial methyl groups and compare their energies. Could get it into a skew boat. It took some effort to get it back to a chair, but I got it after a few tries. Lots of fun. I think I can use this. Thanks. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On May 21, 2010, at 12:03 AM, Robert Hanson wrote: > Mac-side bug fixed. Please do check this out: > > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=135 > > Bob > > On Thu, May 20, 2010 at 9:25 PM, Robert Hanson wrote: > Hmm. OK, we need to get to the bottom of this! > > On Thu, May 20, 2010 at 7:45 PM, rgb wrote: > nada > > Rich > > Robert Hanson wrote: > > so you don't even see a structure? > > > > On Thu, May 20, 2010 at 7:07 PM, Philip Bays > <mailto:pb...@saintmarys.edu>> wrote: > > > > Bob: > > > > I click on the red text in the description which transfers the > > command to the command area under the applet. Clicking on cmd > > results in nothing. (Mac 10.6.3, java 1.6 something.) > > > > Phil > > > > On May 20, 2010, at 7:55 PM, Robert Hanson wrote: > > > >> You sure? It works on my setup. A caching problem? > >> > >> On Thu, May 20, 2010 at 5:54 PM, Philip Bays > >> mailto:pb...@saintmarys.edu>> wrote: > >> > >> Hmm. Bob, I am not seeing anything. > >> > >> Phil > >> > >> On May 20, 2010, at 6:17 PM, Robert Hanson wrote: > >> > >>> Well, sorry, I had to do it. I don't know exactly what to > >>> say about it. Just try it. > >>> > >>> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=135 > >>> > >>> Bob > >>> > >>> -- > >>> Robert M. Hanson > >>> Professor of Chemistry > >>> St. Olaf College > >>> 1520 St. Olaf Ave. > >>> Northfield, MN 55057 > >>> http://www.stolaf.edu/people/hansonr > >>> phone: 507-786-3107 > >>> > >>> > >>> If nature does not answer first what we want, > >>> it is better to take what answer we get. > >>> > >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > >>> > >>> -- > >>> > >>> ___ > >>> Jmol-users mailing list > >>> Jmol-users@lists.sourceforge.net > >>> <mailto:Jmol-users@lists.sourceforge.net> > >>> https://lists.sourceforge.net/lists/listinfo/jmol-users > >> > >> J. Philip Bays > >> Professor of Chemistry > >> Department of Chemistry and Physics > >> Saint Mary's College > >> Notre Dame, IN 46556 > >> (574) 284-4663 > >> pb...@saintmarys.edu <mailto:pb...@saintmarys.edu> > >> > >> > >> > >> > >> > >> -- > >> > >> > >> ___ > >> Jmol-users mailing list > >> Jmol-users@lists.sourceforge.net > >> <mailto:Jmol-users@lists.sourceforge.net> > >> https://lists.sourceforge.net/lists/listinfo/jmol-users > >> > >> > >> > >> > >> -- > >> Robert M. Hanson > >> Professor of Chemistry > >> St. Olaf College > >> 1520 St. Olaf Ave. > >> Northfield, MN 55057 > >> http://www.stolaf.edu/people/hansonr > >> phone: 507-786-3107 > >> > >> > >> If nature does not answer first what we want, > >> it is better to take what answer we get. > >> > >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > >> > >> -- > >> > >> __
Re: [Jmol-users] Jmol model kit and docking
Wow!! *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On May 27, 2010, at 10:30 PM, Robert Hanson wrote: > I have two new demos up at > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm > > 137. set picking dragMinimizeMolecule -- responsive docking > With Jmol 12.0.RC15 you can move a small molecule around and watch it react > to its environment. Grab the caffeine molecule and move it toward the > protein. Holding SHIFT down allows rotation. CTRL-Z undoes an action; CTRL-Y > does a redo. > Finally I think I have a visualization for the "solvent surface"! -- Just > roll the water molecule along and see where it settles. > > > 136. set ModelKitMode > Jmol 12.0.RC15 represents a first attempt at creating a model kit option for > Jmol. Click on the magenta bar in the top left corner. > > > Give them a try! > > Bob > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Same for me with Mac Mail. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jun 1, 2010, at 10:10 PM, rgb wrote: > Otis Rothenberger wrote: >> Bob, >> >> This is the cat's meow. Thanks for the help. I'm still stuck with a >> server side approach (AJAX very frustrating!), but the "Jmol load >> completed" approach seems to work. Cholestane is below. What a slick >> way to communicate 3D models via email: >> >> http://chemagic.com/web_molecules/script_page_large.aspx?smiles=...@h]%28%28c%29c%29[c@H]1CC[C@@H]2[C@@]1%28c...@h]3[c@H]2CCC4[C@@]3%284%29C%29C >> >> For the JME applet on our page, I'm now using a choice of two load >> links - jmeFile or smiles. >> >> I'm interested in how the above link works on Mac. Also, note that the >> jmol javascript command does not work with Windows MSIE 8, so the >> above link does not work on MSIE. On this problem, MSIE ignores the >> following from the console: > In thunderbird 2.0 (on a mac) the link isn't recognised as one (stops at > the first [ character) but if I copy the whole thing and paste it into > FF 3.6 (or safari 4.0) it works just fine. > > You do appear to have misspelled your last name on the page though. :-) > > Rich > > > -- > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Coloring A molecular dynamically....
Jonathan, I'm not sure I understand the goal here. Is it to select a single atom or residue and color it? Is it to select all lysines and color them red? Is it to select residues 50-73 and color them blue? Is it to find all alpha helices and color them purple? Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jun 11, 2010, at 10:24 AM, Jonathan Gutow wrote: > Jay, > > I've actually started to work on a general version of this. Do you > want to help? I am at the stage of outlining behavior and figuring > out the best interface. Here's what I've thought of so far. If your > are interested in working on this let me know and we'll move the > discussion to jmol-developers... > > Interface: > > a) A browser pop-up menu that includes a list of all atoms or residues > (essentially duplicates the list in the Jmol menu). This will require > using callbacks to the applet to get the list of what is in the > displayed molecule(s). There are also some issues with making sure > things update if the displayed molecule changes. > > b) The color could be selected using the colorpicker widget that I > developed for SAGE and is now included for picking the background > color in the Jmol WebExport tool. Some examples of how it looks are at: > > http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Jmol%20Color%20Picker%20Test.html > > (this example needs some updating but will give you an idea of how the > color picker behaves.). > > Jonathan > On Jun 11, 2010, at 7:36 AM, jmol-users-requ...@lists.sourceforge.net > wrote: > >> Message: 1 >> Date: Thu, 10 Jun 2010 15:59:59 -0400 >> From: Jay Vyas >> Subject: [Jmol-users] Coloring A molecular dynamically >> To: jmol-users@lists.sourceforge.net >> Message-ID: >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi : I want to allow users to color atoms in a protein by selecting >> the >> residue numbers, and then selecting a color. Im not sure how to do >> this in >> dynamically. For example, I know I could make a >> "select 1-20 ; color yellow" command. But I want the user to be >> able to >> select both the residue numbers, and the color. Anyone know if >> there is a >> simple way to add this feature using jmol controls ?? >> If not, I think some dynamic javascript could do the trick. >> -- next part -- >> An HTML attachment was scrubbed... >> >> -- >> >> Message: 2 >> Date: Thu, 10 Jun 2010 16:15:36 -0500 >> From: Robert Hanson >> Subject: Re: [Jmol-users] Coloring A molecular dynamically >> To: jmol-users@lists.sourceforge.net >> Message-ID: >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> We have a nice color widget now, and it could be adapted >> Jonathan, does >> the color widget allow you to tie it to any script command? >> >> The basic idea is >> >> 1) set a pick callback so you know what residue(s) were clicked. -- >> or I >> guess just use set picking select. >> 2) in response to a color pick -- say it's "[xFF00FF]" you would >> construct >> the script >> >> var scr = "select within(group, selected);color [xFF00FF]" >> >> and send that to Jmol using >> >> jmolScript(scr) >> > > Dr. Jonathan H. Gutow > Chemistry Department gu...@uwosh.edu > UW-Oshkosh Office:920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/facstaff/gutow > > > > > > > -- > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
Just to clarify. It sounds like the problem Pshemak is having is that when he looks at the vibrations, it is actually switching to another frame or model. These other frames or models do not contain the MOs. The MOs are still there (associated with the first model - or is model 1 the second model?). To see the MOs along with the other models I suppose they could be copied over using some javascript? However, it seems this would look funny with some static MO with the atoms moving relative to it. If what Pshemak wants is to animate through the vibration models and have an MO associated with each vibration model which has been calculated for that model that will be a tough thing to do. It is no longer a Jmol issue but rather how to get Spartan to calculate an MO for each vibration model it is generating then output that in a way that Jmol could read and animate. Probably possible, but I'm not sure exactly how to do it. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jun 30, 2010, at 9:32 AM, Robert Hanson wrote: > When Jmol reads a Spartan smol file, it accesses all vibrations and all > molecular orbitals (supposedly!) They should be accessible via the > right-click menu (or by clicking the "Jmol" logo"). MOs are under > "surfaces"; vibrations are under "model" (at the top). > > Each vibration is another "frame" or "model", and generally one of those > models has the MOs. For some readers that is the first model, some the > second, some the last. It all depends upon the reader. With Spartan, the MOs > should be in model 1, and the vibrations should be the models after that. > > Makes sure you have issued > > vibration on > > if you want to see the vibrations or using that menu, Vibration->ON > > http://chemapps.stolaf.edu/jmol/docs/examples-11/data/C6H6.smol should be a > good example of this. > > Bob > > On Wed, Jun 30, 2010 at 6:19 AM, Pshemak Maslak wrote: > On 6/29/2010 7:20 PM, Robert Hanson wrote: >> >> I'll look into the mep/mo business. Should not be a problem. Just a bug, I >> think. > Thank you very much for your help. > > I do have two related questions: > > 1. Can more than one surface be read from these files by Jmol? > > 2. Can Jmol write jvxl files with multiple surfaces? > > > Since I have just started learning Jmol and have noticed the incredible > amount of work you have put into this project, I would like to take > this opportunity to express my thanks for your contribution to the > development of such an invaluable tool for organic chemists. > > PM > > > >> >> On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak wrote: >> On 6/25/2010 4:51 PM, Greeves, Nick wrote: >> > I have used smol files for vibration >> > e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well >> > without any server side settings. >> > >> > All the best >> > Nick >> > Sent from my iPad >> Thank you very much for the example. Your case indeed clarifies the >> behavior: vibration and surfaces (mep and MOs) appear to be mutually >> exclusive with >> smol files, and if you do not reload, you cannot access the surfaces. >> >> Try the following: start any of the vibrations. Now stop it (check the >> vibration check box twice). Now check if MO's are still in the menu and >> what kind mep loads (not the one form smol, but one generated by Jmol). >> >> This is exactly what I was trying to explain (I am new to Jmol). >> >> That issue was not related to the MIME type question (although both were >> about smol). The same happens on the desktop Jmol. >> >> Thank you for your assistance. >> >> PM >> >> >> >> -- >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does n
Re: [Jmol-users] smol files
OK. So ignore my previous post. I was thinking you wanted to view the vibrations and MOs simultaneously. Obviously not what you want. You said that "MO #" gives a message that no MO coefficient data is available. This would be true unless you are in model 1. I think just stopping vibrations will leave you in whichever model was showing when you stopped vibrations. Unless that happened to be the first model then you wouldn't have any MOs available. Switch to model 1 and the MOs should be available. What other surfaces are you interested in? ******* Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jun 30, 2010, at 10:27 AM, Pshemak Maslak wrote: > On 6/30/2010 9:32 AM, Robert Hanson wrote: >> >> When Jmol reads a Spartan smol file, it accesses all vibrations and all >> molecular orbitals (supposedly!) They should be accessible via the >> right-click menu (or by clicking the "Jmol" logo"). MOs are under >> "surfaces"; vibrations are under "model" (at the top). > Thanks. I am new to Jmol, but not that new. :-) I have no problems > individually visualizing any of the vibrations, or MOs, or mep surfaces from > smol files.. > > The problem (possibly a bug as you have suggested) is that once vibrations > are visualized the MOs or mep are no longer accessible without reloading the > smol file. I am guessing that the "frame" that holds MO and mep data is not > longer read by Jmol after one of the vibrational frames was read. For > example, after stopping vibrations (vibration off) "MO #" would give a > message that no MO coefficient data is available for this frame, and no MO is > displayed. When I choose all vibrational frames (from the menu) I get the > same error message, but the MO loads! > >> >> Each vibration is another "frame" or "model", and generally one of those >> models has the MOs. For some readers that is the first model, some the >> second, some the last. It all depends upon the reader. With Spartan, the MOs >> should be in model 1, and the vibrations should be the models after that. >> >> Makes sure you have issued >> >> vibration on >> >> if you want to see the vibrations or using that menu, Vibration->ON >> >> http://chemapps.stolaf.edu/jmol/docs/examples-11/data/C6H6.smol should be a >> good example of this. >> >> Bob > Coming back to my related questions: > > Can any other surfaces (in addition to MOs and mep) be visualized through > smol files? > > Can Jmol write jvxl files with multiple surfaces (for example selected MOs)? > > Thanks for all your help. > > PM > >> >> On Wed, Jun 30, 2010 at 6:19 AM, Pshemak Maslak wrote: >> On 6/29/2010 7:20 PM, Robert Hanson wrote: >>> >>> I'll look into the mep/mo business. Should not be a problem. Just a bug, I >>> think. >> Thank you very much for your help. >> >> I do have two related questions: >> >> 1. Can more than one surface be read from these files by Jmol? >> >> 2. Can Jmol write jvxl files with multiple surfaces? >> >> >> Since I have just started learning Jmol and have noticed the incredible >> amount of work you have put into this project, I would like to take >> this opportunity to express my thanks for your contribution to the >> development of such an invaluable tool for organic chemists. >> >> PM >> >> >> >>> >>> On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak wrote: >>> On 6/25/2010 4:51 PM, Greeves, Nick wrote: >>> > I have used smol files for vibration >>> > e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well >>> > without any server side settings. >>> > >>> > All the best >>> > Nick >>> > Sent from my iPad >>> Thank you very much for the example. Your case indeed clarifies the >>> behavior: vibration and surfaces (mep and MOs) appear to be mutually >>> exclusive with >>> smol files, and if you do not reload, you cannot access the surfaces. >>> >>> Try the following: start any of the vibrations. Now stop it (check the >>> vibration check box twice). Now check if MO's are still in the menu and >>> what kind mep loads (not the one form smol, but one generated by Jmol). >>> >>> This is exactly what I was trying to ex
Re: [Jmol-users] smol files
Glad that helped. Making it easily accessible to students means doing most of the work for them. In the case of Jmol that means setting up buttons or checkboxes or whatever user interface then scripting what you want the students to see. In the case of viewing the MOs or some other surface you could create a button which the students would click to show the surface. Would be easy enough to include in that script a command to return to model 1 so the MOs would be available to view. Those surfaces in Spartan are basically the electron density surface colored according to other properties. Jmol will certainly allow you to visualize the electron density surface. My understanding is that you can also color it by whatever property you want. There would be some serious scripting involved in doing this. Without knowing exactly what is in the smol file, I would imagine the data for those properties are there somewhere. you would have to grab that data somehow then instruct Jmol to use it as the basis for coloring the surface. I'm no expert on this, but perhaps someone else can help with the details of this. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jun 30, 2010, at 2:09 PM, Pshemak Maslak wrote: > On 6/30/2010 10:38 AM, Jeff Hansen wrote: >> >> OK. So ignore my previous post. I was thinking you wanted to view the >> vibrations and MOs simultaneously. Obviously not what you want. You said >> that "MO #" gives a message that no MO coefficient data is available. This >> would be true unless you are in model 1. I think just stopping vibrations >> will leave you in whichever model was showing when you stopped vibrations. >> Unless that happened to be the first model then you wouldn't have any MOs >> available. Switch to model 1 and the MOs should be available. >> >> What other surfaces are you interested in? > Thanks. I think your comments helped me to figure out how that works. There > is no bug: it is how it is designed: one has to (manually i.e. through menu > or script) return back to the frame with MO info. > As you have said stopping vibration does not automatically return Jmol to > frame (model) 1 (where MO's are). > > I am mostly interested in setting Jmol in such a way that is easily > accesiblke to students. I do not want the Jmol "mechanics" to divert from the > chemistry contents. > > Since Spartan easily calculates various surfaces (density(bonds), > density(HOMO) or density(LUMO to name the few, I was wandering if they are > written into smol files and whether they are accessible through Jmol. > > Thanks! > > PM. > > > > >> >> >> *** >> Jeff Hansen >> Department of Chemistry and Biochemistry >> DePauw University >> 602 S. College Ave. >> Greencastle, IN 46135 >> jhan...@depauw.edu >> *** >> >> >> On Jun 30, 2010, at 10:27 AM, Pshemak Maslak wrote: >> >>> On 6/30/2010 9:32 AM, Robert Hanson wrote: >>>> >>>> When Jmol reads a Spartan smol file, it accesses all vibrations and all >>>> molecular orbitals (supposedly!) They should be accessible via the >>>> right-click menu (or by clicking the "Jmol" logo"). MOs are under >>>> "surfaces"; vibrations are under "model" (at the top). >>> Thanks. I am new to Jmol, but not that new. :-) I have no problems >>> individually visualizing any of the vibrations, or MOs, or mep surfaces >>> from smol files.. >>> >>> The problem (possibly a bug as you have suggested) is that once vibrations >>> are visualized the MOs or mep are no longer accessible without reloading >>> the smol file. I am guessing that the "frame" that holds MO and mep data >>> is not longer read by Jmol after one of the vibrational frames was read. >>> For example, after stopping vibrations (vibration off) "MO #" would give a >>> message that no MO coefficient data is available for this frame, and no MO >>> is displayed. When I choose all vibrational frames (from the menu) I get >>> the same error message, but the MO loads! >>> >>>> >>>> Each vibration is another "frame" or "model", and generally one of those >>>> models has the MOs. For some readers that is the first model, some the >>>> seco
