Re: [Jmol-users] problem to take into account changes to a file.xyz in the Jmol applet
Hello Benjamin Your problem is probaly related to the "Java cache" in the browser. This a browser-specific problem, per user. You can fix it by manually clearing the Java cache before each reload. There are instructions in the Jmol Wiki, Running Jmol, Troubleshooting: http://wiki.jmol.org:81/index.php/Troubleshooting/Java_Problems#Java_c ache I don't think there is any other solution, or an automatic one. Maybe you can disable the Java cache. The only other fix is to use a different filename each time. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] setting hover text only for selected atoms
Thanks, Bob
> well, you can do whatever you want with the callback, right? If you
> want to know if an atom is in a certain set, I think you could use:
>
> if ({whateverSet} and {atomno=_atomHovered})
Yes, I am already following that line -and have a working test-.
It is atomindex, not atomno, isn't it?
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Re: [Jmol-users] user defined covalent radius
It can be done with the frame callback method, but it seems we don't need to go that way. Based on my quick test, the connect command works for all frames in one go without trouble, and the redefined bonds are kept across the animation. So, you may just need to disable autobonding and then apply a single connect command, then play the animation. If you provide an example file and radii, I can demonstrate it. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] user defined covalent radius
Karol, I think what Bob suggested is 1. there is no implementation of custom covalent radii 2. you can use the "connect" command to substitute for that: have Jmol calculate and render bonds base on your radii 3. you must do that for each and every frame in your animation/dynamics The callback is a mechanism by which Jmol send a signal when something happens (in this case, a frame change during animation) and a javascript routine can be invoked (in this case, calling the recalculation of bonds) I'll try to write a prototype and let you know (Bob is currently at a meeting and so probably not following too closely this list) Are you working with the application, or the applet? -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Biomolecule filter broken?
I see (11.5.50, 11.7.28) that the "biopolymers" entry in the pop-up menu is greyed out. May that be a hint? -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: Jmol Assistance
Following my previous post, here are some other ways to do it:
If you want to keep the command in a single place, you can either use
a javascript variable or a function as you were trying to do (even
though I said before it could not be done):
var rotateModel = "rotate {atomno=20} {atomno=30} 90"
jmolInitialize(".")
jmolHtml("RadioGroup Sample: ");
jmolRadioGroup([
[rotateModel, "Rotate"]
]);
jmolBr();
jmolHtml("Menu Sample: ");
jmolMenu([
[rotateModel, "Rotate"]
]);
jmolBr();
jmolHtml("Button Sample: ");
jmolButton(rotateModel,"RotateButton");
or
function rotateModel()
{
return "rotate {atomno=1} {atomno=2} 90"
}
jmolInitialize(".")
jmolHtml("RadioGroup Sample: ");
jmolRadioGroup([
[rotateModel(), "Rotate"]
]);
jmolBr();
jmolHtml("Menu Sample: ");
jmolMenu([
[rotateModel(), "Rotate"]
]);
jmolBr();
jmolHtml("Button Sample: ");
jmolButton(rotateModel(),"RotateButton");
You can also generalize it to:
function rotateModel(x)
{
return "rotate {atomno=1} {atomno=2} " + x
}
and then call it like
rotateModel(90)
rotateModel(45)
etc.
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Re: [Jmol-users] Fwd: Jmol Assistance
Hello Aya
You seem to have several different issues. Let's try to sort out
things with your problem.
Your "function rotateModel" should be a Javascript function. First,
you need the proper javascript syntax (you are lacking the braces and
you should not use "end"). Second, the call to Jmol.js is separate
from any other script; the way you have it, it is just being ignored.
