Re: [Jmol-developers] de.po 404 error
On the other hand, Why http:/_ ? That is not correct You need either two slashes (and then it must be an absolute server url) or no http (relative url) > is a complete unreasonable path. It should be: > http:/_INCLUDE/JSMOL/idioma/de.po that is not correct. You need /_INCLUDE/JSMOL/idioma/de.po Maybe your problem is some code that worked in the Windows server but is not good for the Linux server, after all. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] de.po 404 error
Hello Klaus 1. Yes, the location of the language files cannot be specified. As far as I remember, it always looks for them in a 'idioma' folder which is a sibling of the 'java' folder. I'm not sure what happens when you don't specify the java folder 2. Some javascript error loading the language file is normal and does not prevent it from working Is this your location? http://test.schelm.hhu.de/scheLM_3D/ What I see in the source there may be a cause. you are using an Info.jarPath that is outside the main JSmol folder. Try changing the java folder to be under the JSmol folder, or move the idioma folder to be a sibling of the java folder. Alternatively, if you are not using the java mode, comment out definition of jarPath and see what happens -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] some wrong characters in localization of popup menu
Dear Bob, I have noticed that some characters do not display properly in the pop-up menu, Languages submenu in JSmol-HTML5 Checked in JSmol 14.6.4 and 14.9.1 in two different pages, see snapshot https://ibb.co/hpdWck Many foreign characters display well, but not those few in Russian, Chinese and Ukrainian -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] set antialiasdisplay needs a click to aply changes
Dear Bob, We are finding a strange behaviour in JSmol-html5 within Proteopedia: changing antialiasDisplay does not display any effect until you click on the JSmol canvas. Test case: go to http://proteopedia.org/wiki/index.php/1a2m open the JSmol console and type zoom 300 set antialiasDisplay true // no visible change until one clicks on JSmol set antialiasDisplay false // again Using "refresh" does not make any difference. And Eric just found that this problem is present in the Jmol application (from October 21, 2016) My copy, Jmol 14.10.0 2017-03-25, also does it: load =1a2m zoom 300 cartoon only set antialiasDisplay true Another quirk: in that Proteopedia page, see how the font size of the echo text changes dramatically with antialias --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] scripts persisting after quit or exit
Hi Jeff Glad you are finding a solution. The lack of working of "!exit" straight away is disturbing. "move" is considered an obsolete command and that may be the reason there is no method to interrupt it, but I agree that some things are not easy to reproduce with other commands, as you are seeing. > > One question, when I get the coordinates for moveTo with "show moveto" in > > the console, I end up with a longer command than in your example, for > > example: I am not sure. It is safer that you do not trim the command, but when the last parts tend to remain constant (they are related to rotation radius and other things that do not change with your use of move) they may be omitted, as I did. > I have a move command: move 0 360 0 0 0 0 0 0 4, which does a full rotation > around the y-axis over 4 seconds. How do I covert that to a moveto command? > If I just move to the final coordinates, they are the same as the starting > position, so it does not animate. Indeed! No equivalence there. You can either do two 180º moveTo commands, but that may behave different, or, better, use a rotate command - probably this: rotate y 360 -4.0 (note the minus sign, explained at https://chemapps.stolaf.edu/jmol/docs/#rotate ) --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] scripts persisting after quit or exit
Hi Jeff
I've done a little testing.
It seems that the problem is in the "move" commands, that cannot be
interrupted. I found about "set waitForMoveTo" and "moveTo stop", so this
seems to work:
1.
Edit you spt files to change the move commands to equivalent moveTo
commands.
// move 0 0 0 80 0 -10 0 0 2.0
moveTo 2.0 {588 -641 -493 123.42} 170 0 -10;
//move 0 0 0 -80 0 10 0 0 2.0
moveTo 2.0 {588 -641 -493 123.42} 90 0 0;
(parameters obtained using "show moveto" in the console after manually
entering the original move)
2.
Edit the button code to add the stopping commands, like this:
Jmol.script(jmolview1, '!exit; set waitForMoveTo false; moveTo stop; load
s_dipep.pdb; script animation2.spt;');
3.
You probably need to reset to "set waitForMoveTo true" somewhere, at the
beginning of the scripts I think, so your moves within a script are displayed
sequentially as you want.
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Re: [Jmol-developers] scripts persisting after quit or exit
Hi Jeff That's a little strange. "exit" should do what you wish, at least according to the documentation (I have no direct experience) I suggest that you try this: add !exit as the first line of your script files or the first command of your inline scripts that are callled from buttons. Following your example, I would do this: [1] scene is loaded with: Jmol.script(jmolview1, '!exit; load model.pdb; script initial-view.spt;´); [2] clicking a play button begins the animation with: Jmol.script(jmolview1, '!exit; load model.pdb; script animation.spt;´); [3] combined into [4]: Jmol.script(jmolview1, '!exit; load model.pdb; script initial-view2.spt;´); Let's see if that helps --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Fwd: [sage-cell] Re: Encoding problems for jsmol context menu
Hi Jonathan I've seen this kind of a problem occasionally (my system is configured for Spanish so the JSmol popup menu opens in Spanish, and has accented characters), but have not been able to track it down. I think it may be a bad combination of charsets in the several files involved. I cannot be certain, but the page http://netmath.vcrp.de/downloads/Systeme/Sage/SpatX.html declares UTF-8 while https://sagecell.sagemath.org/embedded_sagecell.js seems to be encoded as "windows-1252" I am assuming this is the JS file that will call JSmol.min.js (not obvious though) Summary: all JS files called from the page should also be encoded as UTF-8 and maybe they need to be declared as such or the server configured to serve them as such. I am not familiar with the particular details. Please try to make sure of that and let's see if that fixes the problem -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] export to IDTF is brokwn
El 18 Oct 2016 a las 23:06, Robert Hanson escribió: > IDTF does work correctly now, but you have to use the additional LaTex file > generated by Jmol to Yes, I had seen that part. However, I was expecting for a way to make a complex PDF (with text, flow, etc) without learning Latex. The PDF generated with Jmol's two files just holds the 3D model. My idea was to design my layout e.g. in Word, leaving empty squares for the models, produce the PDF, then edit it with PowerPDF and insert the u3d files. It works except the model is often either out of view or terribly zoomed in. Will keep trying. > orient it, because that is where the orientation information is. (IDTF was > designed specifically to > not allow specifying of orientation. Go figure!) Wow! Thank you -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] export to IDTF is brokwn
> thank you. fixed. Are people still using IDTF? Yes, hardly anyone, given the amount of information that can be found online. Still, there is some life -- see [1] But I am picking again the idea of producing PDFs with 3D models, and IDTF -> U3D is the only route. I just found that Power PDF fron Nuance lets you insert a u3d file in a PDF, together with all the other content, very easily and visually within the GUI. So I am giving it a try. Seems t work very nicely except for wrong zoom / position of the model. With a price of 39€ for the Education version of the software, it's worth the effort. Much nicer than learning Latex. [1] Embedding and publishing interactive, 3-dimensional, scientific figures in portable document format (PDF) files. Barnes, Vidiassov et al. (2013) doi:10.1371/journal.pone.0069446 -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] export to IDTF is brokwn
Dear Bob, load $aspartate; write IDTF Asp.idtf does nothing, reports nothing Jmol 14.6.4, 2016-10-02 application --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] (bug) set measurement in angstroms
set measurements 0.25 (any width in angstroms) is failing in versions below -- it used to work as expected, giving a not s thick cylinder 14.6.4_2016.10.02 14.6.2_2016.08.28 14.7.0_2016.06.27 14.6.0_2016.06.22 used at Proteopedia --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] cannot write menu to file in 14.6.2
Well, guess what It does not work for me in your page, but it does after I change the language to US English in the popup menu It only likes to save the English menu ;.) Forget it On 17 Sep 2016 at 15:51, Robert Hanson wrote: write menu ? worked fine for me at https://chemapps.stolaf.edu/jmol/jsmol/jsmol/htm On Sat, Sep 17, 2016 at 10:29 AM, Angel Herráez wrote: Ok, thanks I have later been able to do it from Java applet - so it may be that On 17 Sep 2016 at 9:53, Robert Hanson wrote: I don't think write menu was implemented in JSmol. Will take a look. -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson 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 -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] cannot write menu to file in 14.6.2
Ok, thanks I have later been able to do it from Java applet - so it may be that On 17 Sep 2016 at 9:53, Robert Hanson wrote: I don't think write menu was implemented in JSmol. Will take a look. -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] cannot write menu to file in 14.6.2
Is this a bug? On https://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm in the console: " write menu ? " gives this error after requesting the file name: ERROR en guión: TypeError: er.printStackTrace is not a function -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] rendeirng problems with JSmol popup menu
I like CSS solutions; they are very clean and you do not mess up with the js code. > something like "menus that do not contain any menus" --- li with no > containing ul --- I think that can be done in jQuery. Can it be done in CSS? Not actually straightforward, since you cannot apply css to parent nodes based on their children; the logic it's the other way around, top-down. So I don't see how jQuery would do it -- it would have to resort to checking all ul and li elements using JS before deciding. Anyway, why target terminal submenus? It's their height that brings trouble, not their level in hierarchy. -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] rendeirng problems with JSmol popup menu
> The way too long problem is generally solved by dragging the menu higher
on the screen.