Re: [Jmol-users] smol files
Bob, You can do this in Spartan. For example, make a butane molecule and create a dihedral angle constraint. Display the properties window and click on the dihedral angle constraint to show the properties for it. Set it to vary from -180 to 180. Set up an Energy Profile calculation and run it. When it is done, close the original butane molecule so only the results of the Energy Profile calculation are showing. Select the dihedral angle. At the bottom right of the screen, next to where it shows the value of the angle should be a letter P in a yellow box. Click on it. It should enter the dihedral angle values into the spreadsheet. You can also enter values for the energies in whatever units you want or the relative energy (it will set the lowest energy to zero). Now go to the Display menu and choose Plots... Make sure the Properties checkbox is checked. Choose Constraint from the X-axis popup and whatever energy you want from the list for the Y-axis then click OK. This is all in the Mac version. Might be a little different on the Windows version. But it definitely will do it and it isn't too hard. Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 1, 2010, at 12:37 PM, Robert Hanson wrote: > about Spartan -- > > I guess I'll stick with > http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm You > can just drag and drop any Spartan file into that applet, and it will display > the associated clickable graph. Hopefully they will get a feature such as > this into some future edition of Spartan Student. For now this will have to > do. I don't see spreadsheets very appealing unless there is a direct > clickable interface between their data and the actual conformation. It's the > connection between the specific energies and the specific conformations that > my students need to make, not so much the overall energy picture. > > Bob > > > > > I have a Spartan question: How do you construct an energy profile plot > > that allows you to easily correlate specific conformations to specific > > energies (as for example with butane)? I can do that in Sygress/CaCHE > > or using Spartan files with my Jmol/Google plot page, but is there > > some way of doing that directly in Spartan? > > > > Bob > > I am guessing that you would like to have a "clickable" (or otherwise > interactive) graph linking (let's say) energy values with specific > conformers. I do not know how to do that. > > Spartan provides a convenient spreadsheet function that allows one to > collect energy data as a function of torsional angle and plot them (or > even fit the data). A demonstration case is in the Spartan 08 "Tutorial > and User Guide" (p. 98). > > PM > > > > > -- > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- > http://p.sf.net/sfu/sprint-com-first___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
It's actually not that hard to do. No you don't have to enter each dihedral individually into the spreadsheet and yes you can click on any point on the graph and show the corresponding conformation. The hardest part is actually getting the conformations and their energies and it sounds like you already know how to do that. I could show you, but I'm leaving town tomorrow so it would have to wait until I get back. ******* Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 1, 2010, at 3:08 PM, Robert Hanson wrote: > I guess I'll have to have somebody show me how that works. > > If this produces the same result as > http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm? -- I > mean you can click on any point on the graph, and the corresponding > conformation is displayed, that's great. Still, it seems rather involved. Do > you have to enter each dihedral individually into the spreadsheet? > > Bob > > > On Thu, Jul 1, 2010 at 1:22 PM, Jeff Hansen wrote: > Bob, > > You can do this in Spartan. For example, make a butane molecule and create a > dihedral angle constraint. Display the properties window and click on the > dihedral angle constraint to show the properties for it. Set it to vary from > -180 to 180. Set up an Energy Profile calculation and run it. When it is > done, close the original butane molecule so only the results of the Energy > Profile calculation are showing. Select the dihedral angle. At the bottom > right of the screen, next to where it shows the value of the angle should be > a letter P in a yellow box. Click on it. It should enter the dihedral angle > values into the spreadsheet. You can also enter values for the energies in > whatever units you want or the relative energy (it will set the lowest energy > to zero). Now go to the Display menu and choose Plots... Make sure the > Properties checkbox is checked. Choose Constraint from the X-axis popup and > whatever energy you want from the list for the Y-axis then click OK. > > This is all in the Mac version. Might be a little different on the Windows > version. But it definitely will do it and it isn't too hard. > > > Jeff > > > *** > Jeff Hansen > Department of Chemistry and Biochemistry > DePauw University > 602 S. College Ave. > Greencastle, IN 46135 > jhan...@depauw.edu > *** > > > On Jul 1, 2010, at 12:37 PM, Robert Hanson wrote: > >> about Spartan -- >> >> I guess I'll stick with >> http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm You >> can just drag and drop any Spartan file into that applet, and it will >> display the associated clickable graph. Hopefully they will get a feature >> such as this into some future edition of Spartan Student. For now this will >> have to do. I don't see spreadsheets very appealing unless there is a direct >> clickable interface between their data and the actual conformation. It's the >> connection between the specific energies and the specific conformations that >> my students need to make, not so much the overall energy picture. >> >> Bob >> >> > >> > I have a Spartan question: How do you construct an energy profile plot >> > that allows you to easily correlate specific conformations to specific >> > energies (as for example with butane)? I can do that in Sygress/CaCHE >> > or using Spartan files with my Jmol/Google plot page, but is there >> > some way of doing that directly in Spartan? >> > >> > Bob >> >> I am guessing that you would like to have a "clickable" (or otherwise >> interactive) graph linking (let's say) energy values with specific >> conformers. I do not know how to do that. >> >> Spartan provides a convenient spreadsheet function that allows one to >> collect energy data as a function of torsional angle and plot them (or >> even fit the data). A demonstration case is in the Spartan 08 "Tutorial >> and User Guide" (p. 98). >> >> PM >> >> >> >> >> -- >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> ___
Re: [Jmol-users] fwd: Should I use Jmol or ChemDoodle for developing a 3d application?
While I absolutely love Jmol and it clearly is much more capable than this ChemDoodle web components, I've been worried for some time about Jmol eventually running its course like Chime as Java becomes less used. It seems Javascript/HTML5 is on the rise. I wonder what will come after that? Is there any hope of ever achieving a stable cross browser, standards-based solution that won't require relearning a new system? *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 14, 2010, at 4:04 AM, Egon Willighagen wrote: > See: > > http://blueobelisk.shapado.com/questions/should-i-use-jmol-or-chemdoodle-for-developing-a-3d-application > > Eg. > > -- > Post-doc @ Uppsala University > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > -- > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] HTML5 and WebGL
Can you imagine the response you would have received even just 5 years ago if you had complained because your phone didn't do Java? I would guess that in another 5 years or so the response will be similar. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 15, 2010, at 2:40 AM, Egon Willighagen wrote: > I hate the one I do not have: it does not do Java... -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] from Jmol to 3D-PDF (was idtf output for polyhedral structures)
Way cool! Couple of questions or comments. 1. I know nothing about these file formats. I assume there is a good reason that the U3D format can't be written directely? Seems odd that you have to go through some intermediary format. 2. I've got no experience with server side programming. Seems like some clever person could create a web page that allows one to load a molecule into Jmol, display it as they want, write this xxx.idtf file, and send it to some server side script that does the rest and returns the pdf file. Perhaps using something like this http://www.scribtex.com/ *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 17, 2010, at 4:36 PM, Robert Hanson wrote: > OK. Got it! Whew! My work is about done on this. > > Arie, now I REALLY owe you a beer. > > Fellow Jmol users - check this out. You can now export models from Jmol and > have VERY NICE reproductions in a PDF file. I've uploaded some test files > into http://chemapps.stolaf.edu/jmol/docs/examples-11/pdf > > > The workflow looks like this: > > JMOL: write xxx.idtf > > (This process creates TWO files -- .idtf and .idtf.tex. The idtf is > the "intermediate" file format that is needed in the next step to create a > U3D file, which is what goes into the PDF as a 3D "movie"; the idtf.tex files > contains the Jmol state (in a Tex comment) and a bit of TeX code that sets > the zoom correctly (the part I couldn't figure out on my own, Arie) and can > be used to create a sample PDF file using a program such as MikTeX. There are > parameters in there that can be tweaked such as the zoom rotation, and such.) > > I recommend also along with this, > > write xxx.png > > Just so you have the image and associated state if you want that. > > > SHELL: use idtfConverter to create a U3D file from IDTF. > > (I might note that Jmol is VERY EFFICIENT in its use of nodes in creating > these files. If you have ever first created a VRML file and then had another > program create the U3D from that, you will have noticed that a small enzyme > could be 15 Mb of U3D file. Jmol caches all objects and only creates new ones > when it is absolutely necessary.) > > MikTeX/TeXworks or other pdf-creating software: Open and run the idtf.tex file > > That's it! In many cases you will get a nearly EXACT 3D model relative to > what you see in Jmol. > > I was creating PDF documents in less that 10 seconds from the "write" command > once I got it figured out. > > There are several CAVEATS: > > 1) If you move the model rotation center away from screen center, as with > CTRL-ALT-drag, you are going to get a very good, very close, but not quite > perfect reproduction of the model in VRML or U3D. That moving of the center > of perspective is not supported in those virtual reality packages, as far as > I can tell. I guess no one has ever considered it. > > 2) I can't get lighting to work. When I try, I get a light that moves with > the model. So if someone knows how to do that, speak up. > > 3) I can't see how to set the perspective to ORTHOGRAPHIC. If you have used > Jmol you may not even have noticed, but if there is a crystal structure that > structure is being rendered with perspectiveDepth turned off - otherwise the > unit cells are very odd. There is a right-mouse-button option to go into that > mode, but I don't see how to require that up front. Please let me know if you > know how to do that. > > 4) Don't expect the operation of the PDF mouse interface to be like Jmol. In > my hands, at least, it is quite difficult to control. I don't get the mouse > motion model at all, actually, and I particularly don't like the fact that I > can completely lose the rotation center somehow. > > > But, if you can live with that, this is quite cool. > > (more notes below...) > > 2010/7/16 Angel Herráez > > > needed for big objects, and also what you can do to render it more > > fastly. > > > - see one of my earlier mails, notably on the computer power > Well, everytime we have discussed this VRML / X3D / IDTF / U3D / PDF > business, I get rather excited about the possibility --and involved--, but it > the end I think this is not at all comparable to what you get by just setting > a webpage with JmolApplet -- much faster, smoother and smaller. > > > true, but can you do that on an iPhone? [not that iPhones can support U3D > movies within PDF -- or can they? If you have an iPh
Re: [Jmol-users] Access
On my Mac, OS X 10.6.4:
Safari (5.0) - NT1 works fine. NT2 loads the first structure. Clicking the
button does not produce the chlorophyll structure. The message bar says script
started then immediately says script terminated. The javascript debugger shows
this error: "Assertion failed: ReaderArticleFinder aborting CandidateElement
detection due to timeout."
Firefox (3.6.3) - NT1 displays the first structure. Clicking the button
results in an access denied error. NT2 behaves same as in Safari. I'm not
seeing any error messages in firebug.
*******
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 24, 2010, at 10:32 AM, Robert Hanson wrote:
> also, Phil, you will need to be very specific as to browser version. I'm not
> seeing the problem on my Mac with Firefox 3.5.7. But it almost certainly
> related to newer security measures that Firefox has installed. Apparently
> Java access to its cache is considered local file access and is being
> blocked.
>
> Just to make sure, am I right about this:
>
> 1) Mac only
> 2) Firefox/Mozilla only
> 3) Firefox -- what version?
> 4) Only when Firefox is closed and then reopened and sent to the same site
> (what is odd about this is that the Java cache is supposed to be
> cleared automatically in that case)
>
> Ah -- now, does that mean that you have some special setting in Java that
> does not clear the cache when the browser closes. That has always been my
> experience -- and it's important -- that the Java cache is only for a single
> browser session. That's how I test the applet -- close the browser and
> re-open it to ensure that the applet is loaded again.
>
> Bob
>
>
> On Sat, Jul 24, 2010 at 9:12 AM, Robert Hanson wrote:
> you need to report this to Bugzilla.
>
> On Sat, Jul 24, 2010 at 7:09 AM, Philip Bays wrote:
> I think I have just diagnosed the problem, but not the solution.
>
> I have opened the java preferences and completely cleared the cache. (I know
> Angel, you said that in the first place.) Indeed, firefox loads both
> structures as expected and three items now appear in the java cache -- the
> applet and each of the molecule files.
>
> If I now close firefox, reopen it, and access the page, the error occurs. If
> I remove the chlorophyll file from the java cache, then restart firefox, it
> works, again putting chlorophyl in the cache. Upon restarting firefox, the
> error again occurs.
>
> If I turn off java caching, there are no problems. For some reason, Firefox
> does not like chlorophyll in cache.
>
> Phil
>
>
> On Jul 24, 2010, at 7:29 AM, Otis Rothenberger wrote:
>
>> Phil,
>>
>> I'm just curious about something: On a browser that throws the error loading
>> chlorophyll, what happens if you execute the following JavaScript command
>> from the location window (address field) while the first stucture is
>> displayed in Jmol?
>>
>> javascript:jmolScript("load Structures/chlorophyll.pdb")
>>
>> I'm just bypassing the button above to see if the problem is via the button
>> route???
>>
>> Otis
>> Otis Rothenberger
>> chemagic.com
>>
>> On 7/24/2010 6:38 AM, Philip Bays wrote:
>>>
>>> Ok, I got the code right. But it does not work on all browsers. I see
>>> no difference with this code than what I was observing before. Namely, on
>>> the Mac, and the Mac only, and a freshly started mozilla browser (Firefox,
>>> Camino, SeaMonkey), the first structure loads fine, but the chlorophyll
>>> structure throws a java access error with the unsigned applet.
>>>
>>>
>>>
>>> On Jul 23, 2010, at 5:51 PM, Robert Hanson wrote:
>>>
>>>> http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html
>>>> http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT2.html
>>>>
>>>> Ah, yes, these pages look much better. So what are the results?
>>>>
>>>> The page NT1 should load on all platforms with no issues at all. It is
>>>> precisely the stated way of doing things.
>>>>
>>>> Same for NT2. And from this one I can save the state - see attached. (Just
>>>> drag that PNG file into the app or applet.)
>>>>
>>>> Was that just the issue? That Phil was trying to load models before the
>>>> applet was ready?
>>>>
>>>> One of the nice things about the
Re: [Jmol-users] Access
Works fine now on both Safari and Firefox.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 24, 2010, at 11:40 AM, Philip Bays wrote:
> Sorry Otis and perhaps others. The code on NT2 was left from trying to
> reinsert the same structure. It is now updated.
>
> Phil
>
> On Jul 24, 2010, at 11:18 AM, Otis Rothenberger wrote:
>
>> Phil and Bob,
>>
>> With never ending Mac problems of my own, I'm very interested in this
>> chain. Just so I understand:
>>
>> 1) This a suspected Java cache problem - not a browser cache problem.
>> Is that correct?
>> 2) Do you know in what default state a Mac user, or Windows user for
>> that matter, is likely to find Java cache in Firefox - Window and Mac?
>>
>> This latter question relates to the fact that I cannot open the Java
>> console from the Windows Firefox tools menu selection item. There has
>> been some on going Firefox bug fuss on this issue, and I must admit I
>> was hoping that I could ignore this fuss. I'm using FF 3.6.7 on Windows
>> 7. Phil's page NT1 does work on my system. I'm not sure about NT2. The
>> button is doing the following on NT2:
>>
>> jmolButton("load Structures/molecule4.pdb", "Load Chlorophyll");
>>
>> I don't think this is what Phil wanted the button to do. Typo?
>>
>> Otis
>>
>> Otis Rothenberger
>> chemagic.com
>>
>>
>>
>>
>>
>>
>> --
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> J. Philip Bays
> Professor of Chemistry
> Science Hall 172
> Saint Mary's College
> Notre Dame IN 46556
> (574) 284-4663
>
> --
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first --
> http://p.sf.net/sfu/sprint-com-first___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Access
Nope. NT1 gives the access denied error. NT2 works fine.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 24, 2010, at 1:50 PM, Philip Bays wrote:
> Jeff: It works on Firefox the initial time you try. If you shut down
> firefox and try again, does it work?
>
>
> On Jul 24, 2010, at 1:22 PM, Jeff Hansen wrote:
>
>> Works fine now on both Safari and Firefox.
>>
>>
>> *******
>> Jeff Hansen
>> Department of Chemistry and Biochemistry
>> DePauw University
>> 602 S. College Ave.
>> Greencastle, IN 46135
>> jhan...@depauw.edu
>> ***
>>
>>
>> On Jul 24, 2010, at 11:40 AM, Philip Bays wrote:
>>
>>> Sorry Otis and perhaps others. The code on NT2 was left from trying to
>>> reinsert the same structure. It is now updated.
>>>
>>> Phil
>>>
>>> On Jul 24, 2010, at 11:18 AM, Otis Rothenberger wrote:
>>>
>>>> Phil and Bob,
>>>>
>>>> With never ending Mac problems of my own, I'm very interested in this
>>>> chain. Just so I understand:
>>>>
>>>> 1) This a suspected Java cache problem - not a browser cache problem.
>>>> Is that correct?
>>>> 2) Do you know in what default state a Mac user, or Windows user for
>>>> that matter, is likely to find Java cache in Firefox - Window and Mac?
>>>>
>>>> This latter question relates to the fact that I cannot open the Java
>>>> console from the Windows Firefox tools menu selection item. There has
>>>> been some on going Firefox bug fuss on this issue, and I must admit I
>>>> was hoping that I could ignore this fuss. I'm using FF 3.6.7 on Windows
>>>> 7. Phil's page NT1 does work on my system. I'm not sure about NT2. The
>>>> button is doing the following on NT2:
>>>>
>>>> jmolButton("load Structures/molecule4.pdb", "Load Chlorophyll");
>>>>
>>>> I don't think this is what Phil wanted the button to do. Typo?
