Re: [Jmol-users] Slabbing mode
Frieda wrote: > Do these links start to get into the type of thing that would restrict > your development efforts, Miguel? Obviously I do not wish to do that. I > have little feel for it beyond your not using Chime and not having it > installed on your machine- which you have clearly stated. > > If it does get into a gray area, perhaps you could show us what solid > sphere rendering looks like in Jmol, so we can comment. I am not sure exactly what you are asking ... but I will put some energy into this. > Previously, Miguel had said: > >> One of the problems I have had with slab is the various "slabbing >> modes". It is difficult for me to render a solid sphere that has had >> the front of it sliced off. I now have an idea of how to do this in a way that may not be difficult. >> And when it gets past the midpoint these >> turn into solid circles. Not difficult to implement, but rather ugly >> to my eye. > > Hmm, I don't think the Chime solid sphere slab is at all displeasing, The ugliness that I was referring to was specifically 'after it gets past the midpoint'. That is, when you are on the back side of the sphere and it starts shrinking. When that happens there is no shading ... everything is the same solid color. > so I imagine that the Jmol version looks rather different... I guess > the only point of showing it to us in Jmol would be if it could somehow > be modified using our suggestions, or implemented as an optional > slabbing mode. I'll put something together for you. >> It seems to me that perhaps one would want the slabbing mode to be >> different when working with large molecules as opposed to small >> molecules. That is, with large molecules it may be better for atoms to >> disappear completely rather than get sliced away. >> >> Q: What slabbing modes are useful when working with large molecules? >> >> Q: What slabbing modes are useful when working with small molecules >> (or zoomed in on a piece of a large molecule) ? > > For large molecule viewing, having atoms disappear would be superior to > having the empty circle (bubble) appearance that is the current > default. I understand that noone likes the current slab behavior. > But I would have to see it in action to say if it could really > live up to the clarity of a solid face rendering as I know it. > > I don't work much with small molecules so I can't really comment on > that. When working with a somewhat small section of a protein, such as > a beta sheet, or alpha helix (still a far cry from a typical "small > molecule" I think) I found that the solid face rendering continued to > be very useful. > > Are there any other choices for rendering slab besides the bubble, > solid sphere, and disappearing act? For sphere rendering, the bubble is dead ... or should I say 'burst' I will implement a solid hemisphere. Once you get past the center of the atom, it will disappear completely. We will defer further discussion until I implement that and people can take a look at it. Miguel --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] loading cml molecule by javascript from dom.
> Miguel: [Fri, Jul 22, 2005 at 04:06:33PM -0400]: >> >> > Can I use an inline cml document as input to >> > an embedded Jmol instance in my html document? >> >> Loading molecular models as strings into Jmol is supported. This works >> independent of the file type ... cml, xyz, pdb. > > I know - but I don't want to do this. I have a mixed-namespace > xml document, with html interpretable by a web browser, and > cml molecular structures. I can use javascript within this > document to access the cml structure as a tree of DOM nodes. I see. > If I could pass this straight to a Jmol instance, it wouldn't > need to parse the XML - it would already be parsed into nodes > and would be directly manipulable. Well, it would not help Jmol very much. The CML reader does not load the entire xml document. Rather, it uses the 'event trigger' model as it makes a single pass through the text version of the xml document. (I do not know what the proper terminology is to describe this :-) > I could, I suppose, once I've retrieved the relevant cml > node, use javascript to traverse the entire cml > subtree and write out a string of cml to pass to loadInline, but > that seems a very roundabout way to do things. Honestly, I think that is what I recommend. Certainly if you want to get it done in the short term. Since you are working with CML I suspect that you are working with small molecules, so the data is not too big. Egon is interested in XML & CML, so perhaps he would be interested in working on something like this. But he is currently on holiday. > I can't have the cml in my document as a javascript string > literal because the entire document is generated by xslt, so > I have no control over whitespace (including newline) output. I do not understand. I have never used xslt ... but I thought that the whole idea was to allow you to translate into various target formats. Taking a step back ... why aren't you just reading the CML file out of your database rather than trying to stick it inline? I assume that your application wants to do something ... So, just do both ... stick it inline for your application but let Jmol read it out of your database through a separate URL reference. Miguel --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Slabbing mode (was Mac mouse button bug)