I know. But still sometimes it's higher than the screen.
In many pages of mine the JSmol panel is 100% height, locked and cannot
be scrolled down (overflow:none), so it's actually impossible to reach the
lower submenus. That's how I noticed.
Example: http://biomodel.uah.es/en/model1/prot/alfa.htm
> It's a standard jQuery menu.
> So if you can figure out
> how to solve this with that, we could implement your solution in
JSmol.
Indeed. But I found a trick using just css.
See demo at
http://biomodel.uah.es/model1j/prot/alfa.htm
which is using a css patch in the page over regular JSmol.
The code is
.jmolPopupMenu ul.ui-menu { max-height:25em; overflow-y:auto;
overflow-x:hidden; position:fixed; }
That makes scrollable just the Language submenu and those like
Select > Protein > by residue name
However this patch breaks the unfolding of sub-submenus in IE11 (how much we
should care about
that browser, I'm not sure)
There is a trick also to avoid applying the former rules for IE11, though it
uses
a dirty hack:
@media screen and (min-width:0\0) {
.jmolPopupMenu ul.ui-menu { max-height:none; overflow:hidden;
position:absolute; }
}
Additionally, maybe personal taste, so I will not push for these to be
implemented:
to reduce the height of each submenu element:
ul.jmolPopupMenu , ul.jmolPopupMenu ul { line-height:1em; }
/* or maybe 1.1em */
and to reduce the size of the checkboxes and so the height of their submenu
items (like langs):
.jmolPopupMenu input[type="checkbox"] { transform: scale(0.8);
margin-top:-0.2em; }
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Re: [Jmol-developers] rendeirng problems with JSmol popup menu
Fine, Bob The funny thing was that the first string (language name translated to current name) was correct, the second was wrong (language name in the original language). If you siwtch to Russian, you can see in the same line one correct, one wrong. So I understand this is fixed for next release. Great! Regarding the height of the submenu, I think I have a solution via css (see http://biomodel.uah.es/Jmol/test/menu.htm bottom image) but where is the source for that part that generates the popup in JSmol? -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] rendeirng problems with JSmol popup menu
Dear Bob,
I have noticed two issues with the rendering of the pop-up menu in
JSmol-html5
1. The language submenu is way too long, and may become taller than the
screen, so in some page designs the lower half of the languages may be
unreachable.
2. The names of some languages display wrong characters (replaced by
symbols by the browser)
I would like to try and improve these, but I am having trouble locating the
relevant source code where the rendering of the menu is generated. Can you
give me a pointer?
Thanks
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[Jmol-developers] "color darkgrey" is rejected
Bob, I know you worked on this recently. I am testing this on "14.6.2_2016.08.28 2016-08-28 07:48" color gray color grey color lightgray color lightgrey color darkgray // all ok up to here color darkgrey // script ERROR: a color or palette name (Jmol, Rasmol) is required -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] load models {0 0 1} is broken in 14.6.0 seires
load models {0 0 1} filename
is broken in all 14.6.0 releases; it complains the closing brace was not
expected
We are trying to fix a problem in Proteopedia (Jmol 14.4.1) with rendering of
beta strands when the file does not contain SHEET records(note*). I realized
that bug is fixed in 14.6 so we planned to upgrade Proteopedia, but now we
cannot use 14.6 since loading 1st model is a default script in Proteopedia
Note *) rendering broken between 14.3.15_2015.06.19 correct and
14.4.0_2015.11.06 broken. Correct again in 14.6.0
Demo of the problem at first green link in
http://proteopedia.org/w/User:Jaime.Prilusky/Test/green_link
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Re: [Jmol-developers] Reloading current structure fails
The documentation under "data" says
http://chemapps.stolaf.edu/jmol/docs/#data
Using load data instead of just data you can load model data with all of the
loading options of the standard LOAD command.
Also, it says that you should probably use model as part of your data label;
this may be the problem:
If the data type is "model" as in the following example, then the data is
interpreted as an in-line model (and loaded using the default lattice, if
crystallographic).
So maybe you could combine both your load commands into one, i.e.
load DATA "model Abel"|... structure data comes here ...|end "model Abel" {1 1
1} SPACEGROUP "x,y,z;-x,y,1/2-z;-x,-y,-z;x,-y,1/2+z"
I tried with a simple mol2 data and load "" is working fine (see below)
The problem may be either with the symmetry options or with your "mol2
data" label.
zap;
load data "model example"|@MOLECULE|Molecule Name|5
4|SMALL|NO_CHARGES|||@ATOM|1 C1-0. 0.
-0.6300 C 1 fluromethane 0.123871|2 H2 0. 1.0330-0.9980 H 1
fluromethane 0.035745|3 H3-0.8946-0.5165-0.9980 H 1
fluromethane 0.035745|4 H4 0.8946-0.5165-0.9980 H 1
fluromethane 0.035745|5 F5-0.-0. 0.7527 F 1
fluromethane -0.231384|@BOND|1 1 2 1|2 1 3 1|3 1 4 1|4 1 5
1|end "model example"; // this works
load ""; // this works too
load data "model example"|@MOLECULE|Molecule Name|5
4|SMALL|NO_CHARGES|||@ATOM|1 C1-0. 0.