>>>>
>>>> Otis
>>>>
>>>> Otis Rothenberger
>>>> chemagic.com
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> This SF.net email is sponsored by Sprint
>>>> What will you do first with EVO, the first 4G phone?
>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>>> ___
>>>> Jmol-users mailing list
>>>> Jmol-users@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>> J. Philip Bays
>>> Professor of Chemistry
>>> Science Hall 172
>>> Saint Mary's College
>>> Notre Dame IN 46556
>>> (574) 284-4663
>>>
>>> --
>>> This SF.net email is sponsored by Sprint
>>> What will you do first with EVO, the first 4G phone?
>>> Visit sprint.com/first --
>>> http://p.sf.net/sfu/sprint-com-first___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>> --
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first --
>> http://p.sf.net/sfu/sprint-com-first___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> J. Philip Bays
> Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> (574) 284-4663
> pb...@saintmarys.edu
>
>
>
> --
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first --
> http://p.sf.net/sfu/sprint-com-first___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Access
Firefox version is 3.6.8
Java version is 1.6.0_20
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 24, 2010, at 5:07 PM, Robert Hanson wrote:
> Firefox version? Java version? (Java version can be read from the Jmol popup
> menu)
>
> On Sat, Jul 24, 2010 at 3:58 PM, Jeff Hansen wrote:
> Nope. NT1 gives the access denied error. NT2 works fine.
>
>
> *******
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhan...@depauw.edu
> ***
>
>
> On Jul 24, 2010, at 1:50 PM, Philip Bays wrote:
>
>> Jeff: It works on Firefox the initial time you try. If you shut down
>> firefox and try again, does it work?
>>
>>
>> On Jul 24, 2010, at 1:22 PM, Jeff Hansen wrote:
>>
>>> Works fine now on both Safari and Firefox.
>>>
>>>
>>> ***
>>> Jeff Hansen
>>> Department of Chemistry and Biochemistry
>>> DePauw University
>>> 602 S. College Ave.
>>> Greencastle, IN 46135
>>> jhan...@depauw.edu
>>> ***
>>>
>>>
>>> On Jul 24, 2010, at 11:40 AM, Philip Bays wrote:
>>>
>>>> Sorry Otis and perhaps others. The code on NT2 was left from trying to
>>>> reinsert the same structure. It is now updated.
>>>>
>>>> Phil
>>>>
>>>> On Jul 24, 2010, at 11:18 AM, Otis Rothenberger wrote:
>>>>
>>>>> Phil and Bob,
>>>>>
>>>>> With never ending Mac problems of my own, I'm very interested in this
>>>>> chain. Just so I understand:
>>>>>
>>>>> 1) This a suspected Java cache problem - not a browser cache problem.
>>>>> Is that correct?
>>>>> 2) Do you know in what default state a Mac user, or Windows user for
>>>>> that matter, is likely to find Java cache in Firefox - Window and Mac?
>>>>>
>>>>> This latter question relates to the fact that I cannot open the Java
>>>>> console from the Windows Firefox tools menu selection item. There has
>>>>> been some on going Firefox bug fuss on this issue, and I must admit I
>>>>> was hoping that I could ignore this fuss. I'm using FF 3.6.7 on Windows
>>>>> 7. Phil's page NT1 does work on my system. I'm not sure about NT2. The
>>>>> button is doing the following on NT2:
>>>>>
>>>>> jmolButton("load Structures/molecule4.pdb", "Load Chlorophyll");
>>>>>
>>>>> I don't think this is what Phil wanted the button to do. Typo?
>>>>>
>>>>> Otis
>>>>>
>>>>> Otis Rothenberger
>>>>> chemagic.com
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> This SF.net email is sponsored by Sprint
>>>>> What will you do first with EVO, the first 4G phone?
>>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>>>> ___
>>>>> Jmol-users mailing list
>>>>> Jmol-users@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>> J. Philip Bays
>>>> Professor of Chemistry
>>>> Science Hall 172
>>>> Saint Mary's College
>>>> Notre Dame IN 46556
>>>> (574) 284-4663
>>>>
>>>> --
>>>> This SF.net email is sponsored by Sprint
>>>> What will you do first with EVO, the first 4G phone?
>>>> Visit sprint.com/first --
>>>> http://p.sf.net/sfu/sprint-com-first___
>>>> Jmol-users mailing list
>>>> Jmol-users@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>> ---
Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly
Under no circumstances am I now able to get the chlorophyll model to load. I cleared the cache and restarted Firefox and it didn't load chlorophyll. Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8 Java 1.6.0_20 *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 25, 2010, at 11:24 AM, Robert Hanson wrote: > OK, I've tested this on my Mac with a freshly downloaded Firefox 3.6.8. > > No such problem. > > Phil, it looks to me like it might be a bad early version of 3.6.8. > > Mac users -- we need you to try this on Firefox 3.6.8: > > 1. load http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html > 2. click on the link under the applet to display chlorophyl > 3. close the browser > 4. open the browser > 5 repeat steps 1 and 2. > > Phil's experience is that in step 5 the click will not work. > My experience is that it will work. > > Please report EXACT Firefox version. > > Bob > > > > On Sun, Jul 25, 2010 at 10:00 AM, Robert Hanson wrote: > Phil, I went ahead and added a comment to that bug report to see what they > say. I'll try to dig up Firefox 3.6.8 on a Mac around here to get additional > specifics. > > Bob > > > On Sun, Jul 25, 2010 at 8:30 AM, Robert Hanson wrote: > Phil, wait, there are a couple more issues before you go back to them. > > 1) Did you say in that bug report that the signed applet has the same > problem? That would be a BIG and different issue. > > 2) The first structure always loads, right? That indicates that Java can > access its cache appropriately. > > 3) If only the second structure loading does not work, what we have is a > JavaScript thread issue. It is the JavaScript/LiveConnect THREAD that is > being blocked. > > 4) Tests you need to do: > > I. Try opening a console and issuing the load command from there. If it > loads, then it is DEFINITELY a browser liveConnect thread blocking issue. > > II. Try that again using the useCommandThread TRUE. > > Bob > > > > > > On Sun, Jul 25, 2010 at 8:11 AM, Robert Hanson wrote: > You should be able to get any version of Firefox, and in fact, if you search > your Mac applications directory you will probably find it. Just start it. > > OK, I have run a little test: > > 1. Monitor the Java Cache before and after starting the browser and loading > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm > > 2. Close the browser > > 3. Repeat step 1. > > 4. Close the browser > > 5. Upload a NEW caffeine.xyz > > 6. Repeat step 1. > > Findings: > > 1. Java never "clears its cache." It just stores the file and the header that > came from the server associated with that file. That header contains a date. > > 2. It looks like Java just first sends a message to a server asking for a > header, and if the header matches the one in the cache, then the file is not > downloaded, and the cached file is used instead. This is pretty standard > operation. > > > OK, so why the security bug? Obviously it is a Firefox bug. Doesn't happen in > older browsers; only appears with Mac 3.6.8. You need to respond to that bug > report reply and be very clear about that. It would be especially good if you > have verified that it all works with Firefox/Mac 3.5.7. > > > The bug is this (if you can confirm it on your Mac, Phil) > > Observation: Java applet running in Firefox 3.6.8/Mac specifically hit a > security violation when trying to read a file that was previously cached in a > prior browser session. > > Comments: This bug is specific to Firefox 3.6.8/Mac. It does not appear with > other operating systems and it does not appear with Firefox 3.5.7. All works > appropriately within one browser session, but after the browser is closed and > then re-opened, the applet cannot access any locally cached data file from > that previous session opened using Java's URL.openConnection() method. > > > Bob > > > On Sun, Jul 25, 2010 at 7:08 AM, Robert Hanson > > wrote: > Right - that does make sense -- submit a Java bug report, then. Make sure you > have the latest Java available. > > On Sun, Jul 25, 2010 at 6:27 AM, Philip Bays wrote: > Does this response make sense to anyone? If Firefox does not look at java > cache, how can adjusting the cache (removing a file, turning it on or off) > have any affect? Because it is a bug in java that does not affec
Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly
I can confirm the same behavior. I clicked the link for NT3 and it worked
fine. I reloaded NT1 (in another tab) and it worked fine. After restarting
Firefox and loading NT1, it did not work again until NT3 was loaded and I
reloaded the NT1 page.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jul 25, 2010, at 1:14 PM, Philip Bays wrote:
> Bob:
> Several answers and a comment. The signed applet always works fine. In
> fact, once it is run, the unsigned page works fine, IF you do not close down
> firefox, and it correctly loads the unsigned applet..
>
> The first structure always loads fine.
>
>
> I have not done your tests yet. However, let me say this.
>
> As I wrote about the crappy script I originally proposed, I could get even it
> to work if I added:
>
>jmolSetCallback("UseCommandThread","true");
>
> As I recall your response was that I should not use that, so I have not.
> However, I have now added that callback to the script, now located at:
>
> www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT3.html
>
> This script works. What does that tell us about what is going on? And do
> you still need me to run through the tests you have outline below.
>
> Phil
>
> On Jul 25, 2010, at 9:30 AM, Robert Hanson wrote:
>
>> Phil, wait, there are a couple more issues before you go back to them.
>>
>> 1) Did you say in that bug report that the signed applet has the same
>> problem? That would be a BIG and different issue.
>>
>> 2) The first structure always loads, right? That indicates that Java can
>> access its cache appropriately.
>>
>> 3) If only the second structure loading does not work, what we have is a
>> JavaScript thread issue. It is the JavaScript/LiveConnect THREAD that is
>> being blocked.
>>
>> 4) Tests you need to do:
>>
>> I. Try opening a console and issuing the load command from there. If it
>> loads, then it is DEFINITELY a browser liveConnect thread blocking issue.
>>
>> II. Try that again using the useCommandThread TRUE.
>>
>> Bob
>>
>>
>>
>>
>> On Sun, Jul 25, 2010 at 8:11 AM, Robert Hanson wrote:
>> You should be able to get any version of Firefox, and in fact, if you search
>> your Mac applications directory you will probably find it. Just start it.
>>
>> OK, I have run a little test:
>>
>> 1. Monitor the Java Cache before and after starting the browser and loading
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>>
>> 2. Close the browser
>>
>> 3. Repeat step 1.
>>
>> 4. Close the browser
>>
>> 5. Upload a NEW caffeine.xyz
>>
>> 6. Repeat step 1.
>>
>> Findings:
>>
>> 1. Java never "clears its cache." It just stores the file and the header
>> that came from the server associated with that file. That header contains a
>> date.
>>
>> 2. It looks like Java just first sends a message to a server asking for a
>> header, and if the header matches the one in the cache, then the file is not
>> downloaded, and the cached file is used instead. This is pretty standard
>> operation.
>>
>>
>> OK, so why the security bug? Obviously it is a Firefox bug. Doesn't happen
>> in older browsers; only appears with Mac 3.6.8. You need to respond to that
>> bug report reply and be very clear about that. It would be especially good
>> if you have verified that it all works with Firefox/Mac 3.5.7.
>>
>>
>> The bug is this (if you can confirm it on your Mac, Phil)
>>
>> Observation: Java applet running in Firefox 3.6.8/Mac specifically hit a
>> security violation when trying to read a file that was previously cached in
>> a prior browser session.
>>
>> Comments: This bug is specific to Firefox 3.6.8/Mac. It does not appear with
>> other operating systems and it does not appear with Firefox 3.5.7. All works
>> appropriately within one browser session, but after the browser is closed
>> and then re-opened, the applet cannot access any locally cached data file
>> from that previous session opened using Java's URL.openConnection() method.
>>
>>
>> Bob
>>
>>
>> On Sun, Jul 25, 2010 at 7:08 AM, Robert Hanson
>>
>> wrote:
>> Right - that does make sense -- submit a Java bug report, then. Make sure
>> you have the
Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly
Sorry, not sure where to find that. I cleared them from the Firefox Tools menu. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 25, 2010, at 1:25 PM, Philip Bays wrote: > Did you clear the Java cache from the java preferences panel? That seems to > be the key. > > On Jul 25, 2010, at 1:15 PM, Jeff Hansen wrote: > >> Under no circumstances am I now able to get the chlorophyll model to load. >> I cleared the cache and restarted Firefox and it didn't load chlorophyll. >> >> Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.8) >> Gecko/20100722 Firefox/3.6.8 >> Java 1.6.0_20 >> >> >> *** >> Jeff Hansen >> Department of Chemistry and Biochemistry >> DePauw University >> 602 S. College Ave. >> Greencastle, IN 46135 >> jhan...@depauw.edu >> *** >> >> >> On Jul 25, 2010, at 11:24 AM, Robert Hanson wrote: >> >>> OK, I've tested this on my Mac with a freshly downloaded Firefox 3.6.8. >>> >>> No such problem. >>> >>> Phil, it looks to me like it might be a bad early version of 3.6.8. >>> >>> Mac users -- we need you to try this on Firefox 3.6.8: >>> >>> 1. load http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html >>> 2. click on the link under the applet to display chlorophyl >>> 3. close the browser >>> 4. open the browser >>> 5 repeat steps 1 and 2. >>> >>> Phil's experience is that in step 5 the click will not work. >>> My experience is that it will work. >>> >>> Please report EXACT Firefox version. >>> >>> Bob >>> >>> >>> >>> On Sun, Jul 25, 2010 at 10:00 AM, Robert Hanson wrote: >>> Phil, I went ahead and added a comment to that bug report to see what they >>> say. I'll try to dig up Firefox 3.6.8 on a Mac around here to get >>> additional specifics. >>> >>> Bob >>> >>> >>> On Sun, Jul 25, 2010 at 8:30 AM, Robert Hanson wrote: >>> Phil, wait, there are a couple more issues before you go back to them. >>> >>> 1) Did you say in that bug report that the signed applet has the same >>> problem? That would be a BIG and different issue. >>> >>> 2) The first structure always loads, right? That indicates that Java can >>> access its cache appropriately. >>> >>> 3) If only the second structure loading does not work, what we have is a >>> JavaScript thread issue. It is the JavaScript/LiveConnect THREAD that is >>> being blocked. >>> >>> 4) Tests you need to do: >>> >>> I. Try opening a console and issuing the load command from there. If it >>> loads, then it is DEFINITELY a browser liveConnect thread blocking issue. >>> >>> II. Try that again using the useCommandThread TRUE. >>> >>> Bob >>> >>> >>> >>> >>> >>> On Sun, Jul 25, 2010 at 8:11 AM, Robert Hanson wrote: >>> You should be able to get any version of Firefox, and in fact, if you >>> search your Mac applications directory you will probably find it. Just >>> start it. >>> >>> OK, I have run a little test: >>> >>> 1. Monitor the Java Cache before and after starting the browser and loading >>> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm >>> >>> 2. Close the browser >>> >>> 3. Repeat step 1. >>> >>> 4. Close the browser >>> >>> 5. Upload a NEW caffeine.xyz >>> >>> 6. Repeat step 1. >>> >>> Findings: >>> >>> 1. Java never "clears its cache." It just stores the file and the header >>> that came from the server associated with that file. That header contains a >>> date. >>> >>> 2. It looks like Java just first sends a message to a server asking for a >>> header, and if the header matches the one in the cache, then the file is >>> not downloaded, and the cached file is used instead. This is pretty >>> standard operation. >>> >>> >>> OK, so why the security bug? Obviously it is a Firefox bug. Doesn't happen >&g
Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly
Ok. I'm not sure this will add any helpful info, but this is what I tested this morning on Mac OS X 10.6.4 with Firefox 3.6.8 and Java 1.6.0_20. Went to Java Preferences.app and cleared the cache. Started up Firefox and loaded NT1. Clicked the Load Chlorophyll button. Worked fine. Closed Firefox and reopened it. Loaded NT1 and clicked the button. Now chlorophyll doesn't load (file access error). Went to Java Preferences and cleared the cache. Reloaded NT1. Still doesn't work. Closed Firefox, reopened it, and loaded NT1. Now it works. Reloaded NT1, still works. As long as I keep the browser open and reload the page or open it in a new tab, it works. As soon as I close Firefox and restart it, it doesn't work unless the cache has first been cleared. When the chlorophyll is not loading by the button, it loads from the console as Phil has already noted. NT3 works fine in all situations. I downloaded Firefox 3.6.7, 3.6.6, 3.5.11, 3.5.10, and 3.0.19 and observed the same behavior with all of them. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 25, 2010, at 1:55 PM, Philip Bays wrote: > Go to Application/Utilities/Java Preferences.ap. Once open go to the network > tab. Toward the bottom there is a button to view cache files. > If you select them all, and there may be many, click the X at the top to > delete them. Or, if you really want to demonstrate the issue, only remove > the one for the chlorophyll file. > > I have used Cocktail, Firefox, and applejack which each claims to clear the > Java cache. None of them do:-( > This is the only way I have found to do it. > > If you have your system set to clear java cache when the browser is shut down > (however you do that -- I can't figure it out) then you will not observe the > error. > > > > Phil > > On Jul 25, 2010, at 1:47 PM, Jeff Hansen wrote: > >> Sorry, not sure where to find that. I cleared them from the Firefox Tools >> menu. >> >> >> *** >> Jeff Hansen >> Department of Chemistry and Biochemistry >> DePauw University >> 602 S. College Ave. >> Greencastle, IN 46135 >> jhan...@depauw.edu >> *** >> >> >> On Jul 25, 2010, at 1:25 PM, Philip Bays wrote: >> >>> Did you clear the Java cache from the java preferences panel? That seems >>> to be the key. >>> >>> On Jul 25, 2010, at 1:15 PM, Jeff Hansen wrote: >>> >>>> Under no circumstances am I now able to get the chlorophyll model to load. >>>> I cleared the cache and restarted Firefox and it didn't load chlorophyll. >>>> >>>> Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.8) >>>> Gecko/20100722 Firefox/3.6.8 >>>> Java 1.6.0_20 >>>> >>>> >>>> *** >>>> Jeff Hansen >>>> Department of Chemistry and Biochemistry >>>> DePauw University >>>> 602 S. College Ave. >>>> Greencastle, IN 46135 >>>> jhan...@depauw.edu >>>> *** >>>> >>>> >>>> On Jul 25, 2010, at 11:24 AM, Robert Hanson wrote: >>>> >>>>> OK, I've tested this on my Mac with a freshly downloaded Firefox 3.6.8. >>>>> >>>>> No such problem. >>>>> >>>>> Phil, it looks to me like it might be a bad early version of 3.6.8. >>>>> >>>>> Mac users -- we need you to try this on Firefox 3.6.8: >>>>> >>>>> 1. load http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html >>>>> 2. click on the link under the applet to display chlorophyl >>>>> 3. close the browser >>>>> 4. open the browser >>>>> 5 repeat steps 1 and 2. >>>>> >>>>> Phil's experience is that in step 5 the click will not work. >>>>> My experience is that it will work. >>>>> >>>>> Please report EXACT Firefox version. >>>>> >>>>> Bob >>>>> >>>>> >>>>> >>>>> On Sun, Jul 25, 2010 at 10:00 AM, Robert Hanson >>>>> wrote: >>>>> Phil, I went ahead and added a comment to that bug report to see what &
Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly
Failed with Firefox 3.5.11. Didn't notice at first. The page must load problems randomly. The first couple times I tried it loaded the second problem without error because the model hadn't been loaded previously. Once I clicked through several problems then quit Firefox and restarted it then it "reliably" failed to load them with the usual file access error. It may not be the case that the page was failing in Firefox going back that far in time. It might very well work ok with previous versions of Java. I don't have a machine with an older version of Java on it to test that. ******* Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 27, 2010, at 7:20 AM, Philip Bays wrote: > Wow. I find it hard to believe that my Stereochemistry page did not behave > properly that long ago. We are about to leave town so I do not have time to > look at this for another week or so. But it would be interesting to have you > test the following URL with an old version of Firefox: > > www.saintmarys.edu/~pbays/Stereochemistery.html > > Choose option 3. The others use the signed applet at the moment. > > If this is the case, then things point to jmol or Java 1.6, I think. Is it > possible to checK a page out with an old version of jmol and an old version > of firefox? Snow Leopard could also be the culprit. I note that Bob is > running 10.5, not 10.6 and that he does not observe the issue. > > All of the Mozilla browsers use the Java Embedding Plugin to enable java > applets. Disabling that kills jmol altogether. That has not been updated in > awhile and I am wondering if that is an issue. I have written the author > but not received a response. > > I have also confirmed the Firfox 4.0b1 throws the jmol.js error, but does > load chloropyll, even when it is in Java Cache. I will continue to watch the > beta releases to see when they institute something that kills it. > > Phil > > On Jul 26, 2010, at 9:55 AM, Jeff Hansen wrote: > >> Ok. I'm not sure this will add any helpful info, but this is what I tested >> this morning on Mac OS X 10.6.4 with Firefox 3.6.8 and Java 1.6.0_20. >> >> Went to Java Preferences.app and cleared the cache. Started up Firefox and >> loaded NT1. Clicked the Load Chlorophyll button. Worked fine. Closed >> Firefox and reopened it. Loaded NT1 and clicked the button. Now >> chlorophyll doesn't load (file access error). Went to Java Preferences and >> cleared the cache. Reloaded NT1. Still doesn't work. Closed Firefox, >> reopened it, and loaded NT1. Now it works. Reloaded NT1, still works. As >> long as I keep the browser open and reload the page or open it in a new tab, >> it works. As soon as I close Firefox and restart it, it doesn't work unless >> the cache has first been cleared. When the chlorophyll is not loading by >> the button, it loads from the console as Phil has already noted. NT3 works >> fine in all situations. >> >> I downloaded Firefox 3.6.7, 3.6.6, 3.5.11, 3.5.10, and 3.0.19 and observed >> the same behavior with all of them. >> > > J. Philip Bays > Professor of Chemistry > Department of Chemistry and Physics > Saint Mary's College > Notre Dame, IN 46556 > (574) 284-4663 > pb...@saintmarys.edu > > > > > -- > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://ad.doubleclick.net/clk;226879339;13503038;l? > http://clk.atdmt.com/CRS/go/247765532/direct/01/ > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://ad.doubleclick.net/clk;226879339;13503038;l? http://clk.atdmt.com/CRS/go/247765532/direct/01/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] change the visible part of an isosurface without reloading
Alex,
I'm not sure what you are doing on your web page, but it is causing some
strange behavior for me on Safari 5.0 on OS X 10.6.4. Several times it crashed
the browser. It seems to be opening the page and somehow automatically opening
what looks like Firebug, but it is behind the applets so I can't see it well
except for when scrolling.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Aug 16, 2010, at 12:14 PM, Alexander Rose wrote:
> Hi,
>
> - Ursprüngliche Mail -
>> Von: "Robert Hanson"
>> An: jmol-users@lists.sourceforge.net
>> Gesendet: Dienstag, 10. August 2010 14:48:50
>> Betreff: Re: [Jmol-users] change the visible part of an isosurface without
>> reloading
>> On Tue, Aug 10, 2010 at 7:33 AM, Alexander Rose <
>> alexander.r...@weirdbyte.de > wrote:
>>
>> It's certainly an interesting idea, though. Sort of a "hide selected
>> triangles" option, I think. Hmm. We have:
>>
>> isosurface ID "foo" show
>> isosurface ID "foo" hide
>>
>> maybe
>>
>> isosurface ID "foo" show within 2.0 {atomset}
>> isosurface ID "foo" show all
>>
>
> thanks for implementing it as 'isosurface display within 2.0 {atomset}'
>
> Example: http://weirdbyte.de/jmol-test/html/jvxl_vs_ccp4_speed.html
>
> One minor thing: When changing the display params via a jmolscript
> PickCallback (see below), I get a loading indicator which stays until a
> mouseclick. However it works. (Tested on Linux/Firefox, Mac/Firefox/Safari)
>
>
> Alex
>
> --
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev ___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] change the visible part of an isosurface without reloading
Yes, upping the memory given to java seems to have helped. I think in the
process of editing the page you may have messed something else up since the
following is showing at the bottom of the page.
function klick(){
isosurface display within 5.0 ({atomIndex = _atomPicked});
center {atomIndex = _atomPicked};
}
set PickCallback "jmolscript:klick();";
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Aug 16, 2010, at 4:20 PM, Alexander Rose wrote:
> Hi,
>
> Am 16.08.2010 um 20:58 schrieb Jeff Hansen:
>
>> Alex,
>>
>> I'm not sure what you are doing on your web page, but it is causing some
>> strange behavior for me on Safari 5.0 on OS X 10.6.4. Several times it
>> crashed the browser. It seems to be opening the page and somehow
>> automatically opening what looks like Firebug, but it is behind the applets
>> so I can't see it well except for when scrolling.
>>
>
> I'm sorry, forgot about smaller monitors, made the applet smaller.
>
> It was opening FirebugLite, I removed it, wasn't need here.
>
> I also removed one of the applets, the remaining one is enough to make my
> point.
>
> Your browser was probably crashing, because the applet did not had enough
> memory, 512M should be enough
> (http://wiki.jmol.org/index.php?title=Jmol_Applet#Giving_JmolApplet_more_memory_to_work_with).
> I thought stating 'jmolSetMemoryMb("512");' would do the trick, but it it
> seems not to work, neither for the signed nor the unsigned applet.
>
> Sorry for the inconvenience
> Alex
>
>
>
>>
>> Jeff
>>
>>
>> ***
>> Jeff Hansen
>> Department of Chemistry and Biochemistry
>> DePauw University
>> 602 S. College Ave.
>> Greencastle, IN 46135
>> jhan...@depauw.edu
>> ***
>>
>>
>> On Aug 16, 2010, at 12:14 PM, Alexander Rose wrote:
>>
>>> Hi,
>>>
>>> - Ursprüngliche Mail -
>>>> Von: "Robert Hanson"
>>>> An: jmol-users@lists.sourceforge.net
>>>> Gesendet: Dienstag, 10. August 2010 14:48:50
>>>> Betreff: Re: [Jmol-users] change the visible part of an isosurface without
>>>> reloading
>>>> On Tue, Aug 10, 2010 at 7:33 AM, Alexander Rose <
>>>> alexander.r...@weirdbyte.de > wrote:
>>>>
>>>> It's certainly an interesting idea, though. Sort of a "hide selected
>>>> triangles" option, I think. Hmm. We have:
>>>>
>>>> isosurface ID "foo" show
>>>> isosurface ID "foo" hide
>>>>
>>>> maybe
>>>>
>>>> isosurface ID "foo" show within 2.0 {atomset}
>>>> isosurface ID "foo" show all
>>>>
>>>
>>> thanks for implementing it as 'isosurface display within 2.0 {atomset}'
>>>
>>> Example: http://weirdbyte.de/jmol-test/html/jvxl_vs_ccp4_speed.html
>>>
>>> One minor thing: When changing the display params via a jmolscript
>>> PickCallback (see below), I get a loading indicator which stays until a
>>> mouseclick. However it works. (Tested on Linux/Firefox, Mac/Firefox/Safari)
>>>
>>>
>>> Alex
>>>
>>> --
>>> This SF.net email is sponsored by
>>>
>>> Make an app they can't live without
>>> Enter the BlackBerry Developer Challenge
>>> http://p.sf.net/sfu/RIM-dev2dev
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>> --
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
>> Enter the BlackBerry Developer Challenge
>> http://p.sf.net/sfu/RIM-dev2dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> --
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev ___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol problems
Hi all, I've been experiencing some problems with Jmol applet recently and wanted to see if anyone else has these same problems. I first noticed the problem when trying to use Eric Martz's excellent Jmol Tutorial Authoring Template (actually anything from Eric). Basically the page would load but the applet would bail (literally the message bar would say the applet bailed). This is in Safari 5.0.1 on Mac OS X 10.6.4. The pages loaded ok in Firefox (3.6.8). Next I found that Bob Hanson's interactive examples page (http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm) didn't work. The initial Jmol applet load worked ok. When I clicked on the first link (load C6H6.smol) nothing happened and if I persisted or tried to do something else, Safari crashed. Investigating further, I found that turning off extensions fixed both problems. Now both Eric's and Bob's pages work. In other words, there appears to be a problem with Jmol and extensions in Safari 5. However, when I go to Bob's interactive examples page in Firefox, I'm now getting a couple error messages when I click on the C6H6.smol link. They are (in order): Applet jmolApplet0 reports an error of type ScriptException: object: java.security.AccessControlException: access denied (java.util.PropertyPermission http.agent read) load >> "C6H6.smol" << The page at http://chemapps.stolaf.edu says:java.security.AccessControlException: access denied (java.util.PropertyPermission http.agent read) load >> "C6H6.smol" << script ERROR: java.security.AccessControlException: access denied (java.util.PropertyPermission http.agent read) load >> "C6H6.smol" << Anyone else have a similar experience? *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol problems
Ah yes. I remember the Firefox issue now. Glad it isn't just me. Tracked down the offending extension. It is AdBlock. I'm reluctant to turn it off, but I guess I'll have to - at least when I'm using Jmol. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Sep 13, 2010, at 9:47 PM, Philip Bays wrote: > I do not have a problem using Safari (5.0.2) with Bob's page, with or without > extensions. Can we connect it to a particular extension? > > The Firefox issue is one that we discussed some time ago and that still > exists. It is related the the Java Embedding Plugin in Firefox. > > Phil Bays > > On Sep 13, 2010, at 9:26 PM, Jeff Hansen wrote: > >> Hi all, >> >> I've been experiencing some problems with Jmol applet recently and wanted to >> see if anyone else has these same problems. I first noticed the problem >> when trying to use Eric Martz's excellent Jmol Tutorial Authoring Template >> (actually anything from Eric). Basically the page would load but the applet >> would bail (literally the message bar would say the applet bailed). This is >> in Safari 5.0.1 on Mac OS X 10.6.4. The pages loaded ok in Firefox (3.6.8). >> Next I found that Bob Hanson's interactive examples page >> (http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm) didn't work. The >> initial Jmol applet load worked ok. When I clicked on the first link (load >> C6H6.smol) nothing happened and if I persisted or tried to do something >> else, Safari crashed. Investigating further, I found that turning off >> extensions fixed both problems. Now both Eric's and Bob's pages work. In >> other words, there appears to be a problem with Jmol and extensions in >> Safari 5. However, when I go to Bob's interactive examples page in Firefox, >> I'm now getting a couple error messages when I click on the C6H6.smol link. >> They are (in order): >> >> Applet jmolApplet0 reports an error of type ScriptException: >> >> object: >> >> java.security.AccessControlException: access denied >> (java.util.PropertyPermission http.agent read) >> >> load >> "C6H6.smol" << >> >> >> The page at http://chemapps.stolaf.edu >> says:java.security.AccessControlException: access denied >> (java.util.PropertyPermission http.agent read) >> >> load >> "C6H6.smol" << >> >> script ERROR: java.security.AccessControlException: access denied >> (java.util.PropertyPermission http.agent read) >> >> load >> "C6H6.smol" << >> >> >> Anyone else have a similar experience? >> >> >> >> *** >> Jeff Hansen >> Department of Chemistry and Biochemistry >> DePauw University >> 602 S. College Ave. >> Greencastle, IN 46135 >> jhan...@depauw.edu >> *** >> >> >> -- >> Start uncovering the many advantages of virtual appliances >> and start using them to simplify application deployment and >> accelerate your shift to cloud computing. >> http://p.sf.net/sfu/novell-sfdev2dev___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > J. Philip Bays > Professor of Chemistry > Department of Chemistry and Physics > Saint Mary's College > Notre Dame, IN 46556 > (574) 284-4663 > pb...@saintmarys.edu > > > > -- > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol in the Classroom
I just checked this out. I sporadically observed this behavior of zooming instead of rotating. It didn't always happen even after loading several structures. It would happen once or twice then not happen. It was rather random in my case. Each time it happened, a couple of taps on my trackpad would usually get it out of this zooming mode and return it to the normal rotating. A few times it would switch into translating mode but again would eventually get to rotating after tapping a few times on the trackpad. It seems somehow the applet is confusing a single tap and drag for a two finger tap and drag or some other dragging with a key down. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Sep 20, 2010, at 12:51 PM, Philip Bays wrote: > Bob: > > I like this a lot!! > > However --- (there is always a however, isn't there.) On a Mac, using > Safari, I observe something that I think was discussed earlier but I do not > remember if there was a resolution. > > The first two or three structures I request work fine. However, at some > point, the rotate function becomes zoom. That is, left-mouse drag zooms > instead of rotates. If I open the contextual menu, scroll down but do not > select anything, the problem is remedied for that structure, but it recurs > on loading the next. > > I have observed this on an iMac with a Mac mouse, and on a MacPro laptop. I > am running the latest vs. of the OS (10.6.4) and using your web link (below). > > Phil > > > On Sep 20, 2010, at 12:00 PM, Robert Hanson wrote: > >> What do you think of starting a Wiki page "Jmol in the Classroom" -- or >> perhaps, to be consistent, "Classrooms Using Jmol" >> >> People could enter "teachable moments" when they used Jmol in an effective >> way during class. >> >> Here's a possible first installment: >> >> Today, Day 5 of first-semester organic chemistry -- Textbook Smith, 3rd Ed. >> -- Chapter 3 -- Topic "Functional Groups" >> >> I thought it would be fun to get students to suggest examples, so I fired up >> >> http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm >> >> (This page, as of this morning, has a new button on the right that uses the >> PROMPT command in Jmol 12 and taps into the NIH Cactus service using LOAD >> $chemicalName. Look in the page source for that very simple code.) >> >> I just clicked on "Load MOL by NAME" and then asked them to give me a name >> of something they knew, like a medication. >> >> We ended up looking at diphenylhydramine, morphine, THC, heroin, >> hydrocodone, adderall, and tetracycline, writing out several of these >> structures on the board based on the 3D models. This lead to discussions of >> reactivity, hints about the connections between names (even these trade >> names) and functional groups, a little about the blood/brain barrier issue, >> hints about synthesis (it's amazing how simple many of these drugs are). >> >> Great fun. >> >> Bob >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> -- >> Start uncovering the many advantages of virtual appliances >> and start using them to simplify application deployment and >> accelerate your shift to cloud computing. >> http://p.sf.net/sfu/novell-sfdev2dev___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > J. Philip Bays > Professor of Chemistry > Science Hall 172 > Saint Mary's College > Notre Dame IN 46556 > (574) 284-4663 > > -- > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Problem with export to web
I'm having my students do an assignment using Jmol. I had each one download
Jmol 12.0.12 (latest at the time) and rename the folder to Jmol_XXX where XXX
is there initials. I then had them create a subfolder called JmolAssignment
and download 1BF3 from the PDB and save it in the JmolAssignment folder. They
then opened 1BF3, did some stuff and used the export to web command to create a
web page with some buttons to show off the molecule. Once they were done with
it I had them copy the Jmol_XXX folder containing all of their work to a
Dropbox folder I shared with them. I'm copying the folder to my desktop and
opening the html file and the Jmol applet is not loading. I'm getting an error
that says "Result of expression 'applet.script' [undefined] is not a function."
at line line 410 in Jmol.js which is in this section of code in the jmolScript
function.