On Jul 22, 2005, at 4:11 PM, Miguel wrote: Actually, I think we need to know whether or not it was fixed in the Java 1.5 that shipped with 10.4 Tiger. I honestly doubt if Apple will be interested in fixing any Java bugs in anything but their latest release. OK. This will help push me over the edge to install Tiger pretty soon, but there is one outstanding problem I need to solve before I can upgrade. So for now I need to leave this Mac mouse testing to others, until I can return to it with Tiger. Actually the next thing wanted to address is related-- slabbing mode, ie, the appearance of the front plane of the slab as it moves through a large molecule such as a protein. Eric Martz posted on this but I do not see a response when searching the archive. Eric said: SLAB RENDERING Chime's default slab rendering shows each atom cut by the slab plane as a partial sphere with a solid flat face cut by the plane. This is very useful for one of the most important visualizations in proteins, namely, to see the distribution of hydrophobic, polar, charged residues within the core of a domain. Here is a snapshot of an example: http://www.umass.edu/microbio/chime/beta/molslides/slab/slab-chime.gif Here is a snapshot of the same molslide rendered in jmol http://www.umass.edu/microbio/chime/beta/molslides/slab/slab-jmol.gif Do these links start to get into the type of thing that would restrict your development efforts, Miguel? Obviously I do not wish to do that. I have little feel for it beyond your not using Chime and not having it installed on your machine- which you have clearly stated. If it does get into a gray area, perhaps you could show us what solid sphere rendering looks like in Jmol, so we can comment. Previously, Miguel had said: One of the problems I have had with slab is the various "slabbing modes". It is difficult for me to render a solid sphere that has had the front of it sliced off. And when it gets past the midpoint these turn into solid circles. Not difficult to implement, but rather ugly to my eye. Hmm, I don't think the Chime solid sphere slab is at all displeasing, so I imagine that the Jmol version looks rather different... I guess the only point of showing it to us in Jmol would be if it could somehow be modified using our suggestions, or implemented as an optional slabbing mode. It seems to me that perhaps one would want the slabbing mode to be different when working with large molecules as opposed to small molecules. That is, with large molecules it may be better for atoms to disappear completely rather than get sliced away. Q: What slabbing modes are useful when working with large molecules? Q: What slabbing modes are useful when working with small molecules (or zoomed in on a piece of a large molecule) ? For large molecule viewing, having atoms disappear would be superior to having the empty circle (bubble) appearance that is the current default. But I would have to see it in action to say if it could really live up to the clarity of a solid face rendering as I know it. I don't work much with small molecules so I can't really comment on that. When working with a somewhat small section of a protein, such as a beta sheet, or alpha helix (still a far cry from a typical "small molecule" I think) I found that the solid face rendering continued to be very useful. Are there any other choices for rendering slab besides the bubble, solid sphere, and disappearing act? -Frieda Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com
Re: [Jmol-users] loading cml molecule by javascript from dom.
Miguel: [Fri, Jul 22, 2005 at 04:06:33PM -0400]: > > > Can I use an inline cml document as input to > > an embedded Jmol instance in my html document? > > Loading molecular models as strings into Jmol is supported. This works > independent of the file type ... cml, xyz, pdb. I know - but I don't want to do this. I have a mixed-namespace xml document, with html interpretable by a web browser, and cml molecular structures. I can use javascript within this document to access the cml structure as a tree of DOM nodes. If I could pass this straight to a Jmol instance, it wouldn't need to parse the XML - it would already be parsed into nodes and would be directly manipulable. I could, I suppose, once I've retrieved the relevant cml node, use javascript to traverse the entire cml subtree and write out a string of cml to pass to loadInline, but that seems a very roundabout way to do things. I can't have the cml in my document as a javascript string literal because the entire document is generated by xslt, so I have no control over whitespace (including newline) output. Toby --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] loading cml molecule by javascript from dom.
Can I use an inline cml document as input to an embedded Jmol instance in my html document? Or, to show (roughly) what I mean, is something along the following lines possible? (Obviously I can't use jmolApplet as I have below; but is there any way of passing a cml molecule from the DOM tree to jmol?) http://www.w3.org/1999/xhtml"; xmlns:cml="http://www.xml-cml.org/schema/CML2/Core";> Molecule 1 -- Dr. Toby White Dept. of Earth Sciences, Downing Street, Cambridge CB2 3EQ. UK Email: <[EMAIL PROTECTED]> --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac mouse button bug
>> Q: What version of OSX are you running? > > 10.3.9 It would be good to know whether or not this got fixed with 10.4 Tiger. >> Q: Can you understand the output? > > given your interpretation of the above output, I believe so... but I > was not sure if the other info was needed by you, like the four digit > number that starts each second line, or the first line prior to "says > button 3", etc., etc. If that stuff is irrelevant then I imagine I can > figure it out. Actually, I think we need to know whether or not it was fixed in the Java 1.5 that shipped with 10.4 Tiger. I honestly doubt if Apple will be interested in fixing any Java bugs in anything but their latest release. >>> 2. Can you help me with quitting ShiftButtonBug, since when I followed >>> the instruction: >>> To exit give the focus to your terminal window and press ^C >>> >>> nothing happened except >>> ^C >>> appeared in the terminal window... >> >> You did hit 'CTRL-C' ... correct? > > Guess I did not know what ^C *really* means-- I typed ^ literally , as > in SHIFT-6... Not to worry ... it is just jargon/notation ;-) Miguel --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] loading cml molecule by javascript from dom.