-0.6300 C 1 fluromethane 0.123871|2 H2 0. 1.0330-0.9980 H 1
fluromethane 0.035745|3 H3-0.8946-0.5165-0.9980 H 1
fluromethane 0.035745|4 H4 0.8946-0.5165-0.9980 H 1
fluromethane 0.035745|5 F5-0.-0. 0.7527 F 1
fluromethane -0.231384|@BOND|1 1 2 1|2 1 3 1|3 1 4 1|4 1 5
1|end "model example" {1 1 1} ; // no error, model loads
load "" {1 1 1}; // no error, model loads
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Re: [Jmol-developers] myJmol as variable in Jmol.script
Hi Klaus Go to http://chemapps.stolaf.edu/jmol/docs/ and search for "rotationRadius" You will see there is "set rotationRadius" therefore you can try show rotationRadius and it works! Examples of use: show rotationRadius // rotationRadius = 20.94923 rr = rotationRadius; print rr; // 20.94923 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Reloading current structure fails
Ok, Abel So you are not loading a mol2 file, you are loading data. Reloading of data might not be possible, or may need a different syntax. More investigation is needed on this, I cannoy say right now. What happens if you copy that data into a text file and load it into Jmol? Bob will know, but from his silence I guess he may be traveling... I will try to find out a way if I can -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Reloading current structure fails
Hello Abel We need to narrow the problem I've just tested with Jmol 14.6.0_2016.05.24, with a pdb file, a mol file and a mol2 file, and "load" works fine. e.g. load =1crn; load ""; load $caffeine; load ""; load "https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/mol2/csc l.mol2?format=raw"; load ; load ""; So, please, What is the exact version you are using? Is this happening just with a certain file or file type or command? Is it somehow related to the use of the spacegroup filter (I have no experience on this) -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] commit with localization files
Forget that last one -- I found where the language must be added, src\org\jmol\i18n\Language.java I am adding Russian since it is over 95% translated -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] commit with localization files
I just noticed in my local build that Russian (the latest added language) is not available in the pop-up menu. It appears there, though, after I enter this in the console: set language ru and it stays in the menu upon more language changes So I guess there is something that must be changed somewhere, maybe in one of the build scripts? -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] commit with localization files
Bob, I am committing changes in the localization. All the files were old due to lack of a recent rebuild of the POT files. I followed instructions for Nico and rebuilt those files in my Eclipse. That includes some updates of terms in Export to Web ad maybe some string that was not internationalized before. I can see no issues but will appreciate that you take a look for any possible disasters. If all is OK the update should be applied also to the 14.6 branch Thanks -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] update on Export To Web
(Just for the record and to finish this thread) Those changes in the Export to Web interface and the templates it uses for produced pages were finally committed to the trunk a few days ago. They are now used in Jmol 14.6.0 > > As a consequence, I am starting some revision of the page code generated, > > to be more HTML5-compliant and cleaner in terms of tags (e.g. less table > > tags, more div's and css) -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] commits r21103-05
Ok, those were my first commits from within Eclipse, so it took me a few trials and errors. I believe all is well. That was an update to the Export to Web interface, to better match descriptions for JSmol. -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] myJmol as variable in Jmol.script
Hello Klaus
I think that it should be possible to do what you want without using eval(),
which is usually not recommended by javascript gurus.
The variable is indeed an object and not a string, but that is what Jmol
expects.
There may be a problem when the variable has not been defined
beforehand; not sure if it will be your case. The trick in that case is to
define
it first like
myJmol = "myJmol"
Better:
I made a page with your functions and it is working as desired when I use it
like this
but I get the error when I use it like this:
So the issue would be you must pass the object, not the name.
If you don't want to write the object manually, like I did, I suggest that you
use the following instead of eval; one way to refer to objects ny their name is
to use
window[objectname]
That would allow for example this to apply to all Jmol objects named A, B, C,
D:
function setAll() {
for (i=65; i<69; i++) {
KS_AtomeHervorheben( window[String.fromCharCode(i)] )
}
}
> However, one more problem remains. After converting the script to the new
> syntax using
> The code will run in my JSmol enviiroment, but not in the Jmol
> environment.
> either the new syntax is not compatible to the old Jmol using JAVA,
> or that I did not include all necessary files in my html document. Which
> files (beside the old Jmol.js) do I have to include?
It is compatible, but you must be moving to new syntax also for the Java
mode. You must not use Jmol.js any longer, instead just change:
Info.use = 'java'
Info.use = 'html5' // default
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Re: [Jmol-developers] JAVA applet in WebPages
Hi Klaus
The code behind JSmol-HTML5 and Jmol-Java is exactly the same, so all
features must work the same.
I went to
http://schelm.hhu.de/home/Lehre/scheLM/scheLM_3D/start.html
and from there to
http://schelm.hhu.de/home/Lehre/scheLM/scheLM_3D/Butan/Butan.html
Both Jmol panels are displayed using Java, Jmol 14.4.4
When I open the console and paste your script,
moveto /* time, axisAngle */ 1.0 { -665 -743 77 146.14} /* zoom, translation */
80.0 0.0 0.0 /* center, rotationRadius */ {0.2629 0.7225
-1.24549998} 3.6994724443370037 /* navigation center,
translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */ 3.0
0.0 0.0;
it works without errors
So the problem might be in your call to jmolScript
Note that this is an old syntax, which needs conversion to the new
Jmol.script syntax. Are you using an intermediate function for that?