} else {
var applet=_jmolGetApplet(targetSuffix);
if (applet) applet.script(script);
}
}
Any suggestions on what I'm doing wrong?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
--
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Solved my own problem
I found a solution to my problem with Export to Jmol. When I looked at the html file (in both cases I've seen so far) it contained the following. Using directory /Users/andrewpfaff/Desktop/Jmol_ASP/JmolAssignment adding JmolPopIn.js ...jmolApplet0 ...adding CpkColored1BF3WithLigand.png Could not find or open: file:/Users/andrewpfaff/Desktop/Jmol_ASP/JmolAssignment/1BF3.pdb ...adding CpkColored1BF3WithLigand.spt ...jmolApplet1 ...adding BlueHydrophobicGreenPolar1BF3.png Could not find or open: file:/Users/andrewpfaff/Desktop/Jmol_ASP/JmolAssignment/1BF3.pdb ...adding BlueHydrophobicGreenPolar1BF3.spt ...jmolApplet2 ...adding ChargedResidues1BF3WithLigand.png Could not find or open: file:/Users/andrewpfaff/Desktop/Jmol_ASP/JmolAssignment/1BF3.pdb ...adding ChargedResidues1BF3WithLigand.spt ...jmolApplet3 ...adding 1BF3SidechainsWithin10AOfLigand.png Could not find or open: file:/Users/andrewpfaff/Desktop/Jmol_ASP/JmolAssignment/1BF3.pdb ...adding 1BF3SidechainsWithin10AOfLigand.spt When I deleted it, restarted my browser and opened the page again, it was fine. Any ideas where this came from? *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Solved my own problem
The problem does not occur when the students are working in their own local folders. What I showed you was all that I deleted - just text within a tag. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Oct 5, 2010, at 1:57 PM, Angel Herráez wrote: > I'd bet that's a copy of the Log from Export To Web session, but it should > not affect the > working of the applet. > > Maybe there is some bit of code unfinished, like an open tag? > I assume that the problem is not present when your students have the files > in their local > folder, right? > > > > -- > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Solved my own problem
Ok. I just double checked. It appears to be some weird cache thing. The first one I looked at had some problems, I think the 1BF3.pdb file was missing when she did the export to web. When I tried to look at hers I got an error. When I got a second student's work and tried to look at it, I got the same problem. I noticed the stuff in the pre tab and deleted it then restarted my browser. It worked after that. Turns out it must have been restarting the browser that did it, not deleting the stuff from the html file. Now it is working for both of them. Sorry for the confusion. Thought it was weird. Just glad I don't have to open each html file and delete stuff. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Oct 5, 2010, at 2:48 PM, Jonathan Gutow wrote: > Jeff, > > I'm confused. What you deleted should be invisible text that is there > for record keeping, so we can trace errors in creating the page. It > appears that the example you provided was created without the files > being where they were expected to be. I apologize if you've already > explained how the pages were created. I seem to have missed the > beginning of this discussion. > > If the text you deleted is accurate, I don't think the pages created > by export to web should be working. Did you have to go back and put > lots of files in the directory created by Jmol? > > I'm pretty swamped until this weekend, but if things don't get better > zip up and example directory created by export to web and send it to > me. I'll try to look at it as soon as possible. > > Jonathan > On Oct 5, 2010, at 1:35 PM, jmol-users-requ...@lists.sourceforge.net > wrote: > >> Message: 4 >> Date: Tue, 5 Oct 2010 14:34:57 -0400 >> From: Jeff Hansen >> Subject: Re: [Jmol-users] Solved my own problem >> To: jmol-users@lists.sourceforge.net >> Message-ID: <79b07a49-e80e-482c-89d2-da5ec28fe...@depauw.edu> >> Content-Type: text/plain; charset="iso-8859-1" >> >> The problem does not occur when the students are working in their >> own local folders. What I showed you was all that I deleted - just >> text within a tag. > > Dr. Jonathan H. Gutow > Chemistry Department gu...@uwosh.edu > UW-Oshkosh Office:920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/facstaff/gutow > > > > > > > -- > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and SVG
Or perhaps also a tag object. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Apr 17, 2011, at 6:56 AM, Rzepa, Henry wrote: > The introduction of gesture based browsers (for example Safari on the > iPad) has made me realise how valuable scaleable graphics are. Jmol > currently writes out three unscaleable (or at least not without loss) bitmap > formats (gif, jpg and png). Might we consider adding the lossless vector > format SVG to this output? > > I note with surprise and much gratitude that all the major browsers now > support SVG very well indeed (even on the iPad). And as an XML language, > SVG has the advantage of retaining (eg) atom coordinates and much else. > -- > > +44 (020) 7594 5774 (Voice); Blog: http://www.ch.ic.ac.uk/rzepa/blog/ > Dept. Chemistry, Imperial College London, SW7 2AZ, UK. > > (Voracious anti-spam filter in operation for received email. > If expected reply not received, please phone/fax). > > > > -- > Benefiting from Server Virtualization: Beyond Initial Workload > Consolidation -- Increasing the use of server virtualization is a top > priority.Virtualization can reduce costs, simplify management, and improve > application availability and disaster protection. Learn more about boosting > the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New Resolver Version
I guess I'd be a little wary of having my students use this too much. It seems to be reinforcing common mistakes. If they can type in an incorrect name and still get a structure, they may not understand why their answer is not correct. "But professor, the computer gave me the right structure so my name must be correct!" ******* Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Apr 22, 2011, at 1:34 PM, Otis Rothenberger wrote: > It also takes care of our students who don't quite get it! > > http://cactus.nci.nih.gov/chemical/structure/4,4,2-trimethylpentane/image > > Otis > > -- > Otis Rothenberger > Department of Chemistry > Illinois State University Normal, IL 61790-4160 > http://chemagic.org > > -- > Fulfilling the Lean Software Promise > Lean software platforms are now widely adopted and the benefits have been > demonstrated beyond question. Learn why your peers are replacing JEE > containers with lightweight application servers - and what you can gain > from the move. > http://p.sf.net/sfu/vmware-sfemails___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New Resolver Version
Agreed. I think this is a wonderful, powerful tool. Just need to be careful with how students use it in regards to nomenclature. They get confused enough as it is. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Apr 22, 2011, at 2:42 PM, Otis Rothenberger wrote: > Hi Jeff, > > I'm sorry I brought it up ;-) But I agree wholeheartedly with you. It is not > a student tutorial response system! > > That said, don't let my attempt at a bit of humor distract from the > tremendous power of this tool. If the "isooctane" response with the wrong > IUPAC query is indeed not a fluke, I suspect that this was built into the > system as a feature because of the frequency of IUPAC numbering reversals, > even by experienced chemists. I picked "isooctane" simply because it is a > classical student IUPAC naming error. > > With this new addition to Resolver, however, there is a student tutorial > avenue open now that did not exist before: > > http://cactus.nci.nih.gov/chemical/structure/4,4,2-trimethylpentane/iupac_name > > The real power, however, is quickly translating obscure journal names into > structures - 2D and 3D. > > This brings up an interesting thought: What will Resolver respond to the > actual query "isooctane?" Does Resolver have a sense of industrial chemical > history? How will it respond? I'll let you check! > > http://cactus.nci.nih.gov/chemical/structure/isooctane/iupac_name > > Otis > > -- > Otis Rothenberger > Department of Chemistry > Illinois State University Normal, IL 61790-4160 > http://chemagic.org > > From: "Jeff Hansen" > Sent: Friday, April 22, 2011 2:03 PM > To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net > Subject: Re: [Jmol-users] New Resolver Version > > I guess I'd be a little wary of having my students use this too much. It > seems to be reinforcing common mistakes. If they can type in an incorrect > name and still get a structure, they may not understand why their answer is > not correct. "But professor, the computer gave me the right structure so my > name must be correct!" > > > *** > Jeff Hansen > Department of Chemistry and Biochemistry > DePauw University > 602 S. College Ave. > Greencastle, IN 46135 > jhan...@depauw.edu > *** > > > On Apr 22, 2011, at 1:34 PM, Otis Rothenberger wrote: > >> It also takes care of our students who don't quite get it! >> >> http://cactus.nci.nih.gov/chemical/structure/4,4,2-trimethylpentane/image >> >> Otis >> >> -- >> Otis Rothenberger >> Department of Chemistry >> Illinois State University Normal, IL 61790-4160 >> http://chemagic.org >> >> -- >> Fulfilling the Lean Software Promise >> Lean software platforms are now widely adopted and the benefits have been >> demonstrated beyond question. Learn why your peers are replacing JEE >> containers with lightweight application servers - and what you can gain >> from the move. >> http://p.sf.net/sfu/vmware-sfemails___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > Fulfilling the Lean Software Promise > Lean software platforms are now widely adopted and the benefits have been > demonstrated beyond question. Learn why your peers are replacing JEE > containers with lightweight application servers - and what you can gain > from the move. > http://p.sf.net/sfu/vmware-sfemails___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Is there command to rotate protein to show the particular residue
Would it be possible to add an invisible atom in front of the protein and
rotate the protein until the distance from the selected residue to the
invisible atom is minimized?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jun 7, 2011, at 5:40 PM, Robert Hanson wrote:
> yeah, for that you are going to have to do some scripting. It's a classic
> problem -- that of finding the "best" view of a particular part of a protein.
> I think if you have a particular protein in mind, it should be possible, but
> it's really a very big challenge.
>
> What I was trying to point out there is that you should learn a bit about how
> Jmol uses quaternions. These are direct measures of orientation, and that's
> precisely what you need here. They can be multiplied and inverted like
> matrices, and they are just very convenient. So you would do some
> constructing of quaternions and combine them as desired to get the view you
> want. An illustration of this is at the Klotho site, where I am using
> quaternions to orient molecules that are coming from a database and have all
> sorts of odd orientations.
>
> http://chemapps.stolaf.edu/klotho
>
> Basically, you can define a little "xyz frame" in the form of a quaternion
> using any three atoms:
>
> Var q = quaternion({atomno=1} {atomno=2} {atomno=3})
>
> and then you can use that to do all sorts of interesting things.
>
>
> On Tue, Jun 7, 2011 at 7:17 AM, M K wrote:
> Thanks, I have tried this. This is great, but not completely what I need.
> As I understand this command (moveto quaternion { residue as the center of rotation and moves it to the center of the window.
> Unfortunately, residue can be shadowed by other residues of protein.
> What I need is to bring the desired residue to the front. This residue should
> not be new center of rotation.
> OK, if there is no appropriate command I guess I can write script to rotate
> molecule in desired way - to bring particular residue to the front of view.
> For this I should calculate rotational angles that is needed.
> So, my question is where is the zero points of rotational angles?
>
>
> 2011/6/7 Robert Hanson
> Ah, sure. For this I would recommend using quaternion rotation. Basically
> each amino acid is assigned an xyz frame that is positioned in a way that
> depends upon the setting of the "quaternionFrame" -- C, P, or N. Then the
> moveto command has the keyword QUATERNION, which can be followed by a residue
> number:
>
> set quaternionFrame "C"
> moveto quaternion {5}
>
> This orients the molecule relative to that residue.
>
>
> On Mon, Jun 6, 2011 at 5:57 PM, M K wrote:
> Dear all,
>
> Form my web-page that incorporates Jmol applet I would like to issue command
> to show particular residue of protein (to rotate molecule by the appropriate
> angle) in response to the pressing the button by user.
> Is there the appropriate command in Jmol?
> If not, I guess I could write a script which rotate molecule by the
> appropriate angel. But where is the zero angle of molecule? How is it defined?
>
> Thanks,
> seven32
>
> --
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> --
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/l
Re: [Jmol-users] 404 (Not Found) error in jmol
Whatever the problem is I don't think you can blame it on Safari. All three links are fine for me in Safari 5.1, OS 10.6.8. No error messages in the console. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Aug 23, 2011, at 12:31 PM, Robert Hanson wrote: > 1) I don't think that's a JavaScript error. And it's not coming from Jmol.js. > 2) Code looks fine; operation in Firefox/Windows works fine > 3) Not having a Mac, I can't field test this right now (in Valladolid, Spain) > > A Safari bug? Can't imagine what that's about. I suggest you ignore it if all > is fine. > > On Mon, Aug 22, 2011 at 8:40 AM, Yingjie Lin wrote: > Hi Bob, > > I am very sorry. There was a problem with the links. > http://scbx.mssm.edu/sitecomp/1kna/22.html (uses jmol-12.0.22) > http://scbx.mssm.edu/sitecomp/1kna/39.html (uses jmol-12.0.39) > http://scbx.mssm.edu/sitecomp/1kna/48.html (uses jmol-12.0.48) > > - Yingjie > > On Aug 22, 2011, at 6:14 AM, jmol-users-requ...@lists.sourceforge.net wrote: > >> Whatever those are, they are not pages on your server. >> >> On Thu, Aug 18, 2011 at 1:35 PM, Yingjie Lin wrote: >> >>> Hi Bob, >>> >>> I just created three example pages each using a different version of Jmol. >>> >>> http://scbx.mssm.edu/sitecomp/1kna/output_22.html (uses jmol-12.0.22) >>> http://scbx.mssm.edu/sitecomp/1kna/output_39.html (uses jmol-12.0.39) >>> http://scbx.mssm.edu/sitecomp/1kna/output_48.html (uses jmol-12.0.48) >>> >>> The error messages I mentioned show up in Javascript error console. Thanks. > > > -- > uberSVN's rich system and user administration capabilities and model > configuration take the hassle out of deploying and managing Subversion and > the tools developers use with it. Learn more about uberSVN and get a free > download at: http://p.sf.net/sfu/wandisco-dev2dev > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-generated animations on mobile devices
Its a start. Still a long way to go. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Sep 13, 2011, at 10:16 PM, Quinn, Greg wrote: > For those interested in interactive molecular rendering on mobile devices, > the Protein Data Bank released the latest version of its website which uses > HTML5 sprite-based molecular animations as an alternative to the Jmol applet > when "Discussed Entry" web pages are viewed with a mobile device (currently > some issues with interactivity on the native Android web browser). The > animations are created using a Jmol-generated sprite strip, and javascript is > used to cycle through the images drawn in a Canvas object, upon touch > (requires a browser that supports the Canvas object plus the absence of Java > support, e.g. Mobile Safari on the iPad and iPhone). > e.g. http://www.rcsb.org/pdb/101/motm_disscussed_entry.do?id=3pe4 > Cheers > Greg > -- > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > Learn about the latest advances in developing for the > BlackBerry® mobile platform with sessions, labs & more. > See new tools and technologies. Register for BlackBerry® DevCon today! > http://p.sf.net/sfu/rim-devcon-copy1 > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerry® mobile platform with sessions, labs & more. See new tools and technologies. Register for BlackBerry® DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Butane's conformation and energy graph.