Third, you cannot call the Jmol script directly but must pass it
trough jmolScript():
function rotateModel()
{
jmolScript('rotate {atomno=1} {atomno=2} 90;')
}
Then, you can call that javascript function, but not inside
jmolRadioGroup or JmolButton:
So, that's not the best way to do it. Let's try something different:
jmolInitialize(".")
jmolHtml("RadioGroup Sample: ");
jmolRadioGroup([
["rotate {atomno=1} {atomno=2} 90", "Rotate"]
]);
jmolBr();
jmolHtml("Menu Sample: ");
jmolMenu([
["rotate {atomno=1} {atomno=2} 90", "Rotate"]
]);
jmolBr();
jmolHtml("Button Sample: ");
jmolButton("rotate {atomno=1} {atomno=2} 90","RotateButton");
jmolApplet(290,"load models/practice.pdb;select all;spacefill
25%;wireframe .15;color cpk;zoom 120",0)
Note I have added a call to jmolInitialize(). This is not completely
complusaory, but it is highly recommended (unless you know well what
you are doing).
> I am working on something of a webpage project, where I must utilize
> a java applet, Jmol, in an html page. I don't know if this is a lack
> of knowledge in html, java, or jmol (most likely all three) that is
> hindering me from being productive, but I am having a hard time
> finding where to place the java functions and the code that
> references them relative to the html formatting. Any suggestions?
1. You don't need to know any Java language.
2. There are no Java functions involved. It's Javascript, no Java.
Most is done with Javascript thaks to the Jmol.js library that
interfaces with Jmol.
> No matter where I put my function, if I try calling it in the same
> script When I put the functions in the same
Your function was malformed.
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Re: [Jmol-users] How to pan the view?
> I often wondered > why there isn't another way to do it---a different command key or > command key combination. There's also Ctrl + right-drag (if you have a mouse with more than one button) -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Use of Java in teaching?
> "a) Java allows malicious activity that could damage the system" "Letting users use the computer allows malicious activity that could damage the system" ;-) And, does this mean that Flash is foolproof? > "b) Java is an outmoded way to provide educational resources as everyone > is using Flash now" Outmoded? A software that's being updated every month or so... I would'n dare to say that. And the key is: can Flash do what the Java applets do? I don't mean only Jmol. Everyone? Everyone is using Flash now to substitute html on their pages. Does that mean that html is outmoded? Open source vs. proprietary, of course Whoever is deciding the (no) installation is rather short-sighted. One has to consider the functionality, not make generalizations based on ... what evidence? -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] SelectionListener
Alex, it is possible to do that from the javascript side with the applet, using pickCallback, as well as from the JmolScript language: http://jmol.sourceforge.net/jslibrary/#jmolSetCallback http://chemapps.stolaf.edu/jmol/docs/#setcallback so I bet that there is a way inside the code to have it done at an inner level (but cannot help you out there) -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] selecting list of atoms
Hi Dan
I'm afraid there is not much that can be done:
1. you can put commas instead of "or"
select atomno=3,atomno=5,atomno=18,atomno=26
2. if the file is MOL format (not sure about others like XYZ,
certainly not in PDB), you can use a combination of element symbol +
atom number, like
select C3,O5,C18,C26
3. there is a chance that there is a Jmol math syntax to do that in
some way like {3,5,18,26} but I cannot help with that, if even
possible. Bob can tell you.
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Re: [Jmol-users] Chime to Jmol translation
Hello Inbal Time ago, someone wrote a script for doing that (maye in Perl, not sure now) but I'm not sure if it is still available and how trustable it may result, particularly for recent Jmol versions; in any case, I'd rather do it manually. The tasks are: 1. substitute embed tags by applet calls 2. check that scripts are working Things change a little depending on whether scripts are in separate files or in the page source, but it doesn't really make a difference in functional terms. Most commands are fully portable from RasMol/Chime to Jmol, but there are a few that break scripts ad those must be located by eye. I can give some help if you hit some stones in the process, just ask --or if you are in the situation, I will also be happy to do it in exchange for money or a publication ;-) http://sourceforge.net/services/project_services.php?project_id=23629 -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Multiple viewports in JMol?