Please, clarify where/how you are running that script that gives the error; I
could not find it in the page
I can see that your Java page is using a Jmol.js file, labeled "Jmol 12.0"
There might be a problem with that. You should be using JSmol.min.js also
for the Java page
The JSMol page
has two JSmol-HTML5 panles that report a different version, Jmol 14.4.1
So in order to get the same behaviour you should use the same JSmol files
and just change the Info.use parameter in the source code
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alcalá de Henares (Madrid), Spain
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Re: [Jmol-developers] JAVA applet in WebPages
Hello Klaus Yes, the files are now different since JSmol. It is recommended that you change to the new JSmol Object syntax (see the Wiki for guidance) Otherwise, you could possibly still run it the old way. The Java applet files are inside the "java" folder which is inside the "jsmol.zip" file inside the downloaded zipfile You would in that case need to keep your old copy of Jmol.js -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] "nihResolverFormat" cannot be set
It seems this previous post (4th April) went unnoticed > Bob, > > This parameter can be shown but not set: > > $ print _versionDate > 14.4.4_2016.03.29 2016-03-29 22:33 > $ show nihResolverFormat > nihResolverFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE"; > $ set nihResolverFormat = > "https://cactus.nci.nih.gov/chemical/structure/%FILE"; > ERROR en guión: no se reconoce el parámetro SET: nihResolverFormat > > set <<< "https://cactus.nci.nih.gov/chemical/structure/%FILE"; > > -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] "nihResolverFormat" cannot be set
Bob, This parameter can be shown but not set: $ print _versionDate 14.4.4_2016.03.29 2016-03-29 22:33 $ show nihResolverFormat nihResolverFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE"; $ set nihResolverFormat = "https://cactus.nci.nih.gov/chemical/structure/%FILE"; ERROR en guión: no se reconoce el parámetro SET: nihResolverFormat set <<
Re: [Jmol-developers] Java 9 issue
if I may throw a suggestion, "L10N" is a term commonly associated to localization It could also be used for the current "idioma" folder in the jsmol package (I am happy with idioma, but others may not understand what it is for) -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] problem parsing DNA from assembly mmCIF (PDBe)
Thanks, Bob As far as I've seen, for whatever reason the EBI PDBe people are doing changes in the CIF format of those files; in several respects they do not match their regular CIF files. They remove some fields and others change names. I talked to them and basically they say that's how it's going to be. Regarding "biomolecule 1", you'd better talk to Jaime and Joel. What I've gathered is that biomolecule 1 is assigned automatically, there may be several of them, not the same, while this assembly has been hand-picked to be biologically reliable. So Jaime is hosting copies of the files in Proteopedia, and I'm helping in adapting Proteopedia scripts to handle those files as well as the classic pdb ones. For example, the nr. of models in a file, very easy to read from a pdb file, is harder or even absent is some mmCIF assembly files. Regarding the reordering on models, I noted that a 20-model pdb trimer becomes 60 models, and not always in the "logical" order, but I have not done a systematic analysis. Up to now, only that particular assembly file has shown problems with our Proteopedia scripts, in the initial "simplified model" rendering. Indeed, the "full model" rendering includes the DNA, and now I see why. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] problem parsing DNA from assembly mmCIF (PDBe)
We are starting to work on reading mmCIF files from PDBe, for "assemblies". This means the actual biological unit of the molecule, be it monomer, dimer, tetramer, etc -- manually checked since there are often several automatically prepared biological units in PDB Apparently EBI has been applying some variation in which CIF dta fields are retained in the assemby CIF file So far we have managed (Proteopedia) to handle those idiosyncrasies, but I have hit some weird problem with 2LEV It has protein + DNA, several models. Jmol 14.4.1 Jan 15 fails to render the DNA at all These are my checks: load http://www.ebi.ac.uk/pdbe/entry-files/download/pdb2lev.ent // PDB file -- ok load http://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divide d/pdb/le/pdb2lev.ent.gz // PDB file (gz) -- ok load http://www.ebi.ac.uk/pdbe/entry-files/download/2lev_updated.cif // Updated mmCIF file -- ok load http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz // Assembly 1 (mmCIF; gz) -- DNA is not displayed select dna //19040 atoms selected hide all //37340 hidden atoms display all //0 hidden atoms // in all cases, no rendering of DNA -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] update on Export To Web
Dear developers, in particular Bob and Jonathan, Over the last weeks I was teaching a course where whe learned to produce webpages from Jmol Export to Web. As a consequence, I am starting some revision of the page code generated, to be more HTML5-compliant and cleaner in terms of tags (e.g. less table tags, more div's and css) I have managed to do a new setup of Eclipse in my computer and so I am again able to locally test my builds of Jmol. This message is a warning to avoid any clashes in case some of you may think of changing the source meanwhile. I will discuss with you and commit my changes once I'm satisfied with the result. Jonathan, I've noticed that the widgets are not yet implemented in the current (JSmol) version. I am not sure if I will understand your approach and so may or not change that part. Right now I am working just on the html source of the templates. Best, Angel -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] partially selected state in checkbox groups
Yes, it's working through all levels (tested with 3, see http://biomodel.uah.es/JSmol/test_cbGroup.htm On 13 Nov 2015 at 16:25, Robert Hanson wrote: > > Did you get the sub-group business working? > > On Fri, Nov 13, 2015 at 1:46 PM, Angel Herráez < angel.herr...@uah.es> wrote: > Dear Bob > > I've being working on checkbox groups, to implement the display of > partially > selected state --which is a supported feature in html5. > > https://sourceforge.net/p/jmol/feature-requests/228/ > > Can you consider this for inclusion in next release? > I don't know where that should be located in the source code tree. > > > > -- > ___ > Jmol-developers mailing list > Jmol-developers@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department 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 > -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] partially selected state in checkbox groups
Dear Bob I've being working on checkbox groups, to implement the display of partially selected state --which is a supported feature in html5. https://sourceforge.net/p/jmol/feature-requests/228/ Can you consider this for inclusion in next release? I don't know where that should be located in the source code tree. -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] How to display smoothly varying XYZ geometries in Jmol?
Hello Krishna, and welcome to Jmol community
There are probably several ways you can try for your purposes (although I
am not sure to closely understand your setup). Here are some tips:
1. Do not use "zap", as it clears one model before starting to load the next.
Maybe just
load file1.xyz; load append file2.xyz;
or
load files "file1.xyz" "file2.xyz";
http://chemapps.stolaf.edu/jmol/docs/#loadappend
http://chemapps.stolaf.edu/jmol/docs/#loadfiles
2. If the atoms and bonds are the same in all models, you can try
load trajectory
but probably that may not be done with several files, only with a multimodel
file
http://chemapps.stolaf.edu/jmol/docs/#loadtrajectory
3. If you are calculating the coordinates, there is no need to save files, you
could try loading the data using the "data" or "load data" commands
http://chemapps.stolaf.edu/jmol/docs/#loaddata
4. It is indeed possible to change atom coordinates of the current model
inside Jmol, avoiding the need to load a second, third... files. For this, you
access and set the atom properties (x, y, z, xyz, atomX, atomY, atomZ). See
http://chemapps.stolaf.edu/jmol/docs/#atomproperties
Example:
{atomno=3}.x = 0.123;
{atomno=3}.y = 2.03;
{atomno=3}.z = -0.31;
I am quite sure if you explore those you will find your solution. Jmol
scripting
is very flexible and powerful.
Good luck and let us know the outcome,
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Re: [Jmol-developers] xml files?
> I am trying to convert the Jmol source code to JSmol using Java2Script. > I've made some changes to it and I want to know how they affect JSmol. I > got the code from here: http://jmol.sourceforge.net/#Obtain%20Jmol Ah, ok That's a purely developer-programmer issue, then. It's clear now. I cannot help on that, sorry. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] xml files?