> Can I use an inline cml document as input to > an embedded Jmol instance in my html document? Loading molecular models as strings into Jmol is supported. This works independent of the file type ... cml, xyz, pdb. See jmolAppletInline and jmolLoadInline at http://www.jmol.org/jslibrary At the bottom of the demonstration page (http://jmol.sourceforge.net/demo/) there is a link to a small sample (http://jmol.sourceforge.net/demo/jssample2/). Do a View -> Source on this page. Miguel --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac mouse button bug
On Jul 22, 2005, at 11:34 AM, Miguel wrote: I followed these directions that were displayed by ShiftButtonBug in Terminal's window: These were old instructions from the bug report that I submitted to Apple. OK. do a Shift Right-click and see that Button1 is also being returned. And when you release the mouse state says that Button1 is still pressed Here is the output I got in the Terminal window: e.getButton() says button 3 5184 -> Shift+Button1+Button3 e.getButton() says button 3 1088 -> Shift+Button1 So, this bug did not get fixed in the version of OSX that you are running. Q: What version of OSX are you running? 10.3.9 Open a terminal and type 'java -version' Q: What version of java are you running? terminal says: java version "1.4.2_05" Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_05-141.3) Java HotSpot(TM) Client VM (build 1.4.2-38, mixed mode) Now, 2 questions: 1. Do I repeat this process with the keystoke combos we are interested in for slabbing, and send the results (output) to you as above? Yes, I suppose ... Q: Can you understand the output? given your interpretation of the above output, I believe so... but I was not sure if the other info was needed by you, like the four digit number that starts each second line, or the first line prior to "says button 3", etc., etc. If that stuff is irrelevant then I imagine I can figure it out. 2. Can you help me with quitting ShiftButtonBug, since when I followed the instruction: To exit give the focus to your terminal window and press ^C nothing happened except ^C appeared in the terminal window... You did hit 'CTRL-C' ... correct? Guess I did not know what ^C *really* means-- I typed ^ literally , as in SHIFT-6... but now I know... Will get back to you (and the list) with info from testing. Frieda If that does not work, then 1. click on the gui close box to shut down the terminal 2. consider filing a bug report with Apple ;-) Miguel --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] loading cml molecule by javascript from dom.
Can I use an inline cml document as input to an embedded Jmol instance in my html document? Or, to show (roughly) what I mean, is something along the following lines possible? (Obviously I can't actually use jmolApplet as I have below; but is there any way of passing a cml structure from the DOM tree to jmol?) http://www.w3.org/1999/xhtml"; xmlns:cml="http://www.xml-cml.org/schema/CML2/Core";> Molecule 1 -- Dr. Toby White Dept. of Earth Sciences, Downing Street, Cambridge CB2 3EQ. UK Email: <[EMAIL PROTECTED]> --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] molecular surfaces
Hi to all I know Miguel is trying to make progress with this, so I have being testing the possibilities of rendering molecular surfaces (solvent-accesible, I guess). I have set-up a testing page, which is linked from http://wiki.jmol.org/ProteinCommunity Please, post any comments or experience in this list. --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac mouse button bug
> On Jul 21, 2005, at 7:58 PM, Miguel wrote: > >> Here is some source code and object code to test mouse events. >> >> Runs on any system with java 1.4 or greater >> >> You can run it by saying. >> >> Download it to some directory >> bring up a terminal >> go to that directory and type the command: >> java ShiftButtonBug > > OK, I did this and ShiftButtonBug is running in Terminal. > > I followed these directions that were displayed by ShiftButtonBug in > Terminal's window: These were old instructions from the bug report that I submitted to Apple. > do a Shift Right-click > and see that Button1 is also being returned. > And when you release the mouse state says that Button1 > is still pressed > > Here is the output I got in the Terminal window: > > e.getButton() says button 3 > 5184 -> Shift+Button1+Button3 > > e.getButton() says button 3 > 1088 -> Shift+Button1 So, this bug did not get fixed in the version of OSX that you are running. Q: What version of OSX are you running? Open a terminal and type 'java -version' Q: What version of java are you running? > Now, 2 questions: > > 1. Do I repeat this process with the keystoke combos we are interested > in for slabbing, and send the results (output) to you as above? Yes, I suppose ... Q: Can you understand the output? > 2. Can you help me with quitting ShiftButtonBug, since when I followed > the instruction: > To exit give the focus to your terminal window and press ^C > > nothing happened except > ^C > appeared in the terminal window... You did hit 'CTRL-C' ... correct? If that does not work, then 1. click on the gui close box to shut down the terminal 2. consider filing a bug report with Apple ;-) Miguel --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] RE: more .xyz