Hello Umanga If you mean seeing the 5 models side by side at the same time, no. You'll need 5 applets. You can load the 5 files into a single applet and show them one by one using the "load files" or the "load append" command. Or show them superimposed at the same time, but they will overlap. -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Custom menus in Jmol
Yes, Dan, it is implemented. I put it into practice recently and found a bug which has been fixed. Read it all in the Wiki, including 2 examples. http://wiki.jmol.org:81/index.php/Custom_Menus -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac OS X
> Can you say to me where I can downloaded Jmol? http://jmol.org and follow the links -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bonds not showing in Jmol 11.6
Hi Ewen That's pdb format, right? I've done a quick test and it's working for me in both 11.4.6 and 11.6.16 Check the column positions of the atom numbers, might be that. Not an explanation for your problem, but you could also dispose of CONECT records and use Jmol "connect" command -- it's cleaner and more flexible (partial bonds for example). And you can embed it in the pdb file if you don't want to run a separate script. http://wiki.jmol.org/index.php/File_formats#Script_inline_within_a_mol ecular_coordinates_file -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] computing volume and surface area of isosurfaces
Hello Yi Not sure it this is enough to solve your problem; I don't think Jmol can do the calculation of surface and volumen but, yes, you can save the isosurface data. >From application and signed applet, you can directly save to disk, using write isosurface >From unsigned applet, you can send the data to the console, then copy- paste from there into a text file: show isosurface For details on the commands, see the doc page http://chemapps.stolaf.edu/jmol/docs/#isosurface Good luck! -- Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and GROMACS?
Egon, this page of mine http://biomodel.uah.es/en/water/p3.htm was built from Gromacs data of a molecular dynamics simulation. Since Jmol did not read the gro file, I converted the data to pdb format (see details at the bottom of the page). We discussed about providing Jmol support for gro files, but I think it was not done -- if I remember correctly, Bob needed good sample files for proteins, which I don't have. See the discussion at http://sourceforge.net/tracker/?func=detail&atid=379136&aid=1876675&gr oup_id=23629 -- Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] good idea?
This is an interesting feature, and rather surprising to me. One never ends to marvel at Jmol wonders. Great work, Bob! And now that I'm sensitive to the topic (having mused around it for my home page in the last few days), this feature would contribute to web accesibility, if the arrow, plus, minus keys could be included (that may be hardly cross-platform maybe): use Jmol without the mouse. An interesting subproject or junior task maybe. Here are my two euro cents (or are they 4?): 1. I do not think that having it active by default is a good idea, at least in blind mode. I'd make it either (a) inactive by default or (b) active by default but with set showKeyStrokes true. I'd rather prefer (a); (b) may be dangerous or confusing to non-aware users. Remember that many users are not expected to know how to use the command language; that's one of the purposes of having an applet, to provide a ready-to-use environment. 2. I agree that a named echo is better than bottom left (e.g. name it "KeyStrokes"). And if put a line above the bottom, there's less chance to obscure an existing echo. A different default color (maybe different font face too, monospaced?) could be helpful. 3. Activating both the feature and the showKeyStrokes should be available from the pop-up menu. If you need to open the console for that, then there is less usefulness in having the commands displayed inside the applet, since you already see them in the console. 4. I agree that if the pop-up menu is blocked, the feature should be blocked too. (For those pages where we really do not want the user to mess around) -- Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with local installation
Hello Norman That's quite unexpected. The Java installation should take care of everything. I have never seen such problem. Some things to try, as non-privileged user: * Can you see Jmol applets in web pages? * Can you open another Java application (another .jar file)? * Is this happening only when you double-click on Jmol.jar, or on a molecule file. If the latter, how have you set-up the file association? * Try opening Jmol from the command line rather than from double- click * Try to reinstall / update Java Let us know the outcome -- Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol in Powerpoint
Hi Arjan It is possible, provided that: - you use Windows - you use a PC where you have installed a certain piece of software - but you really are embedding a webpage that includes a Jmol applet; this has the advantage that you can also include controls like butttons and so on The software is called LiveWeb. Check compatibility with PPT versions (I have only used it with Office2003) It is a complement or plugin installed into PowerPoint, and requests permissions for being run (its an ActiveX). I must say that I don't particularly recommend this solution, unless you like it better and you are using your own PC for the presentation. In most setups, if is easier to just use Jmol app or and applet in a webpage. You'd rather jump to the Jmol window, or to the JmolApplet page, in the middle of your presentation, and back to this after showing the models. Or you put a hyperlink to the page inside the presentation. Another advantage is that you have the Jmol page open in advance, prepared behind the presentation, so you don't have to wait for Java and the applet and model to load when you go to the next slide. This has been discussed a few times in the list. I think it's a good topic for a FAQ in the Wiki. Wil post it there. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] loading multiple unit cells and CIF files
Steve, It sees to me that instead of
"RELOAD {444 666 1}"
what you want may be the next menu entry,
"RELOAD {444 666 1}; display 555;"
Is it so?