I'm not sure where your problem is, but look here for a solution to this. Perhaps it will help you with yours. Bob Hanson also has a nice solution. http://web.me.com/jhansen4/iWeb/Jmol/svgGraphTest5.xhtml *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Oct 30, 2011, at 12:56 PM, Mio_libero wrote: > Hi, friends, i am rewriting a page that shows the free rotation around the > c2-c3 bond of butane while the energy value is diplayed are in messagebox > area and grph too is shown below as in this page > This page works locally with Jmol 12.2. from my site it is not work. I cannot > find the error. Can anybody help me? > Pino > -- > Get your Android app more play: Bring it to the BlackBerry PlayBook > in minutes. BlackBerry App World™ now supports Android™ Apps > for the BlackBerry® PlayBook™. Discover just how easy and simple > it is! http://p.sf.net/sfu/android-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World™ now supports Android™ Apps for the BlackBerry® PlayBook™. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol and Moodle
My university is currently trying Moodle as an alternative to Blackboard for a Course Management System. One of the things I like about Moodle is that it supports Jmol. However, we have had some problems so far. I have put a couple of Jmol pages on my Moodle site. I am able to view the molecules just fine in Safari but not in Firefox (Mac OS X 10.4.8). In Firefox, it loads the applet just fine but fails to load the molecule. I get a black box which, when I control click, gives the pop-up menu which indicates no atoms are loaded. We are using Jmol 10.2. I have asked them to switch to 11.0, but it hasn't happened yet. If anyone has any suggestions about what is going wrong that I could forward to our Moodle site administrator I would really appreciate it. I haven't yet had the chance to test on any other systems so I don't know how it behave there. Thanks. ********* Jeff Hansen Department of Chemistry DePauw University Greencastle, IN 46135 [EMAIL PROTECTED] * - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and Moodle
Thanks for your help Bob. I went to Console.app and checked out the Java log and found the following. org.jmol.applet.Jmol load time = 2 seconds FileManager.openFile(../../file.php/11/1a3n.pdb) SmarterJmolAdapter:The Resolver thinks:null error opening http://moodle.depauw.edu/file.php/11/1a3n.pdb unrecognized file format openFile(../../file.php/11/1a3n.pdb) 1202 ms This is pretty much what Dean found earlier. As he mentioned, this seems to be a Firefox on OS X issue only. Jeff This is usually an indication that your server is not properly finding the files. It's a directory issue. Be sure to open the Java contol panel -- argh on a Mac -- ah, look at the Java log in the System logs folder -- and see what it is telling you. It will say something like "file not found -- JmolApplet.jar" or something like that. Then we could know what "loads the applet just fine" means. Be sure to try on a PC as well using Firefox. Bob Jeff Hansen wrote: My university is currently trying Moodle as an alternative to Blackboard for a Course Management System. One of the things I like about Moodle is that it supports Jmol. However, we have had some problems so far. I have put a couple of Jmol pages on my Moodle site. I am able to view the molecules just fine in Safari but not in Firefox (Mac OS X 10.4.8). In Firefox, it loads the applet just fine but fails to load the molecule. I get a black box which, when I control click, gives the pop-up menu which indicates no atoms are loaded. We are using Jmol 10.2. I have asked them to switch to 11.0, but it hasn't happened yet. If anyone has any suggestions about what is going wrong that I could forward to our Moodle site administrator I would really appreciate it. I haven't yet had the chance to test on any other systems so I don't know how it behave there. Thanks. * Jeff Hansen Department of Chemistry DePauw University Greencastle, IN 46135 [EMAIL PROTECTED] * - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and Moodle
Bob Hanson wrote: OK, you're on track. Check that file from the machine that is causing the problem. When you go to that exact URL with that browser, do you get a login message from the server? When I go there, I get a log in screen. Ah, so I'm betting only one of your browsers is passing on the secure password to the server when Jmol makes that call. Something like that. I'm going to change this error message to display the first 1000 characters of the file. That should be very helpful in general. Yes, ok, that's done. Jmol 11.1.12 will have this feature. When you look in the log file you will see the first three lines of the file. Also, this will display in the applet window. (a feature of 11.1) Bob When I do as you asked I get a window that asks me what I want to do with the file: open or save. No request for a password. I'm already logged in so probably it doesn't need my login while you weren't logged in when you tried it. ***** Jeff Hansen Department of Chemistry DePauw University Greencastle, IN 46135 [EMAIL PROTECTED] * - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Moodle and Jmol again
Let me try this one more time with a little more information. I tried Phil Bays' suggestion and got the java embedding plug-in. After installing it and restarting Firefox and trying to load the page with the Jmol applet I got basically a blank page. No black box for the applet as before. Interestingly a look at the Java log showed nothing either. Uninstalling the java embedding plug-in returned to the original behavior. The java applet loaded as shown by the black box on the page. Right clicking the black box brought up the Jmol menu which indicated no atoms had loaded. The Java log showed the following. MRJ Plugin for Mac OS X v1.0.1 [starting up Java Applet Security @ Fri Feb 16 11:24:29 EST 2007] <<< ProxyClassLoader: defined LiveConnectProxy class. >>> <<< Here're the permissions you've got: >>> <<< [EMAIL PROTECTED] ( (java.net.SocketPermission moodle.depauw.edu connect,accept,resolve) ) >>> java.lang.NoSuchMethodError: doubleValue at netscape.oji.JNIRunnable.run(Native Method) at netscape.oji.LiveConnectProxy.run(LiveConnectProxy.java:48) Fri Feb 16 11:24:30 EST 2007 JEP creating applet JmolApplet (http:// moodle.depauw.edu//mod/resource/type/jmol/) WrappedAppletLoader.run(org.jmol.applet.Jmol) English: no need for gettext wrapper AppletRegistry.checkIn(jmolApplet0) (C) 2006 Jmol Development Jmol Version 10.2.0 2006-04-14 20:06 java.vendor:Apple Computer, Inc. java.version:1.5.0_06 os.name:Mac OS X appletDocumentBase=http://moodle.depauw.edu/mod/resource/view.php?id=115 setting color scheme to:jmol loadImage:jmol75x29x8.gif urlImage=jar:http://moodle.depauw.edu//mod/resource/type/jmol/ JmolApplet0.jar!/jmol75x29x8.gif successfully loaded jmol75x29x8.gif [EMAIL PROTECTED] org.jmol.applet.Jmol load time = 2 seconds FileManager.openFile(../../file.php/11/Structures/1a3n.pdb) SmarterJmolAdapter:The Resolver thinks:null error opening http://moodle.depauw.edu/file.php/11/Structures/1a3n.pdb unrecognized file format openFile(../../file.php/11/Structures/1a3n.pdb) 1093 ms * Jeff Hansen Department of Chemistry DePauw University Greencastle, IN 46135 [EMAIL PROTECTED] * - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-users Digest, Vol 9, Issue 18
Thanks for the response Angel. On Feb 18, 2007, at 11:51 PM, jmol-users- [EMAIL PROTECTED] wrote: Date: Fri, 16 Feb 2007 19:44:44 +0100 From: "Angel Herraez" <[EMAIL PROTECTED]> Subject: Re: [Jmol-users] Moodle and Jmol again To: jmol-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=US-ASCII Hi Jeff I have not any experience close to your situation, and I'm a Windows person, but sometimes a fresh brain can help. Let's start stating what I have got from your posts: 1.- You have a problem only with Firefox, not Safari. That points to a Java plugin problem. However, as it has been noted, new versions of Firefox are reported not to need the plugin. Also, your installation of the plugin has't helped. Correct here. The Firefox version I am using is 2.0.0.1. 2.- The error message in the Java console looks like Jmol is not understanding the PDB format (it usually says "SmarterJmolAdapter:The Resolver thinks:pdb" instead of "SmarterJmolAdapter:The Resolver thinks:null"). However, this should affect Safari too, as would any Moodle configuration problem. 3.- I suppose you have tried other Jmol pages using your Firefox? That will rule out plugin problems and take us to Moodle problems. Correct here also. Other Jmol pages work. I did find that one of the Jmol demonstration pages (the one using frames) doesn't work in either Firefox or Safari but this seems to be an unrelated issue. And it seems Dean got the same on another Moodle site... So it's some Moodle trick? 4.- It seems that Jmol loads correctly, so it may be a Java security restriction specific to the Moodle environment... but again, then Safari shouldn't work either. I know I am not giving any solution, but sometimes thinking aloud helps --and I felt you needed some answer--. Good luck. And make sure to write down the answer when you find it. The Wiki has a secton on Jmol in Moodle. Thanks again. It seems this is most likely a Moodle problem rather than Jmol so I'll see if I can get some help from the Moodle community. I'll be sure to bring any solutions I may find back here. Jeff - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Weird problem with Jmol
I've come across a strange problem with Jmol that I'm hoping someone can help me resolve. The problem came up with a web page containing the Jmol applet that a group of my students made for a class presentation. Here is the problem: When we first load the page it loads just fine. However, if we reload the page the applet doesn't load and none of the buttons or links they created with Jmol.js are there either. If I load another page at this point, it doesn't work either (same behavior). If I restart the browser and load a different page, it works fine. If I load the "offending" page it loads fine. If I reload the page it once again doesn't work and loading another page thereafter also doesn't work. I've just checked and I can load pages offsite such as the Jmol demonstration pages at Sourceforge, but pages on the same site don't load. Again, restarting the browser and opening "good" page seems to clear things out and the "bad" page loads fine. Reloading the "bad" page mucks things up and loading any page on the site thereafter also doesn't work. Just for your information I've been testing this using Safari 2.0.4(419.3) and Mac OS X 10.4.9. On Firefox on the the same Mac the same thing happens except that the "bad" file doesn't work at all. The files in question can be found at: http://people.depauw.edu/jhansen/Presentations/Jessica.html - Bad file http://people.depauw.edu/jhansen/Presentations/ CarbonicAnhydrase.html - Good file Any help you can provide would be appreciated. Thanks. Jeff * Jeff Hansen Department of Chemistry DePauw University Greencastle, IN 46135 [EMAIL PROTECTED] * - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Student Jmol pages
I taught a course on Enzyme Mechanisms for the first time this semester. The course is an organic chemistry course that looks at the organic reaction mechanisms of enzyme reactions. At the end of the semester the students did group presentations on a particular enzyme that is assigned to them. I had them do the molecular visualization using Jmol and make a web page to go along with the presentation. I thought some of you might be interested in seeing their work. It isn't fantastic but not too bad for starting from zero and getting to this in 3 or 4 weeks. The pages are at: http://people.depauw.edu/jhansen/Presentations/ * Jeff Hansen Department of Chemistry DePauw University Greencastle, IN 46135 [EMAIL PROTECTED] * - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] loading files from RCSB directly
I thought I would try setting up a page to load files from the RCSB
site. I've tried using the code suggested below. If I use that code
as shown in a jmolButton it doesn't work. The button does not show
up. If I remove the quotes from the load files command the button
displays but the files don't load. I get the following message
displayed in the applet: "java.security.AccessControlException:
access denied (java.net.SocketPermission www.rcsb.org:80
connect.resolve)"
Here is the relevant code from the page:
jmolInitialize("JmolFolder","JmolAppletSigned.jar");
jmolApplet(600, "background [x99];");
...
</pre><tt>jmolButton("set echo top left; echo Loading files; refresh; load
</tt><tt>files =1crn =1blu =1hje; set echo bottom left; echo 1CA2;", "Load
</tt><tt>files");
</tt><pre style="margin: 0em;">
jmolBr();
I guess I don't have to use this, but it seems a desirable option to
be able to load any file and not have to actually have the files on
your computer or the server.
Any help would be appreciated.
Bob Hanson wrote:
BTW, what's with the "=" before the file names? Just curious.
that was SUPPOSED to read:
load files "=1crn" "=1blu" "=1hje"
It means "Go get these files from RCSB directly; I don't have them on my
computer"
I'm starting to use this so that anyone can run the script and it should
work for them same as for me. No files required!
*
Jeff Hansen
Department of Chemistry
DePauw University
Greencastle, IN 46135
[EMAIL PROTECTED]
*
-
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] loading files from RCSB directly
Angel Herraez wrote:
Hi Jeff
this sounds like the typical quotes rpoblme with javascript. But
maybe I haven't read thoroughly your code.
I will suggest a quick fix; if it doesn't work, write again
Basic principles:
1) Jmol needs double quotes for certain parameters, file names are
one of them.
2) Javascript needs alternating double and single quotes and
sometimes escaping them
jmolButton('set echo top left; echo Loading files; refresh; load
files "=1crn" "=1blu" "=1hje"; set echo bottom left; echo 1CA2;',
"Load
files");
jmolBr();
Angel,
Thanks for the suggestion. I tried it and the button does display
using the code you suggested. However, I still get the same error
message "java.security.AccessControlException: access denied
(java.net.SocketPermission www.rcsb.org:80 connect.resolve)" when I
click on the button. So it looks like your suggestion of using
single quotes around the whole command and double quotes around the
pdb names does the same thing as my code which used double quotes
around the whole command and no quotes around the pdb names. Either
way I get a java security error message. Any other suggestions?
Jeff
*
Jeff Hansen
Department of Chemistry
DePauw University
Greencastle, IN 46135
[EMAIL PROTECTED]
*
-
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] loading files from RCSB directly
Ok. I'm kinda confused now. I started this when I saw the following. On May 14, 2007, at May 14, 5:52 PM, Bob Hanson wrote: Ah, Frieda, you MUST use file.model notation with multiple files anywhere you would like to say "model n". Especially with PDB files, "set backgroundModel 1" would be too ambiguous. For example: load files "=1crn.pdb" "=1blu.pdb" "=1hje.pdb" animation mode palindrome animation fps 1 set backgroundmodel 1.1 frame range 1.1 3.1 frame play So I think it's just that one command. This works perfectly when I do not have my state script between the load and the animation commands. But I have a state script to load and set up all the file display options, then the anim is triggered with a button. Any idea where to start looking for the problem? what's the problem, again? BTW, what's with the "=" before the file names? Just curious. that was SUPPOSED to read: load files "=1crn" "=1blu" "=1hje" It means "Go get these files from RCSB directly; I don't have them on my computer" I'm starting to use this so that anyone can run the script and it should work for them same as for me. No files required! So were those commands issued from the console? Is it not possible to include them in a button? Incidentally, I'm using the signed applet and Jmol 11.1.39. And it works fine from the console, just not from a button. Trying Bob's page at http://www.stolaf.edu/academics/chemapps/jmol/temp/signed/test.htm I can of course load file using the load a PDB file link although technically that doesn't load a file it rewrites the page and loads the file. However, typing load "=1crn" into the text box and clicking execute gives the java security error. If it isn't possible that is fine. Just seemed like it would be nice to do it this way so I thought I would give it a try. I guess it won't work. * Jeff Hansen Department of Chemistry DePauw University Greencastle, IN 46135 [EMAIL PROTECTED] * - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] getting info from Jmol applet
I'm having difficulty getting info from the Jmol applet. Here is my
code (basically copied from a post from Bob Hanson):
jmolInitialize("jmol");
jmolApplet(500, "load ../Jmol/jmol/models/1bf3.pdb");
var atomSet =
document
.getElementById("jmolApplet0").getProperty("atomInfo","atomno<5");
alert (atomSet.get(0).get("info"));
This code displays the applet with the molecule loaded but does not
display the alert box at all. I must admit I am relatively new to
javascript. Any help getting started with this would be most
appreciated. Ultimately I am looking to get other types of info out
such as the energy of a molecule from a spartan file. Thought I would
start with something simple that has been done, but I'm having some
trouble with it.
Thanks in advance for any help you can give.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-users Digest, Vol 27, Issue 24
Thanks Bob. That certainly works. So basically anytime I want to pull
out some info from the molecule file I need to do that in the
jmolApplet command. Or is there a way to do that prior to loading the
molecule into Jmol? I'm looking ahead to situations where I'll want
to dynamically load a structure into an applet, grab some data out of
it and do some stuff with it. Now I'm wondering how I'll be able to
update other parts of the web page based on this data if the applet
hasn't finished loading the file yet.
Is there a way to find out what properties are accessible from the
applet? I'm looking at getting a protein's sequence into an array or
a small molecule's energy. If these aren't directly accessible can
the entire file be brought into a string variable and then dig the
info out of it?
Thanks again.
*******
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 20, 2008, at 3:43 PM, [EMAIL PROTECTED]
wrote:
Message: 4
Date: Wed, 20 Aug 2008 14:42:00 -0500
From: "Robert Hanson" <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] getting info from Jmol applet
To: jmol-users@lists.sourceforge.net
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Jeff,
The mistake here is timing. You cannot query an applet while the
page is
loading (prior to and completion of applet initialization).
In some
cases this crashes browsers; in others it just causes an error; in
others it
permanently disables the applet communication.
The simple fix is to place the JavaScript code in a function defined
in the
block, and then add a JavaScript call to that function in the
start-up Jmol script, after the file is loaded. No need for form tags.
function appletReady() {
var atomSetArray = jmolGetPropertyAsArray("atomInfo","atomno<5");
alert (atomSetArray[0].info);
}
jmolInitialize("jmol");
jmolApplet(500, "load ../Jmol/jmol/models/1bf3.pdb;javascript
appletReady()");
</pre><blockquote style="border-left: #EE solid 0.2em; margin: 0em; padding-left: 0.85em"><pre style="margin: 0em;">
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] script in string
Can anyone help me figure out what is wrong with this line of code? var loadJmol = "addJmol(molecule, divInc);"; What is happening is the is not being recognized or something and everything from the closing quotation mark on, including the next several lines until the next , is being displayed as text on the web page. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] A little more javascript help please?
I've posted a couple of questions in the past few days and several of you have given me some very good help that has put me in the right direction. Now let me give you a little background on what I'm trying to do. I'm working on learning javascript and the DOM and thought a good project to do this would be to make a page that would create a new div and put a jmol applet in it. Thanks to your help I am making some progress on this. At this point I've got a menu that sends a reference to a pdb file to a function which creates the new div and starts the jmol applet. The code is below. I'm having two problems with it. The first problem is how the jmol applet appears on the page when I call this function. It is basically clearing the page so that the only thing that shows is the applet. The original applet that was there and the pulldown menu disappear. I tried using newDiv.appendChild instead of newDiv.update but this didn't work at all. If I comment out the jmolApplet(400... line then [object Object] appears on the page below the pulldown menu (where I expect it). The second problem is that when the new applet is added to the page no molecule is loaded in it. The alert command just before the jmolApplet line shows just what I expect it to show, but I still only get a blank jmol applet. So if you have any suggestions to help me get the rest of the way to where I'm trying to get I'd really appreciate it. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] A little javascript help please? again
Oops. Sorry I forgot the code. Here is the message again this time
with the code.
I've posted a couple of questions in the past few days and several of
you have given me some very good help that has put me in the right
direction. Now let me give you a little background on what I'm trying
to do. I'm working on learning javascript and the DOM and thought a
good project to do this would be to make a page that would create a
new div and put a jmol applet in it. Thanks to your help I am making
some progress on this. At this point I've got a menu that sends a
reference to a pdb file to a function which creates the new div and
starts the jmol applet. The code is below. I'm having two problems
with it. The first problem is how the jmol applet appears on the page
when I call this function. It is basically clearing the page so that
the only thing that shows is the applet. The original applet that was
there and the pulldown menu disappear. I tried using
newDiv.appendChild instead of newDiv.update but this didn't work at
all. If I comment out the jmolApplet(400... line then [object Object]
appears on the page below the pulldown menu (where I expect it). The
second problem is that when the new applet is added to the page no
molecule is loaded in it. The alert command just before the
jmolApplet line shows just what I expect it to show, but I still only
get a blank jmol applet. So if you have any suggestions to help me
get the rest of the way to where I'm trying to get I'd really
appreciate it.
var jmolObject = Class.create();
jmolObject.prototype = {
initialize: function(molecule){
jmolInitialize("jmol");
var loadString = "\"load ../Jmol/jmol/models/" +
molecule + "\"";
alert(loadString);
jmolApplet(400, loadString);
}
};
var divInc = 0;
function newJmolDiv(molecule) {
var newDiv = document.createElement('div');
var jmolID = 'jmolDiv_' + (divInc++);
newDiv.id = jmolID;
document.body.appendChild(newDiv);
newDiv.update(new jmolObject(molecule));
}
function appletReady() {
var atomSetArray =
jmolGetPropertyAsArray("atomInfo","atomno<5");
alert (atomSetArray[0].info);
}
jmolInitialize("jmol");
jmolApplet(500, "load ../Jmol/jmol/models/1bf3.pdb; javascript
appletReady();");
1bf3.pdb
1CA2.pdb
211hexane.smol
benzene.smol
pentane.pdb
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-users Digest, Vol 27, Issue 32
Dean,
Many thanks. I've got it working perfectly now. The only tweak I had
to make to your suggestion was to change loadString to
eval(loadString). From my reading I had thought that innerHTML was
not part of the Standard and so I was trying not to use it.