> Hi Miguel, > > Thanks, it works in the Jmol application fine, > even the very large file. Good. > The smaller ones work fine over the web, but the big one > is very slow. I may just forget this one as it is not > that important. I do have one question though, once I have > turned off the bonding is there a way I can generate > bonds for a select small group of atoms? Currently not implemented > I was using a group of sulfur atoms > in a wireframe display as scale bars. > > **2 minutes later** > > I just took a look at the axes Jmol displays, am I correct > in assuming that the size of the axes is determined by the > maximum X Y and Z coordinate for an atom in the file? Yes There is a 'boundbox' that is defined by min/max coordinate value along the x, y & z axes. set boundbox on The axes extend to the centers of the faces of the boundbox set axes on The following commands will be interesting for you. color boundbox orchid color axes yellow font axes 28 serif italic set axes on # axes of 1 pixel set axes 5 # 5 pixel axes set axes 0.1 # 0.1 angstrom radius You can use the following to show coordinate values select atomno=1 label " my x coordinate is %x" color label orange font label 20 select atomno=2 label "%x,%y,%z" color label turquoise font label 18 monospaced > If so I can use these to indicate the scale of the > images. Good. Miguel - Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] - --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac mouse button bug
On Jul 21, 2005, at 7:58 PM, Miguel wrote: Here is some source code and object code to test mouse events. Runs on any system with java 1.4 or greater You can run it by saying. Download it to some directory bring up a terminal go to that directory and type the command: java ShiftButtonBug OK, I did this and ShiftButtonBug is running in Terminal. I followed these directions that were displayed by ShiftButtonBug in Terminal's window: do a Shift Right-click and see that Button1 is also being returned. And when you release the mouse state says that Button1 is still pressed Here is the output I got in the Terminal window: e.getButton() says button 3 5184 -> Shift+Button1+Button3 e.getButton() says button 3 1088 -> Shift+Button1 Now, 2 questions: 1. Do I repeat this process with the keystoke combos we are interested in for slabbing, and send the results (output) to you as above? 2. Can you help me with quitting ShiftButtonBug, since when I followed the instruction: To exit give the focus to your terminal window and press ^C nothing happened except ^C appeared in the terminal window... Frieda Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol / Chime / JCAMP
I've been working with students building a java applet to display jcamp data. You can see the project in its current state at http://jchemapplet.sourceforge.net/. There's still a fair amount of work to do--tweaking the decompression algorithms to get them just right, adding axes, adding integration for proton NMR, etc. When we get those done we'll work on getting the molecular structures and the spectral data to communicate with Jmol the way it currently works in chime. Our work has stopped for the summer but we plan to continue again in the fall. We'd be happy to have collaborators if Marie or others are interested. Please check out what we've done and submit comments/suggestions at the site or directly to me ([EMAIL PROTECTED]). -Jennifer -Original Message- Message: 8 Date: Thu, 21 Jul 2005 12:41:22 -0400 (EDT) From: "Miguel" <[EMAIL PROTECTED]> To: [EMAIL PROTECTED], [EMAIL PROTECTED] Subject: [Jmol-users] Jmol / Chime / JCAMP Reply-To: jmol-users@lists.sourceforge.net Marie posted the question below to jmol-developers I believe that some of you have worked with tying JCAMP plots to display in Jmol. Any suggestions/advice for Marie? Miguel Mensaje original ---= - Asunto: =5BJmol-developers=5D questions about CHIME and JMOL De: =22marie Le Dorner=22 Fecha: Mie, 20 de Julio de 2005, 4:46 Para: jmol-developers=40lists.sourceforge.net -= - I am french and I am doing a website for the chemical and physical = Department of the University of Oxford. I have chosen JCAMP to plot my graphs, since I know that It is possible t= o connect a graph and a molecule in motion ( I would to show OH stretches ), I know that I can do that with CHIME , but I don't understand the difference between CHIME, and JMOL. I went to this site :http://jmol.sourceforge.net/ . Could you please give me some answers ? Thank you in advance . Melle M.LEDORNER : minipouce451=40hotmail.com --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] prerelease 10.00.22 + mouse slab gestures