Hi, Sam > I'm looking for these files that were mentioned in the readme in > the main Jmol download: > build_01_fromjmol.xml > build_02_fromjspecview.xml > build_03_tojs_stable.xml I cannot advise on those, which I don't know at all --and never saw before. They might be recent, or developer-related i.e. for building the released files. Not used regularly from the user side. Bob will tell you about them. > I am trying to convert my Jmol code to JSmol using Java2Script, however > I am getting errors. I read that you guys had to heavily augment > Java2Script for it to work, what's the scoop on that? This is confusing. Do you want to convert Jmol source code? Or Jmol commands / scripts? These need no conversion, as they work equally in JSmol. Please, clarify what "your" Jmol code is about · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Changing Console Location and Adding a New Menu
> Wow, that's very helpful, thank you! So I assume if you can create a > permanent console in Jsmol, > it's possible in Jmol as well. Java is a different business, the console IS a java window so you cannot fix it in the page. Example test: http://biomodel.uah.es/JSmol/test_console.htm?_USE=JAVA > would it be possible to instead > customize the right click menu Yes. Please see http://wiki.jmol.org/index.php/Custom_Menus http://wiki.jmol.org/index.php/Recycling_Corner#Custom_pop-up_menus > and have the right click menu be permanent? That will be tricky, but you might follow the same method as for the console. and http://chemapps.stolaf.edu/jmol/docs/#menu -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical & virtual servers, alerts via email & sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Changing Console Location and Adding a New Menu
Sam, Nearly there, just with CSS as I envisaged: http://biomodel.uah.es/JSmol/test_console.htm -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical & virtual servers, alerts via email & sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Changing Console Location and Adding a New Menu
It seems that the console div is created when either the "console" command is executed or the popup menu option is picked. It is appended after the BODY tag, with this content: etc So you need to fing where is that code generated. Maybe search for class="jmolConsole" in the source -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical & virtual servers, alerts via email & sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Changing Console Location and Adding a New Menu
Hello Sam Note there are no windows, it's all html in the single page, so my bet is you can do it (maybe) just using CSS, rather than modifying the source. I am not sure though whether the console panel is created every time or is always present and hidden. Case 2 will suit CSS, while case 1 will require code changes. Sorry I cannot tell you where in the code the console panel is created (Bob will know, but he is away for a week) If you try to explore the page elements while the console is displayed, you can find if a CSS solution is feasible. -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical & virtual servers, alerts via email & sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Bug Found
Hi Sam What you describe is very uncommon. Please, describe the procedure you have used to load the files. example: load files "=4KKS" "=1PD6" Hey! I see now! The particular 1PD6.pdb is a structure resolved by NMR as so it contains 28 different structures (conformations) -- taht's the reason for what you are seeing You probably want to load just one model, see http://chemapps.stolaf.edu/jmol/docs/#loadmodels -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Displaying Multiple Structures and Manipulating Coordinates
Hello Sam, and welcome (This rather belongs into jmol-users list) > I'm emailing to ask a few questions about JMol. From what I've > found on your emailing archives, it seems like it is possible to load > multiple structures at once, but how exactly would one do that using the > frame commands? You use the "load" command. The "frame" command controls display of one or another, later on. in brief, load files "file1.pdb" "file2.pdb" for details, see http://chemapps.stolaf.edu/jmol/docs/#loadfiles > In addition, I was wondering if it was possible in JMol > to manipulate a structure's coordinates and then save those coordinates. Yes, it is possible. There are a few ways to move atoms, like "rotateSelected" and "translateSelected" They can also be moved with the mouse, after activating the proper mode (see the "picking" command and more). Then, you use the "write coords" command Everything at http://chemapps.stolaf.edu/jmol/docs though it takes some time to master those issues Good luck! -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] ligand contacts are broken in PDB
Dear Bob, I thought you'd like to know that the ligand contacts view, "View Pocket in Jmol" in the PDB website seem to be broken. When I click on the link, nothing happens. Maybe a consequence of their updates in viewers. (I've tried to reproduce that nice display manually via the console, and I can get the contact surface fine, but I don't know how to slab the surface so that only the rear half or backdrop is displayed) -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] DOCUMENTATION AnimFrameCallback
Dear Bob, http://chemapps.stolaf.edu/jmol/docs/#setcallback set AnimFrameCallback says 9 parameters are returned. I only see 8; I think that maybe "isAnimationRunning" and "animationDirection" are merged into one? 14.2.14_2015.06.11 Regards, Angel -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Loop speed optimization potential
Hi Rolf I was about to suggest what Bob is putting forward: if Javascript is faster, you might take part of the code out from JmolScript into JavaScript. I believe he has demo'ed how. Another idea: I found that in Javascript there is much improvement in loops when they are decrementing instead of incrementing the control variable. Namely, changing for (i=0; ihttp://goparallel.sourceforge.net/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] rotate selected @variable fails in recent versions
I am seeing a problem in using COMPARE() and ROTATE SELECTED with
only recent versions:
My script is of the type
load a.pdb // 10 frames
load append b.pdb // single frame
select protein; trace only; color trace gray;
rotMx = compare({2.1 & alpha}, {1.10 & alpha});
show rotMx;
select 2.1; color trace blue;
rotate selected @rotMx;
// alternative: rotateSelected @rotMx;
The 2.1 model moves far away to the other side of the 1.10 model
In former versions this works fine.
The rotMx variable looks the same in all versions, so it's ROTATE that fails
Failure:
14.3.12_2015.02.11b (zip from St.Olaf)
14.3.12_2015.02.07 (zip from St.Olaf)
These are OK:
14.3.3_2014.08.01a
14.2.9_2014-11-23
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[Jmol-developers] problem loading multimodel pdb file in jmol-14.3.12_2015.02.11b
Bob, A 10-model pdb file that loads fine in previous versions (up to jmol-14.3.12_2015.02.07.zip) breaks jmol-14.3.12_2015.02.11b.zip from St.Olaf load 3o80_3o8m_altB_17-485_508362-32078.pdb ERROR en guión: ERROR creating model: java.lang.NoSuchMethodError: org.jmol.modelsetbio.AminoMonomer.getExplicitNH()Ljavajs/util/P3; load >> "3o80_3o8m_altB_17-485_508362-32078.pdb" << -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] list bounces
El 23 Jan 2015 a las 7:02, Robert Hanson escribió: > Who is handling these? Anyone? > jmol-users-boun...@lists.sourceforge.net I've done it a couple of times, but in others when I logged in, the problem had already been taken care of (Nico, maybe?) On the other hand, I suspect I have admin access only for one of the lists, either users or developers -- I need to check -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] setAppletCss
It seems that setAppletCss() is not working, tested in JSmol 14.3.10
Case example: the button has red border, but the JSmol object has not:
.grayBox { border:1px solid red; }
Jmol.setAppletCss('grayBox');
Jmol.setButtonCss('grayBox');
Jmol.getApplet('myJmol', Info);
Jmol.jmolButton(myJmol, ' ', 'test')
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Re: [Jmol-developers] JSmol as network viewer