Interestingly my previous approach (creating a new jmol object) now
works if I use eval(loadString) as long as I do not include the
jmolSetDocument(false). In this case it wipes the page and correctly
displays the jmol applet. When I add the jmolSetDocument(false) it
writes [object Object] where the applet should be. So the
jmolSetDocument(false) is somehow messing up creating the jmol object
correctly. Dean, you were a great help. Might someone help me figure
out this other way too? I would like to be as standards compliant as
possible.
Here is the current code that works (thanks Dean):
var divInc = 0;
function newJmolDiv(molecule) {
var newDiv = document.createElement('div');
var jmolID = 'jmolDiv_' + (divInc++);
newDiv.id = jmolID;
document.body.appendChild(newDiv);
var loadString = "\"load ../Jmol/jmol/models/" + molecule +
"\"";
jmolInitialize("jmol");
jmolSetDocument(false);
newDiv.innerHTML = jmolApplet(400, eval(loadString));
}
function appletReady() {
var atomSetArray =
jmolGetPropertyAsArray("atomInfo","atomno<5");
alert (atomSetArray[0].info);
}
Here is the code that almost works. Without jmolSetDocument(false) it
clears the page and loads the applet. With jmolSetDocument(false) it
puts [object Object] in the new div.
var jmolObject = Class.create();
jmolObject.prototype = {
initialize: function(molecule){
jmolInitialize("jmol");
jmolSetDocument();
var loadString = "\"load ../Jmol/jmol/models/" +
molecule + "\"";
alert(loadString);
jmolApplet(400, eval(loadString));
}
};
var divInc = 0;
function newJmolDiv(molecule) {
var newDiv = document.createElement('div');
var jmolID = 'jmolDiv_' + (divInc++);
newDiv.id = jmolID;
document.body.appendChild(newDiv);
newDiv.update(new jmolObject(molecule));
}
function appletReady() {
var atomSetArray =
jmolGetPropertyAsArray("atomInfo","atomno<5");
alert (atomSetArray[0].info);
}
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 23, 2008, at 11:47 AM, [EMAIL PROTECTED]
wrote:
> Jeff,
>
> I remember being similarly confused when I first started playing with
> Javascript and the DOM. By default, the Jmol.js library functions
> write the
> necessary HTML to the current document when they are called. So in
> your
> case, calling jmolApplet is overwriting everything, including your
> controls. To change this behavior, you need to call
> jmolSetDocument(false).
> The beauty of the Jmol.js library is that all of the functions
> return HTML
> that you can then assign to a variable.
>
> The other thing I've found very useful is innerHTML (some people
> love it,
> others hate it; I've learned to live with it). In your case, you
> can do
> something as simple as:
>
> jmolSetDocument(false);
> newDiv.innerHTML = jmolApplet(400, loadString);
>
> (Of course, within your example, you will need to decide where you
> want to
> put this - but I hope it gives you some idea where to go.) Good
> luck with
> your pages.
>
> Dean
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-users Digest, getting data from Jmol
Bob, I've been looking through the documentation and trying to figure this out. I'm not having much success. I don't think I quite understand the syntax for doing this. I also don't understand what properties are available and where to find them and which file formats are supported. I'm not finding the help I need in the documentation or at least I'm not understanding well enough the help that is there. So lets say that I wanted to have a file with several related models and find the energy of the molecule in each model (actually that is what I want to do). I'm not looking for the code to do this, just another pointer in the right direction to move me in the right direction. Sorry if I'm too much of a bother. Robert Hanson Fri, 22 Aug 2008 07:22:24 -0700 oh, yes! You can do all that. Check the Jmol wiki for lots of tips. Commands include jmolEvaluate (my favorite), and jmolGetPropertyAsArray() or jmolGetPropertyAsString() *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-users Digest, getting data from Jmol
I'm working with Spartan 04 .smol files. I could use Spartan 06 files if necessary. I'm making progress. I'm able to use jmolGetPropertyAsArray and pull a value out of that. I would like to show the contents of the entire array so I could see what is there and how it is organized, but I'm having trouble figuring out how to do that. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** On Aug 26, 2008, at 12:41 PM, Robert Hanson wrote: The properties supported do depend upon the file type. What file type are you working with? Generally you can check this by using getproperty auxiliaryinfo which is a general holder for all sorts of molecular info. Bob On Mon, Aug 25, 2008 at 7:50 AM, Jeff Hansen <[EMAIL PROTECTED]> wrote: Bob, I've been looking through the documentation and trying to figure this out. I'm not having much success. I don't think I quite understand the syntax for doing this. I also don't understand what properties are available and where to find them and which file formats are supported. I'm not finding the help I need in the documentation or at least I'm not understanding well enough the help that is there. So lets say that I wanted to have a file with several related models and find the energy of the molecule in each model (actually that is what I want to do). I'm not looking for the code to do this, just another pointer in the right direction to move me in the right direction. Sorry if I'm too much of a bother. Robert Hanson Fri, 22 Aug 2008 07:22:24 -0700 oh, yes! You can do all that. Check the Jmol wiki for lots of tips. Commands include jmolEvaluate (my favorite), and jmolGetPropertyAsArray() or jmolGetPropertyAsString() *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-users Digest, getting data from Jmol
Thanks Paul. That is very helpful. I was able to use it to display the data in the array in a text area on the web page. Should prove useful for figuring out how to mine the data. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** On Aug 26, 2008, at 2:51 PM, Paul Pillot wrote: I use the following dump() script when I want a detailed content of an object/array in javascript : http://binnyva.blogspot.com/2005/10/dump-function-javascript-equivalent-of.html Paul Le 26 août 08 à 20:37, Jeff Hansen a écrit : I'm working with Spartan 04 .smol files. I could use Spartan 06 files if necessary. I'm making progress. I'm able to use jmolGetPropertyAsArray and pull a value out of that. I would like to show the contents of the entire array so I could see what is there and how it is organized, but I'm having trouble figuring out how to do that. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** On Aug 26, 2008, at 12:41 PM, Robert Hanson wrote: The properties supported do depend upon the file type. What file type are you working with? Generally you can check this by using getproperty auxiliaryinfo which is a general holder for all sorts of molecular info. Bob On Mon, Aug 25, 2008 at 7:50 AM, Jeff Hansen <[EMAIL PROTECTED]> wrote: Bob, I've been looking through the documentation and trying to figure this out. I'm not having much success. I don't think I quite understand the syntax for doing this. I also don't understand what properties are available and where to find them and which file formats are supported. I'm not finding the help I need in the documentation or at least I'm not understanding well enough the help that is there. So lets say that I wanted to have a file with several related models and find the energy of the molecule in each model (actually that is what I want to do). I'm not looking for the code to do this, just another pointer in the right direction to move me in the right direction. Sorry if I'm too much of a bother. Robert Hanson Fri, 22 Aug 2008 07:22:24 -0700 oh, yes! You can do all that. Check the Jmol wiki for lots of tips. Commands include jmolEvaluate (my favorite), and jmolGetPropertyAsArray() or jmolGetPropertyAsString() *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux
[Jmol-users] problem in firefox
My apologies. This is really more of a javascript/html question but
it is on a Jmol project I am working on. Could someone explain to me
what is the problem with the following code? The appletReady()
function works just fine in Safari and the page validates as HTML 4.01
strict, but the appletReady() function doesn't work in Firefox.
Firebug reports an error and says jmolText is not defined.
function appletReady() {
var _dataInfo = jmolGetPropertyAsArray("auxiliaryInfo");
jmolText.value = dump(_dataInfo);
}
...
The page is at http://web.mac.com/jhansen4/Jmol/NewJmolDiv.html if
that will help.
*******
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem in firefox
Dean,
Yeah, I thought of that and tried it, but that didn't work either. In
that case Firebug reports that getElementById is not defined. So it
seems for some reason Firefox isn't recognizing the textarea's id.
Incidentally, I get a similar error when I try the same with the
textDiv div instead.
Jeff
*******
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 27, 2008, at 11:19 AM, Dean Johnston wrote:
Jeff,
No apologies needed. Giving an id to a does not create a
Javascript object automatically (at least in Firefox). You will
have to use something like:
var myText = document.getElementById('jmolText');
and then say
myText.value = dump(_dataInfo);
It's interesting that it does work in Safari.
Dean
On Wed, Aug 27, 2008 at 11:05 AM, Jeff Hansen <[EMAIL PROTECTED]>
wrote:
My apologies. This is really more of a javascript/html question but
it is on a Jmol project I am working on. Could someone explain to me
what is the problem with the following code? The appletReady()
function works just fine in Safari and the page validates as HTML 4.01
strict, but the appletReady() function doesn't work in Firefox.
Firebug reports an error and says jmolText is not defined.
function appletReady() {
var _dataInfo = jmolGetPropertyAsArray("auxiliaryInfo");
jmolText.value = dump(_dataInfo);
}
...
The page is at http://web.mac.com/jhansen4/Jmol/NewJmolDiv.html if
that will help.
*******
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win
great prizes
Grand prize is a trip for two to an Open Source event anywhere in
the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win
great prizes
Grand prize is a trip for two to an Open Source event anywhere in
the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem in firefox
Thanks. Bob. Using document.getElementById('jmolText'); worked.
Thanks for sharing your .js file as well. I'll probably take a look
at it at some point. I'm working towards my own at this point and I'm
afraid looking at yours will just prevent my learning how to do it
myself.
*******
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 27, 2008, at 11:57 AM, Robert Hanson wrote:
Right -- "name" attribute is quite problematical. In some browsers
"id" is accessible as "name", but that's not acceptable. And in some
browser versions the name of an element in a form is under the form
name rather than the document.
Always use "id" and, as Dean points out, then access it only using
document.getElementById()
Most of us create a scrap of JavaScript that we put in all our pages
that provides us these services.
One I use is http://www.stolaf.edu/depts/chemistry/gca/divs.js
Bob
On Wed, Aug 27, 2008 at 10:19 AM, Dean Johnston
<[EMAIL PROTECTED]> wrote:
Jeff,
No apologies needed. Giving an id to a does not create a
Javascript object automatically (at least in Firefox). You will
have to use something like:
var myText = document.getElementById('jmolText');
and then say
myText.value = dump(_dataInfo);
It's interesting that it does work in Safari.
Dean
On Wed, Aug 27, 2008 at 11:05 AM, Jeff Hansen <[EMAIL PROTECTED]>
wrote:
My apologies. This is really more of a javascript/html question but
it is on a Jmol project I am working on. Could someone explain to me
what is the problem with the following code? The appletReady()
function works just fine in Safari and the page validates as HTML 4.01
strict, but the appletReady() function doesn't work in Firefox.
Firebug reports an error and says jmolText is not defined.
function appletReady() {
var _dataInfo = jmolGetPropertyAsArray("auxiliaryInfo");
jmolText.value = dump(_dataInfo);
}
...
The page is at http://web.mac.com/jhansen4/Jmol/NewJmolDiv.html if
that will help.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win
great prizes
Grand prize is a trip for two to an Open Source event anywhere in
the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win
great prizes
Grand prize is a trip for two to an Open Source event anywhere in
the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win
great prizes
Grand prize is a trip for two to an Open Source event anywhere in
the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem in firefox
Believe me I've been doing plenty of that, but I also have been finding trial and error to be very instructive too. I did take a look at your divs.js file. I don't yet understand all of it. I tried your divFind and divWrite functions and I'm pretty sure I'm understanding what they do. Unfortunately the divWrite doesn't do what I want. I want to put a Jmol applet into the div and this function appears to only write text into a div. I tried divWrite(jmolID, newJmol) and divWrite(jmolID, eval(newJmol) where jmolID is a variable that holds the div's id and newJmol is a Jmol applet object. Unfortunately both off these do the same thing which is to write the function used to create the Jmol applet object into the into the div as text. I've also tried the following code: document.getElementById(jmolID).appendChild(newJmol); which produces the following error message in FireBug: uncaught exception: Node cannot be inserted at the specified point in the hierarchy (NS_ERROR_DOM_HIERARCHY_REQUEST_ERR) document.getElementById(jmolID).update(newJmol); gives the error: document.getElementById(jmolID).update is not a function I've tried several variations. I got it to work once using: newDiv.update(jmolApplet(400, eval(_jmolApplet.loadString))); where newDiv was a reference to a div element, but this only worked in Safari and not Firefox. Unfortunately, everywhere I've read about adding something to a div element the something being added is text. I can't find anywhere that gives an example off adding some other kind of object. Perhaps I should give it up. I thought it would be possible to create a Jmol applet object and add it to the web page. Then I would be able to include methods in the Jmol applet object constructor to change jmol parameters and such. Obviously there are other ways to do that, but this just seems an attractive way to me for some reason. ******* Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** On Aug 27, 2008, at 2:14 PM, Robert Hanson wrote: >> I'm working towards my own at this point and I'm afraid looking at yours will just prevent my learning how to do it myself. Shame! NEVER say that! The way to learn this is by adapting anything you can find. That's the great thing about JavaScript. Learn how these code fragments work by testing it in your own application. You will learn lots. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem in firefox
Thanks for your help Angel. This is getting me very nearly there. To
recap. I am trying to create a web page in which a div element is
created and a new Jmol applet is displayed in that new div. Your
suggestion to take a look at the Jmol homepage was very helpful. That
is essentially what I needed to do. Based on that I came up with the
following code. It creates the new div and puts a Jmol applet in it.
However, it does not load the molecule file into the the applet. The
message bar at the bottom of the window shows the following error
message: script compiler ERROR: command expected>>>>"load ../
Jmol/jmol/Models/benzene.smol;"<<<<
Additionally, the alert(result1) (see code below) displays undefined
in the alert box and alert(result2) displays a blank alert box. So
I'm wondering what is going on with that.
Here is the code. molecule refers to a structure filename. Thanks to
Bob for the divFind and divWrite functions.
function divFind(name,issilent){
var d=document.getElementById(name);
// if(!d&&!issilent&&debugPrint)debugPrint("couldn't find "+name,1)
return d
}
function divWrite(name,what){
result1 = jmolGetStatus("scriptStatus");
alert(result1);
var d=divFind(name);
if(!d)return 0;
try{d.innerHTML=what}catch(error){alert(error)};
result2 = jmolGetStatus("scriptStatus",divInc);
alert(result2);
return d;
}
function jmolObject(molecule, divID){
jmolSetDocument(false);
this.loadString = "\"load ../Jmol/jmol/Models/" + molecule + ";" +
"\"";
alert(this.loadString);
divWrite(divID,jmolApplet(400, this.loadString,divInc));
}
var divInc = 0;
function newJmolDiv(molecule) {
var newDiv = document.createElement('div');
newDiv.id = 'Div' + (++divInc);
document.body.appendChild(newDiv);
jmolObject(molecule, newDiv.id);
}
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 2:41 PM, Angel Herráez wrote:
> Hi Jeff
>
> Not sure after the flurry of messages if you have solved your problem.
>
> On 27 Aug 2008 at 16:21, Jeff Hansen wrote:
>
>> Unfortunately both off these do the same thing which is to write the
>> function used to create the Jmol applet object into the into the
>> div as text.
>
> That may be due, as Bob has pointed out, to the need to use
> jmolSetDocument(0)
>
>
>> being added is text. I can't find anywhere that gives an example
>> off adding some other kind of o
>
> Have you checked out the method used in Jmol homepage? I'm not sure
> if that's what you
> are after. A similar solution is what I once called "pop-in" method
> for inserting Jmol applet
> upon user request. This is used in Jmol app Export to Web module
> (Pop-in Template) and
> in
>
> I haven't tested those in Firefox 3 though (I'm yet sticking to 2.0
> until my favorite add-ons
> are updated).
>
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem in firefox
Sorry I wasn't clear about this, but the applet corresponding to result1 is loaded when the page loads. I'll try jmolScriptWait to see if that does anything for the result2. f *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** On Aug 28, 2008, at 5:41 PM, Angel Herráez wrote: > On 28 Aug 2008 at 15:59, Jeff Hansen wrote: > >> Additionally, the alert(result1) (see code below) displays undefined >> in the alert box and alert(result2) displays a blank alert box. So >> I'm wondering what is going on with that. > > I would say that with result1 you are trying to read from the applet > before it has been > created, so it's not surprising thayt you get undefined. > As for result2, I'm not sure because I don't know the try/catch > command, but anyway it may > be too soon to have the applet ready. Javascript goes much faster > than loading Java + > Jmol. > > > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem in firefox
Thanks. New it had to be something simple like that. For some reason
I needed the \" earlier and it was still there.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 4:57 PM, Robert Hanson wrote:
remove the \" around the load command. It's just:
this.loadString = "load ../Jmol/jmol/Models/" + molecule;
On Thu, Aug 28, 2008 at 2:59 PM, Jeff Hansen <[EMAIL PROTECTED]>
wrote:
Thanks for your help Angel. This is getting me very nearly there. To
recap. I am trying to create a web page in which a div element is
created and a new Jmol applet is displayed in that new div. Your
suggestion to take a look at the Jmol homepage was very helpful. That
is essentially what I needed to do. Based on that I came up with the
following code. It creates the new div and puts a Jmol applet in it.
However, it does not load the molecule file into the the applet. The
message bar at the bottom of the window shows the following error
message: script compiler ERROR: command expected>>>>"load ../
Jmol/jmol/Models/benzene.smol;"<<<<
Additionally, the alert(result1) (see code below) displays undefined
in the alert box and alert(result2) displays a blank alert box. So
I'm wondering what is going on with that.