El 21 Jul 2005 a las 12:17, Miguel escribió: > >> CTRL-SHIFT-LEFTdrag # control slab > >> CTRL-SHIFT-LEFTdouble-click-drag # control depth > >> ALT-CTRL-SHIFT-LEFTdrag # move both slab and depth, maintaining the > >> thickness of the displayed slice. > >> I want you folks to play with this. I can confirm that this works as expected on Windows (Firefox 1.0.4, 2-button+wheel Genius mouse, Java 1.5.0-b64, Jmol 10.00.22 with a user-friendly pop-up menu in Spanish ;-) ) Miguel, the "move both slab and depth" is a nice option for travelling through a protein; when you make the slider, try to implement this. --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] slider vs mouse gestures
Frieda Reichsman wrote: On Jul 21, 2005, at 6:56 PM, Miguel wrote: I think that the slab slider would appear after execution of 'slab on' :-OOh!! Cool! But I can also easily imagine a situation in which an author decides not to have it showing, but I as a user would benefit from slabbing. That's why I think the mouse gestures are very good. If I were to do a slider my inclination would be to say that it always appeard when you were in 'slab on' mode. If the author did not want to offer it by default, you could turn it on via the popup menu. I think you have completely resolved my doubts about the slider. Nifty stuff! Frieda I have not had the time yet to try out version 10.00.22 but want to bring another point into the discussion. It may be more comfortable to use a slider for controlling slab, but any control popping up in the applet window has a disadvantage: it needs a more or less big part of the window, disturbing the view of the structures shown. Especially if someone wants to make a screenshot it might be annoying and would at least require additional steps to get it out of the image. So I would suggest that the slider should get its own switch for hiding it without switching slab off. By default it could be switched on so that it would be shown if slab is switched on. Regards, Rolf --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] slider vs mouse gestures
El 21 Jul 2005 a las 18:56, Miguel escribió: > I think that the slab slider would appear after execution of 'slab on' [...] > If I were to do a slider my inclination would be to say that it always > appeard when you were in 'slab on' mode. [...] > If the author did not want to offer it by default, you could turn it on > via the popup menu. I think this is a perfect solution, Miguel. Great job! I have to set up a testing page and verify the mouse gestures under Win, then will write them into the Wiki MouseManual page · · · · · · · · · · · · · · · · · · · · · · · · · · · · · Dr. Angel Herraez Dep. Bioquimica y Biologia Molecular, Universidad de Alcala E-28871 Alcala de Henares (Madrid), Spain fax: +34-91 885 45 85 --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] mouse gesture wiki page feedback - Mac
> Might I presume to suggest the following? > -Add "click on molecule" to the Translation row > -Move the Reset and Center row up to just beneath the Translation row. Done, but translation works both clicking ON the molecule and AWAY from it. Reset works only AWAY. > Hope I am not being *too* presumptuous by making specific suggestions > like this. Not at all. The Wiki is supposed to be a collaborative effort. In fact, somebody already made a new contribution (selecting atoms) by straight edition of the page. --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] x,y,z to x,y,z lines
Brandon Hespenheide wrote: There was a post a few days ago asking whether it was possible to script Jmol to display straight lines from one 3D point to another 3D point, and a reply asking for what use this would be. I would find this functionality extremely useful for displaying/undisplaying hydrogen bonds and hydrophobic interactions (which are defined by our software). We currently offer these predefined selections in our PyMol scripts (produced by our software), and I would like to make it available on our web-based version of the software. for displaying bonds I suggest to implement the RasMol bond + command (unbond), which is used to CONECT any two atoms, allowing double bond wireframe rendering in PDB files (and may be, in future Jmol versions, structure manipulations). In general, any user-defined interaction could be displayed this way (such as the small-world and contact-order networks some people use to understand protein folding rates). A draw command for any geometric object is an other construction site, e.g. draw line [x1,y1,z1] [x2,y2,z2] Regards, Jan --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