Hi Rolf This is interesting but not what I can really discuss about, but I'd contribute one or two hints: One really nice thing (I've seen it in other tree viewers) would be the ability for the user to pull a node and have the whole thing rearrange dynamically. That's a force field and Jmol already does this with dragMinimze. However, probably not easy to achieve seeing the complexity of your trees (i.e. many "bonds" tied to an "atom"). > Q: Does JSmol allow that an atom is part of more than one residue or > would this interfere with something? Quick answer: no atom can belong to 2 residues. But I would forget about "residues". I'd just define Jmol variables as atom sets and assign each node to as many of them as you wish (using a script). It is as easy to select by user variables / atomsets as by residue. Another possibility is to assign custom atom properties, instead of atom sets. -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] chainCaseSensitive is forced true in 14.3.7
Bob, that sounds fully reasonable to me. The way I see it, old PDB files used to have just uppercase chain IDs and in many old scripts we just got used to use lowercase. When some Upper+Lowercase PDB files started, set chainCaseSensitive appeared so the user could cater for those and still the legacy default was kept. > (1) If files loaded have no lower-case chain labels and all are > single-character, match them as always, based on the setting of > chainCaseSensitive; default for which is FALSE: OK > The idea is that the original idea of chainCaseSensitive was to allow > ":a" to match "A" in a PDB file, not so much to allow ":A" to match > "a" in the PDB file. > > Correct? Yes > (2) If any one of the current files loaded has lower-case chain > characters or multi-character chains, then it seems to me Jmol should > disregard the setting of chainCaseSensitive and just consider its > value to be TRUE. OK Or maybe instead of ignoring the setting, force change it to true? That way if can be verified "show chainCaseSensitive" Thank you! -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] cartoon for Calpha-only is broken
9 Sep 2014, 2:58, Robert Hanson wrote: > In addition to that, the chain read from then HELIX record was not > stored the same way, so helixes and sheets were not read for any > chain that was outside the range "A" - "Z". Partly solved, but with another glitch now present: > in 14.3.7_2014.09.08b > load =1LMB > cartoon only // ok for dna, not for protein in 14.3.7_2014.09.14 load =1LMB cartoon only // ok for protein, nothing is displayed for DNA -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] cartoon for Calpha-only is broken
sorry, that's not Calpha-only But the problem is present --now I don't know the reason -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce. Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] cartoon for Calpha-only is broken
in 14.3.7_2014.09.08b cartoon is broken for Calpha-only files It used to render cartoons, now it just renders trace load =1LMB cartoon only // ok for dna, not for protein -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce. Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] chainCaseSensitive is forced true in 14.3.7
There is also a problem with numeric chain IDs: load =1LMB; select *:1; //selects chains 1 and 2 select *:2; // same atoms select *:3; //selects chains 3 and 4 select *:4; // same atoms I notice that hover display quotes around the ID, like [DG]37:"2".O3' so I tried select *:"1" without change -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce. Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] chainCaseSensitive is forced true in 14.3.7
in 14.3.7_2014.09.08b "chainCaseSensitive" is being ignored and acts as true That is, load =1crn select *:a //0 atoms selected select *:A // 327 atoms selected irrespective of the setting of chainCaseSensitive -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce. Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Jmol.resizeApplet
Bob, are both syntaxes supported? Jmol.resizeApplet(appletid, w, h) Jmol.resizeApplet(appletid, [w,h]) I only had the 2nd documented http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Functions#resizeApple t -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] still problmes with MOVETO after MOVE
Dear Bob, After the last update of Jmol, 29th July, I am still having trouble when my page runs a script with "move" command and later a "moveto" or "zoomto". I've prepared a simplified test-demo page at http://biomodel.uah.es/en/model4/dna/_test_.htm That's using an older version of Jmol, but the same problem is still here with 14.3.3_2014.07.29 (tested locally, as I cannot update in the server rigth now) After clicking the "spin" button, the next action on the "end" or "zoom" buttons does nothing. A second button push does work. -- Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] Script error: missing ] after element list
Dear Bob, I am getting this error when running a page in Firefox 30 from local disk (file:// protocol), in an alert box wehn loading the page: [Java2Script] Script error: missing ] after element list ../../JSmol/j2s/core/corescript.z.js [Exception... "Access to restricted URI denied" code: "1012" nsresult: "0x805303f4 (NS_ERROR_DOM_BAD_URI)" location: ""] Then models do not load from a script atteched to a button in the page. That's Jmol 14.3.3 downloaded yesterday from StOlaf (it reports being 14.2.3) The page runs fine from server. It was also running wthout warnings before, using either 14.2.2 or 14.1.10 I think I really cannot isolate the details, but I thought to report in case it ticks something that you can fix. -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Jmol to Jsmol - issues
Hello Priya Nothing has changed? That's surprising I've visited your page and in the source code I can see nothing related to J(S)mol Can you please give a better pointer? -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] reg: certificate for java applets - for JMol
Hello Krithika First, the correct email address you should use is the distribution list for developers, jmol-developers@lists.sourceforge.net Second, the Jmol applet at the Jmol website is obsolete. Please read more updated documentation in the Jmol Wiki, particularly http://wiki.jmol.org/index.php/Jmol_JavaScript_Object Jmol is, since version 14, properly signed by "Integrated Graphics". That is the version included in the Jmol distribution. 15 Jul 2014, 11:09, Krithika Bhuvaneshwar [kb472@georgetown.edreg: certificate for java applets - for JMol wrote: > > Hello, > > We use the Jmol Jar files. Ever since Java SE7 was introduced in > early 2014 requiring all Java Applets to be signed with a trusted > certificate, we have been experiencing issues with the Java Applets. > > Can you please provide updated jar files with a valid signed > certificate for the java applet? > > If I do a browser check from your web site, this is what I get: > width='200' height='200' > type='application/x-java-applet' > > > > > > > > > > > > > > > > You do not have Java applets enabled in your web browser, or your > browser is blocking this applet. > Check the warning message from your browser and/or enable Java > applets in > your web browser preferences, or install the Java Runtime Environment > from www.java.com /> > > PS:We do have the proper license for Jmol shown here: > https://gdoc.georgetown.edu/content/documents/gnuLGPL2_1.pdf > > Thanks > Krithika > -- > > Ms. Krithika Bhuvaneshwar > Bioinformatician/Data Manager > Innovation Center for Biomedical Informatics (ICBI) > Georgetown University Medical Center, Washington, DC > Email: kb...@georgetown.edu ; krithika...@gmail.com > Phone: 202-687-6850 ; Fax: 202-687-5011 > http://icbi.georgetown.edu/ > -- > - > · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] "move" breaks any further movement
FYI,
this was broken between 14.1.10 and 14.1.11
> In 14.1.16 and 14.2.2, issuing a "move" command works, but any
> further "moveto" or "zoom" does nothing
load $caffeine;
moveto 1.0 { 916 -393 -75 38.89} 65.75 0.0 0.0 {-0.45 0.19 -0.065} 5.5 {0 0 0}
0 0 0 3 0 0;
move 90 0 0 0 0 0 0 0 5 30; // 90 degrees around X
moveto 1.0 { 916 -393 -75 38.89} 65.75 0.0 0.0 {-0.45 0.19 -0.065} 5.5 {0 0 0}
0 0 0 3 0 0;
zoomto 1 *0.5;
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[Jmol-developers] "move" breaks any further movement
Dear Bob,
In 14.1.16 and 14.2.2, issuing a "move" command works, but any
further "moveto" or "zoom" does nothing
load $caffeine;
moveto 1.0 { 916 -393 -75 38.89} 65.75 0.0 0.0 {-0.45 0.19 -0.065}
5.5 {0 0 0} 0 0 0 3 0 0;
move 90 0 0 0 0 0 0 0 5 30; // 90 degrees around X
moveto 1.0 { 916 -393 -75 38.89} 65.75 0.0 0.0 {-0.45 0.19 -0.065}
5.5 {0 0 0} 0 0 0 3 0 0;
zoomto 1 *0.5;
I know "move" is rather obsolete, but I have not found an equivalent
for a timed rotation. We use it a lot in the DNA Tutorial.
I've tried
rotate X 90 -5;
but that seems to run in a separate thread and so the subsequent
script does not wait for the rotation to finish.