Here is the code. molecule refers to a structure filename. Thanks to
Bob for the divFind and divWrite functions.
function divFind(name,issilent){
var d=document.getElementById(name);
// if(!d&&!issilent&&debugPrint)debugPrint("couldn't find
"+name,1)
return d
}
function divWrite(name,what){
result1 = jmolGetStatus("scriptStatus");
alert(result1);
var d=divFind(name);
if(!d)return 0;
try{d.innerHTML=what}catch(error){alert(error)};
result2 = jmolGetStatus("scriptStatus",divInc);
alert(result2);
return d;
}
function jmolObject(molecule, divID){
jmolSetDocument(false);
this.loadString = "\"load ../Jmol/jmol/Models/" + molecule +
";" +
"\"";
alert(this.loadString);
divWrite(divID,jmolApplet(400, this.loadString,divInc));
}
var divInc = 0;
function newJmolDiv(molecule) {
var newDiv = document.createElement('div');
newDiv.id = 'Div' + (++divInc);
document.body.appendChild(newDiv);
jmolObject(molecule, newDiv.id);
}
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 2:41 PM, Angel Herráez wrote:
> Hi Jeff
>
> Not sure after the flurry of messages if you have solved your
problem.
>
> On 27 Aug 2008 at 16:21, Jeff Hansen wrote:
>
>> Unfortunately both off these do the same thing which is to write
the
>> function used to create the Jmol applet object into the into the
>> div as text.
>
> That may be due, as Bob has pointed out, to the need to use
> jmolSetDocument(0)
>
>
>> being added is text. I can't find anywhere that gives an example
>> off adding some other kind of o
>
> Have you checked out the method used in Jmol homepage? I'm not sure
> if that's what you
> are after. A similar solution is what I once called "pop-in" method
> for inserting Jmol applet
> upon user request. This is used in Jmol app Export to Web module
> (Pop-in Template) and
> in
>
> I haven't tested those in Firefox 3 though (I'm yet sticking to 2.0
> until my favorite add-ons
> are updated).
>
>
>
-
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win
great prizes
Grand prize is a trip for two to an Open Source event anywhere in
the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
__
Re: [Jmol-users] problem in firefox
I tried jmolScriptWait but couldn't get it to not break the load command. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** On Aug 28, 2008, at 6:03 PM, Jeff Hansen wrote: > Sorry I wasn't clear about this, but the applet corresponding to > result1 is loaded when the page loads. I'll try jmolScriptWait to see > if that does anything for the result2. > > f > ******* > Jeff Hansen > Department of Chemistry and Biochemistry > DePauw University > 602 S. College Ave. > Greencastle, IN 46135 > [EMAIL PROTECTED] > *** > > > On Aug 28, 2008, at 5:41 PM, Angel Herráez wrote: > >> On 28 Aug 2008 at 15:59, Jeff Hansen wrote: >> >>> Additionally, the alert(result1) (see code below) displays undefined >>> in the alert box and alert(result2) displays a blank alert box. So >>> I'm wondering what is going on with that. >> >> I would say that with result1 you are trying to read from the applet >> before it has been >> created, so it's not surprising thayt you get undefined. >> As for result2, I'm not sure because I don't know the try/catch >> command, but anyway it may >> be too soon to have the applet ready. Javascript goes much faster >> than loading Java + >> Jmol. >> >> >> >> - >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win >> great prizes >> Grand prize is a trip for two to an Open Source event anywhere in >> the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem in firefox
Thanks Bob. If gas prices weren't so high and my family wouldn't miss
me too much I would take you up on the offer.
Of course jmolScriptWait didn't break anything, just my failed
attempts to use it broke something.
I tried your second alternative (callbacks are still a mystery to me
although that code doesn't look too bad). So after loading the file I
called a function.
this.loadString = "load ../Jmol/jmol/Models/" + molecule +
";javascript myFunc();";
divWrite(divID,jmolApplet(400, this.loadString,divInc));
In the function I tried to use jmolGetStatus.
function myFunc(){
var result = jmolGetStatus("scriptStatus",divInc);
alert(result);
}
As with all of my attempts thus far this displayed "undefined." I
guess I still don't get how this works.
I think ultimately I will put the load command along with some other
commands in a script file rather than continuing to make these long
(and going to get longer) strings.
I'm making progress and having fun. Does that make me a geek?
Thanks for the help and encouragement.
You can see how far I've come at http://web.mac.com/jhansen4/Jmol/NewJmolDivSTD.html
.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 10:47 PM, Robert Hanson wrote:
Jeff, why don't you come over to St. Olaf and I'll show you how this
works! :)
Seriously, hang in there. You are trying to do a lot all at once,
and you will catch on. This is precisely what this list is for. Just
keep at it.
"jmolScriptWait" would not "break" anything.
jmolScriptWait should only be used if you absolutely have to pause
the JavaScript until that operation is complete. There are times
this is necessary, but it's not a great idea.
Most Jmol commands are given "asynchronously" using jmolScript()
rather than jmolScriptWait(). Jmol has a built-in queuing system, so
you can fire as many commands at it as you wish, and they will be
processed in order as processing becomes available. You can also
clear the queue using
!exit
and you can abort a specifically running script (but continue
processing later scripts) using
!quit
An alternative to waiting is to have the issued script notify the
web page when it is complete. Eric Martz and Tim Driscoll
masterminded this idea using "scriptcallback" methods that see a
comment go by and then know it is time to do something. Something
like this:
set scriptcallback "myfunc";set debugscript true;load whatever;#--
file is loaded
then myfunc() gets a message every time a script command is
executed, and the "#--file is loaded" message comes through as well:
function myfunc(app, msg) {
var s = "" + msg // converts Java string msg into a JavaScript
string
if (s.indexOf("#--file is loaded") == 0) {
[do something]
}
}
Alternatively, I've used the following quite effectively:
jmolScript("load whatever;javascript modelLoaded()")
That would run the JavaScript function
function modelLoaded() {
}
as soon as the model is loaded.
Basically, good "event driven" code is asynchronous. Nothing waits
for anything. Things happen because they get a message that they
need to happen. The more you can do that, the better.
Still, I do use jmolScriptWait() myself at times. Also
jmolEvaluate() is synchronous, and I use that a lot as well.
Bob
On Thu, Aug 28, 2008 at 6:30 PM, Jeff Hansen <[EMAIL PROTECTED]>
wrote:
I tried jmolScriptWait but couldn't get it to not break the load
command.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 6:03 PM, Jeff Hansen wrote:
> Sorry I wasn't clear about this, but the applet corresponding to
> result1 is loaded when the page loads. I'll try jmolScriptWait to
see
> if that does anything for the result2.
>
> f
> ***
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> [EMAIL PROTECTED]
> ***
>
>
> On Aug 28, 2008, at 5:41 PM, Angel Herráez wrote:
>
>> On 28 Aug 2008 at 15:59, Jeff Hansen wrote:
>>
>>> Additionally, the alert(result1) (see code below) displays
undefined
>>> in the alert box and alert(result2) displays a blank alert box.
So
>>> I'm w
Re: [Jmol-users] problem in firefox
I guess I really didn't need the jmolGetStatus() I just wanted some
way to check that the applet was being loaded and I could communicate
with it. I'll just forget using that.
Getting the zeroPoint wasn't too bad. This is what I did.
var _dataInfo = jmolGetPropertyAsArray("auxiliaryInfo");
var _jmolText = document.getElementById('jmolText');
var Energy = _dataInfo['ZEROPOINT'];
Of course your way is more succinct so I'll probably do that from now
on. I'm sure it will also be faster. Grabbing all the auxiliaryInfo
can take some time.
I'll update to RC11 today. Changes come too fast for me to keep up
with, which is a good thing.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 29, 2008, at 10:40 AM, Robert Hanson wrote:
mosty I think you will find that the jmolGetStatus() business won't
be helpful. I'm probably the only who ever used that. It was an
early attempt to get around callbacks, and I can't think of any good
reason to use it now.
Try something else, like the following:
alert(jmolGetPropertyAsString("auxiliaryinfo", "", divInc))
For getting that property, these days I just use:
var x = jmolEvaluate('getProperty("auxiliaryInfo.zeroPoint")')
rather than doing all the translation of the auxiliaryInfo array
into JavaScript just to get that one element.
But you are using Jmol 11.6.RC6 -- be sure to upgrade that to
11.6.RC11.
Bob
On Thu, Aug 28, 2008 at 11:00 PM, Jeff Hansen <[EMAIL PROTECTED]>
wrote:
Thanks Bob. If gas prices weren't so high and my family wouldn't
miss me too much I would take you up on the offer.
Of course jmolScriptWait didn't break anything, just my failed
attempts to use it broke something.
I tried your second alternative (callbacks are still a mystery to me
although that code doesn't look too bad). So after loading the file
I called a function.
this.loadString = "load ../Jmol/jmol/Models/" + molecule +
";javascript myFunc();";
divWrite(divID,jmolApplet(400, this.loadString,divInc));
In the function I tried to use jmolGetStatus.
function myFunc(){
var result = jmolGetStatus("scriptStatus",divInc);
alert(result);
}
As with all of my attempts thus far this displayed "undefined." I
guess I still don't get how this works.
I think ultimately I will put the load command along with some other
commands in a script file rather than continuing to make these long
(and going to get longer) strings.
I'm making progress and having fun. Does that make me a geek?
Thanks for the help and encouragement.
You can see how far I've come at http://web.mac.com/jhansen4/Jmol/NewJmolDivSTD.html
.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 10:47 PM, Robert Hanson wrote:
Jeff, why don't you come over to St. Olaf and I'll show you how
this works! :)
Seriously, hang in there. You are trying to do a lot all at once,
and you will catch on. This is precisely what this list is for.
Just keep at it.
"jmolScriptWait" would not "break" anything.
jmolScriptWait should only be used if you absolutely have to pause
the JavaScript until that operation is complete. There are times
this is necessary, but it's not a great idea.
Most Jmol commands are given "asynchronously" using jmolScript()
rather than jmolScriptWait(). Jmol has a built-in queuing system,
so you can fire as many commands at it as you wish, and they will
be processed in order as processing becomes available. You can also
clear the queue using
!exit
and you can abort a specifically running script (but continue
processing later scripts) using
!quit
An alternative to waiting is to have the issued script notify the
web page when it is complete. Eric Martz and Tim Driscoll
masterminded this idea using "scriptcallback" methods that see a
comment go by and then know it is time to do something. Something
like this:
set scriptcallback "myfunc";set debugscript true;load whatever;#--
file is loaded
then myfunc() gets a message every time a script command is
executed, and the "#--file is loaded" message comes through as well:
function myfunc(app, msg) {
var s = "" + msg // converts Java string msg into a JavaScript
string
if (s.indexOf("#--file is loaded") == 0) {
[do something]
}
}
Re: [Jmol-users] problem in firefox
I spoke too soon.
var x = jmolEvaluate('getProperty("auxiliaryInfo.zeroPoint")')
isn't working for me. It returns an error message about the
getProperty command.
*******
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 29, 2008, at 10:40 AM, Robert Hanson wrote:
mosty I think you will find that the jmolGetStatus() business won't
be helpful. I'm probably the only who ever used that. It was an
early attempt to get around callbacks, and I can't think of any good
reason to use it now.
Try something else, like the following:
alert(jmolGetPropertyAsString("auxiliaryinfo", "", divInc))
For getting that property, these days I just use:
var x = jmolEvaluate('getProperty("auxiliaryInfo.zeroPoint")')
rather than doing all the translation of the auxiliaryInfo array
into JavaScript just to get that one element.
But you are using Jmol 11.6.RC6 -- be sure to upgrade that to
11.6.RC11.
Bob
On Thu, Aug 28, 2008 at 11:00 PM, Jeff Hansen <[EMAIL PROTECTED]>
wrote:
Thanks Bob. If gas prices weren't so high and my family wouldn't
miss me too much I would take you up on the offer.
Of course jmolScriptWait didn't break anything, just my failed
attempts to use it broke something.
I tried your second alternative (callbacks are still a mystery to me
although that code doesn't look too bad). So after loading the file
I called a function.
this.loadString = "load ../Jmol/jmol/Models/" + molecule +
";javascript myFunc();";
divWrite(divID,jmolApplet(400, this.loadString,divInc));
In the function I tried to use jmolGetStatus.
function myFunc(){
var result = jmolGetStatus("scriptStatus",divInc);
alert(result);
}
As with all of my attempts thus far this displayed "undefined." I
guess I still don't get how this works.
I think ultimately I will put the load command along with some other
commands in a script file rather than continuing to make these long
(and going to get longer) strings.
I'm making progress and having fun. Does that make me a geek?
Thanks for the help and encouragement.
You can see how far I've come at http://web.mac.com/jhansen4/Jmol/NewJmolDivSTD.html
.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 10:47 PM, Robert Hanson wrote:
Jeff, why don't you come over to St. Olaf and I'll show you how
this works! :)
Seriously, hang in there. You are trying to do a lot all at once,
and you will catch on. This is precisely what this list is for.
Just keep at it.
"jmolScriptWait" would not "break" anything.
jmolScriptWait should only be used if you absolutely have to pause
the JavaScript until that operation is complete. There are times
this is necessary, but it's not a great idea.
Most Jmol commands are given "asynchronously" using jmolScript()
rather than jmolScriptWait(). Jmol has a built-in queuing system,
so you can fire as many commands at it as you wish, and they will
be processed in order as processing becomes available. You can also
clear the queue using
!exit
and you can abort a specifically running script (but continue
processing later scripts) using
!quit
An alternative to waiting is to have the issued script notify the
web page when it is complete. Eric Martz and Tim Driscoll
masterminded this idea using "scriptcallback" methods that see a
comment go by and then know it is time to do something. Something
like this:
set scriptcallback "myfunc";set debugscript true;load whatever;#--
file is loaded
then myfunc() gets a message every time a script command is
executed, and the "#--file is loaded" message comes through as well:
function myfunc(app, msg) {
var s = "" + msg // converts Java string msg into a JavaScript
string
if (s.indexOf("#--file is loaded") == 0) {
[do something]
}
}
Alternatively, I've used the following quite effectively:
jmolScript("load whatever;javascript modelLoaded()")
That would run the JavaScript function
function modelLoaded() {
}
as soon as the model is loaded.
Basically, good "event driven" code is asynchronous. Nothing waits
for anything. Things happen because they get a message that they
need to happen. The more you can do that, the better.
Still, I do use jmolScriptWait() myself at times. Also
jmolEvaluate() is synchronous, and I use that a l
[Jmol-users] which jmol applet?
If I use a function like this:
function getEnergy() {
var _jmolText = document.getElementById('jmolText');
var Energy =
jmolEvaluate('getProperty("auxiliaryInfo.zeroPoint")');
var text = "Energy = " + Energy + " kJ/mol\n";
var node = document.createTextNode(text);
_jmolText.appendChild(node);
}
and I have more than one Jmol applet on the page, how do I select
which applet I'm getting the info from?
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] which jmol applet?
Thanks. That appears to do the trick.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 30, 2008, at 6:28 AM, Angel Herráez wrote:
> Hi Jeff
>
> That shuld be in the doc... No! "jmolEvaluate" is not documented in
> http://jmol.sourceforge.net/jslibrary/
>
> Let me take a look at Jmol.js code...
> function jmolEvaluate(molecularMath, targetSuffix)
>
> So, you work as with jmolScript. That would be:
>
> var Energy =
> jmolEvaluate('getProperty("auxiliaryInfo.zeroPoint")' , 0 );
>
> using "0" for the first applet, "1" for the second, etc., or their
> names if you set them.
>
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bond picking -- and getProperty in general
So for example, could I use the following to get the zero point energy
from the third model in the first file loaded into the second applet
of several applets on a page?
var Energy = jmolEvaluate('getProperty("auxiliaryInfo.zeroPoint",
{1.3}, 1)')
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 30, 2008, at 11:45 PM, Robert Hanson wrote:
getProperty can be a very inefficient function. The algorithm is
designed to return the entire property set, then do the selections.
So, for example, if you say:
print getProperty("atomInfo[3]")
and there are 3 atoms, then first a vector containing 3
elements is produced and only after that is one selected.
I'm reminded that I thought of that and had a solution to it but
forgot. The alternative format:
print getProperty("atomInfo", {atomIndex=3})
is far more efficient, as it only creates a single atomInfo entry --
an array with one element.
I've checked in code now that combines these:
print getProperty("atominfo[1].sym", {atomIndex=3})
creates only one entry and then selects the information about atom
symbol from that single entry. ([0] would work as well, because that
means "the last entry", and there is only one)
In checking through the code, I also noticed that "bondInfo" works
similarly, but both atoms of the bond must be selected. I've now
changed that so that if you specify just one atom, then "bondInfo"
gives you what you think it would -- the bond info for that atom:
print getProperty("bondInfo", {atomno=2})
[[ information about all bonds to atom #2 are displayed ]]
Similarly,
print getProperty("bondInfo[1]", {atomno=2})
give information about just the first bond to atom #2.
In addition, getProperty("modelInfo") was not allowing an atom
expression, but it seems to me that would make sense as well:
print getProperty("modelInfo", {atomIndex=2})
or perhaps
print getProperty("modelInfo", {1.3})
So I have added that.
Finally, getProperty("auxiliaryInfo") also could allow for
specifying the model, so I have added that as well:
print getProperty("auxiliaryInfo", {1.3})
These changes should make for much more efficient extraction of
information.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win
great prizes
Grand prize is a trip for two to an Open Source event anywhere in
the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] javascript command fails in Safari?
I don't know about from the console, but I've used it successfully in
a web page on Safari.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Sep 5, 2008, at 9:18 PM, Eric Martz wrote:
> It appears to me that the javascript command of Jmol does not work in
> Safari on Mac OS X.
>
> Examples, typed into the Jmol console:
>
> javascript alert("hi")
> or
> javascript alert(document.location.href)
>
> These display the alert in Firefox on Windows or Mac OS X, but not in
> Safari on Mac OS X.
>
> If this is a known limitation, I suggest that it be documented for
> the javascript command in the Jmol reference manual.
>
> Thanks, Eric
>
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