And move was working until recently
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Re: [Jmol-developers] language localization fails
> And > http://127.0.0.1/biomodel/JSmol/idioma/ > definitely exists? Oh yes > I'm not sure where the vertical bar in the file:/// path is coming > from, do you? I think it's (at least) a Firefox thing, it's taking the place of the colon after the drive letter. On the other hand, there seems to be some interference between application of language and loading a custom popup menu definition. I found that somehow my custom menu was incompatible with the new J(S)mol version. After I edited the menu, the language seems to be loading fine. But still I'm puzzled as to why the "set language" from the console was failing. Don't put too much time into it. But still the Jmol application is not loading initially in Spanish, even though Spanish is ticked in the language submenu. Thanks -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] language localization fails
> > JV.Viewer.appletCodeBase http://127.0.0.1/biomodel/model3j/../JSmol/j2s/ file:///F|/webs/biomodel/model3j/../JSmol/j2s/ > JV.Viewer.appletIdiomaBase http://127.0.0.1/biomodel/model3j/../JSmol/idioma file:///F|/webs/biomodel/model3j/../JSmol/idioma i.e. both have the relative path broken · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] internal version number in JSmol is not updated to Jmol version number
Bob, some internal string needs to be fixed. I am seeing different version numbers in the pop-up menu depending on where I look: About > Jmol > gives the correct version, 14.2.2 2014.06.29 About > System > gives a wrong JSmol version, 14.1.14 Apr 27, 2014 -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] language localization fails
Dear Bob,
The Jmol JSconsole has provided some hints as why the language is not
loading:
Loading language resource
file:///F|/webs/biomodel/model3j/../JSmol/idioma/es.po
FileManager opening 3
file:/F|/webs/biomodel/model3j/../JSmol/idioma/es.po
FileManager opening 1 file:/F
0 translations loaded
Jmol getValue doTranslate null
language=es
So the relative path is being set wrong:
file:///F|/webs/biomodel/model3j/../JSmol/idioma/es.po
should be
file:///F|/webs/biomodel/JSmol/idioma/es.po
When I run it from local web server, it loads in Spanish but the path
problem is still there:
Loading language resource
http://127.0.0.1/biomodel/model3j/../JSmol/idioma/es.po
FileManager opening 1
http://127.0.0.1/biomodel/model3j/../JSmol/idioma/es.po
562 translations loaded
Jmol getValue doTranslate null
language=es
This is an excerpt of my page code:
var JmolPath="../JSmol";
var myInfo = {
serverURL: JmolPath + '/php/jsmol.php',
j2sPath: JmolPath + '/j2s',
jarPath: JmolPath + '/java',
jarFile: "JmolApplet0.jar",
isSigned: false,
use: 'html5',
debug: false
};
This used to work with 14.0.17
I'm rather confused. Any hints?
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Re: [Jmol-developers] problems with custom popup and with language
You are right, I see now that both auto-language and lang-switch are both working fine at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.14.2/jsmol.htm Sorry. So I need to isolate the problem in my page, and will come back if needed. Thanks -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] language localization fails
I agree it's quite tricky. I will have to setup a test page maybe On 1 Jul 2014 at 14:23, Robert Hanson wrote: > > How can we test this? > -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] problems with custom popup and with language
When I enter load menu mine.mnu in the console, I get this output: Available callbacks include: animframeCallback appletreadyCallback atommovedCallback clickCallback dragdropCallback echoCallback errorCallback evalCallback hoverCallback loadstructCallback measureCallback messageCallback minimizationCallback pickCallback resizeCallback scriptCallback syncCallback structuremodifiedCallback So maybe something in my menu? But I tried loading the standard menu (produced using "show menu") and it gives the same output -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] problems with custom popup and with language
Precedents, for reference:
29 Jan 2014, 11:55, Bob Hanson wrote:
> ___JmolVersion="14.1.8_dev_2014.01.29"
> bug fix: show MENU write MENU load MENU all broken in 12.2
>
> [feature-requests:#213] custom pop-up menus
> Status: open
> Created: Tue Jan 28, 2014 11:08 AM UTC by Angel Herraez
> Last Updated: Tue Jan 28, 2014 11:08 AM UTC
> Owner: nobody
> It seems that the customized pop-up menus feature has been lost in
> J(S)mol 14.
> It would be nice to have it back
> http://wiki.jmol.org/index.php/Custom_Menus
30 Jan 2014, 21:33, Robert Hanson wrote:
> Ah, OK. "callback" is just another name for "parameter" and now all
> the parameters are in Info. So try:
>
> Info = {
> ...
> menuFile: "myfile.mnu",
>
> }
>
> and see if that works. Looks in the code like it will.
>
> Bob
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[Jmol-developers] problems with custom popup and with language
Jmol 14.2.2_2014.06.29 both in HTML5 and Java modes 1. The pop-up opens in English, not Spanish (I already reported this earlier today) 2. My page applies a language command that is being ignored (in fact, it is somehow applied since the language submenu has Spanish ticked, but the interface is in English) 3. My page tries to load a custom popup menu. It does not load, either using Info.script = 'load menu "mine.mnu"' or Info.menuFile: "mine.mnu" So I tried the corresponding commands at the console: 4. set language "es" // reports language = "es" // but fails to update the popup menu 5. load menu "mine.mnu" // fails to load the menu -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] language localization fails
Hi Bob 14.2.2_2014.06.29 application, the interface opens in English instead of Spanish. The pop-up language shows Spanish ticked, when I click on that the interface changes to Spanish. So the switch works, it's just the initial display where the language is not applied correctly. I haven't tested inside a webpage of my own yet. http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm, using 14.1.16, opens OK in Spanish in HTML5 mode -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] write("coord") gives original, not transformed, coordinates
Dear Bob,
Some time ago we addressed the issue of writing transformed
coordinates in MOL format, either using write command or write()
function.
I think it was fixed in some 14.1.x version, but right now I am
finding that
zz = write("coord")
zz = write("coord", "t.mol")
are delivering the original coordinates and not the transformed
coordinates.
The command,
write coord "t.mol"
does save a file with the correct transformed coordinates.
I've tested this on 14.2.0, 14.0.17, 14.1.16
Has the bug reappeared?
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Re: [Jmol-developers] is source code missing at SF ?
Thank you, Jaime In fact, my usual target is http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/ but since I got nothing, I climbed up the tree :) -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] is source code missing at SF ?
There is nothing at http://sourceforge.net/p/jmol/code/ I used to go there for seeing the code. What has changed? -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] bug in the script for ligand pockets in PDB
> yes, OK, but that's not a general solution. I suppose that happens in Java > and JavaScript? Not sure, but I will try to check today. It is happening in the PDB site, I think it was Java Jmol. I guess I can use the ?_USE=HTML5 there for testing. Why is it not general? Just avoid uppercase in scripts. -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] bug in the script for ligand pockets in PDB
Bob, I think you are not getting my point.
I think this happens because there is an upercase "ID" text in the source
code of that "gotoligand" function.
For some reason, Jmol goes later to convert that to lowercase.
But if the "gotoligand" function had just lowercase "id", then I believe no
harm
would happen.
That is,
http://www.rcsb.org/pdb/Viewers/jmol-14.1.1//jsmol/spt/ext/rcsb/gotoLigand.s
pt
has these:
// contact surface
contact ID "surf" {ligandAtoms} surface
contact slab 60 fullylit
// hydrogen bonds
contact ID "hb" {ligandAtoms} hbond
select within(3.3,ligandAtoms)
Those two 'contact ID ' should be changed to 'contact id ' and see if the
problem goes away.
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Re: [Jmol-developers] bug in the script for ligand pockets in PDB
Yes, I had read about such a problem. The issue is, however, that it is not a user-given ID with Turkish characters, but the "ID" token in the source code. -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] bug in the script for ligand pockets in PDB
Dear Bob,
You're going to love this bug report. It's thrilling!
I was today demonstrating the new PDB "ligand pocket" view that uses the
"contact" command. Guess what... it breaks in Turkish computers, nothing is
displayed but the standard protein rendering.
I think I have tracked down the issue. This is the error in the console history:
line 23 command 20 of function gotoligand:
contact id >> "surf" << { ligandatoms } surface
gotoligand ( "" , "IBP" )
Note that Turkish "i" without the dot. I guess the uppercase ID (that you
usually use) is being somewhere converted to lowercase, and in Turkish that
means without the dot on the i, and Jmol chokes.
That happens while working directly on the PDB site (Jmol Java), at least
with Chrome and Firefox, and does not happen on my Spanish laptop in the
same room and network. This means all Turkish users are deprived of the
nice display of ligands within the contact-colored surface.
For clarification, Turkish is unique in having 2 kinds of "i" in both upper and
lowercase and the matching makes it different:
i --> I
i --> I
while in any other language:
i --> I
(I hope the Unicode characters don't get lost in the email)
Probably changing the original code into lowercase "id" will avoid the issue.
We can test up to next Friday.
Cheers,
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Re: [Jmol-developers] What is the second Canvas2d for that shows up below the active one when using JSmol?
Hi Removing the assignment of Info.coverImage makes the problem go. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] What is the second Canvas2d for that shows up below the active one when using JSmol?
I'm having a similar problem as Jonathan's. Two canvas2d objects are
created.
I believe there is something wrong with Jmol.getAppletHtml()
The problem does not happen when I use Jmol.getApplet() directly in the div.
Note: I am using jquery-1.10.2.min.js plus JSmol.min.nojq.js
Symptoms:
- The page is taller (scroolbar) than its intended contents.
- A square area below the actual JSmol square is sensitive to right-click
opening of the popup menu and also to zoom by mouse wheel.
- Firefox Inspector gives this source code:
This is my code in the page:
/* viewerMolec is a global object-variable defined before, that holds many
parameters for the page.
*/
viewerMolec.infoJmol = {
color: '#'+viewerCfg.bkg,
height: '100%',
width: '100%',
j2sPath: viewerMolec.pathJmol + 'j2s',
jarPath: viewerMolec.pathJmol + 'java',
jarFile: 'JmolAppletSigned0.jar',
isSigned: true,
serverURL: viewerMolec.pathJmol + 'php/jsmol.php',
loadstructcallback: 'viewer_OnModelLoad',
pickcallback: 'viewer_OnAtomOrBondPicked',
measureCallback: 'viewer_OnMeasures',
script: 'set frank off; /*etc*/ ',
zIndexBase: 15,
z: 15,
deferUncover:true,
coverImage:'cover.png',
use: 'html5'
};
$(document).ready( function() {
$('#viewerViewer').html(Jmol.getAppletHtml('JmolOb',viewerMolec.infoJmol))
;
});
#viewer { width:800px; height:400px; position:relative; }
#viewerTools { width:49%; height:100%; position:absolute; left:0; top:0;
overflow:hidden; }
#viewerViewer { width:50%; height:100%; position:absolute; left:50%; top:0; }
// etc.
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Re: [Jmol-developers] Jmol web site
Not a bit of work, I'm afraid, but quite a lot. There is a lot of information there that is obsolete. I have done --long time ago-- updates to the website files and I committed then, but then Nico had to do the "building" or whatever is the name to get the actual website updated. I may have time to do this but not too soon. -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] documentation
Bob, the text for set cartoonLadders OFF is duplicated from set cartoonRockets OFF and makes no sense, of course :) -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] cameraDepth seems broken
Am I getting paranoid, or is "set cameraDepth" again not working? in 14.1.12_2014.03.22, both Java applet and JSmol JmolVersion="14.1.12_2014.03.13" bug fix: set cameraDepth disabled -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] loading binary files in Chrome from local host
Well, even if unexpected it is welcome ;-) > and see what's going on. The message is expected; successful local file > loading is not. I do not consider "localhost" or "http://127.0.0.1"; to be LOCAL -- it should be the same as SERVER. So, the alert should not be displayed and then the file loads successfully as expected from a server with php support. Thanks -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] loading binary files in Chrome from local host
Dear Bob, You have implemented an alert that says "JSmolCore.js: synchronous binary file transfer is requested but not available" when trying to load a binary file. In Chrome, I get this alert when trying to load a pdb.gz file from disk -- correct. but I also get it when I load the page and file from 127.0.0.1 (localhost) and the file does load successfully! I have two shortcuts to Chrome and one explicitly adds the --allow-file-access-from-files parameter to the command line (maybe the other has it too by default but not in my shortcut properties). Both are loading the file. I guess this is difficult to track, just want you to know. -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] bug in translucent background for echo
Translucent background for echos seems broken now: Jmol Application, 13.0.10 #works fine, yellow text on translucent background load =1crn; set echo coment4 50% 50%; echo "example"; color echo yellow; background echo gray translucent 0.4; Jmol Application, 14.0.10 #wrong Background is opaque yellow, while text is translucent gray? -barely visible -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] cameraDepth seems broken
Hi I cannot make set cameraDepth to work in 14.0.11 or 14.1.8 It does have an effect in Jmol 12.0.5, 13.0.10 (Jmol application) load $cubane set cameraDepth 10 set cameraDepth 2 set cameraDepth 0.2 set cameraDepth 0.02 set cameraDepth 0.002 -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] meaning of struts mp.added ?
org\jmol\scriptext\CmdExt.java
May I ask the meaning or context of this phrase?
{0} struts mp.added
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[Jmol-developers] GuiMao phrases that are split in 2 lines pose a translation question
Any reason for these phrases split between two variables?
I am not sure how should I split them when translating.
org\openscience\jmol\app\jmolpanel\GuiMap.java
"GT_script_button_template.html_LOADING",GT.escapeHTML(GT._("Once
the molecule file is fully loaded the image at right will become live. At that
time the \"activate 3-D\" icon")),
"GT_script_button_template.html_DISAPPEAR",GT.escapeHTML(GT._("will
disappear.")),
"GT_script_button_template.html_JAVACAPABLE",GT.escapeHTML(GT._("I
f your browser/OS combination is Java capable you will get snappier
performance if you")),
"GT_script_button_template.html_USEJAVA",GT.escapeHTML(GT._("use
Java.")),
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Re: [Jmol-developers] [Jmol-users] last chance before Jmol 14.1.11; JJSME/JSpecView
I usually commit the Spanish updates directly into SVN, so we can test this first without worrying about merging the Launchpad files. Once it works, that's a second part to address. For example, the Capture menu entries have already Spanish translations which I added a few days ago. Now I see them in the po file at SVN, so I guess all is going well. I can also see (untranslated yet) entries for "Export", "Open local file" etc. I will submit the pending translations this evening -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