And this is what these menu entries do, respectively:
save orientation; load "" {444 666 1} ; restore orientation; center;
and
save orientation; load "" {444 666 1} ; restore orientation;
unitcell on; display cell=555; center visible; zoom 200;
So, for 3x3x3 cells out of 5x5x5, you may try
load "myFile.cif" {333 777 1} ;
unitcell on;
display
cell=444,cell=445,cell=446,cell=454,cell=455,cell=456,cell=464,cell=46
5,cell=466,cell=544,cell=545,cell=546,cell=554,cell=555,cell=556,cell=
564,cell=565,cell=566,cell=644,cell=645,cell=646,cell=654,cell=655,cel
l=656,cell=664,cell=665,cell=666;
center visible; zoom 200;
Or, if the file is already loaded, change the first line for:
save orientation; load "" {333 777 1} ; restore orientation;
etc.
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Re: [Jmol-users] surface calculation and rendering time
Jaime, I was writing a post for the Proteopedia list explaining just this. Here is my advice: I haven't looked at the source code, but this may help: the sensible thing for pre-programmed surfaces in web pages is to have Jmol save them as jvxl files, then make the page load that file - - much faster than calculating it every time. Also, I would add a message inside Jmol itself while the model loads. It is discouraging to have a white empty square. See http://wiki.jmol.org/index.php/Recycling_Corner#Providing_a_.27please_ wait.27_notice_while_the_applet_loads You could also add a warning (using echo) while the surface is calculated or loaded. A typo: "of the hemes by toogling off the spin" should be "toggling", right? -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Advice on display of cyclic DNA: more ...
Henry, I've devised a (very) dirty solution: duplicate residue 1 as nr. 9 The trace or cartoon is very sharp at the connection, so things get better if we shift the residue numbering, such as making 1 -> 6 2 -> 7 3 -> 8 4 -> 1 5 -> 2 6 -> 3 7 -> 4 8 -> 5 9 is a copy of the new residue 1 (former 6); this is in the straightest part of the chain, so the conection looks better. You must reorder the data so that the residues are in order 1..9 in the file. If you still don't like the bent joining, duplicate another residue (new 10 = new 2); you will then see two close stretches of trace: hide the added 9,10 residues using "hide" so that duplicate atoms, bonds and trace are not seen, but the trace trajectory will still be smooth. Dirty, as I said, but good-looking enough ;-) And the hidden state of added residues is something not easy to be changed by users. I will attach a sample in a separate message off-list -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Advice on display of cyclic DNA: more ...
Well, it is not based on residue numbering. A possible way to deal with this ould be to parse the pdb information in LINK records. Henry's file (2HK4.pdb) has them: LINK P C A 1 O3* T A 8 LINK P C B 1 O3* T B 8 They are meant to supplement info in CONECT records, and to be used for: 1. Bonds between HET groups or between a HET group and standard residue, 2. Inter-residue linkages not implied by the primary structure 3. etc. Point 2 looks to me like the current case. Point 1 would also be interesting (not sure now whether Jmol currently links hetgroups and residues in cartoons, will check) This is the PDB spec: ·· The LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. [snip] Record Format COLUMNS DATA TYPE FIELD DEFINITION - 1 - 6 Record name"LINK " 13 - 16 Atom name1 Atom name. 17 Character altLoc1 Alternate location indicator. 18 - 20 Residue name resName1Residue name. 22 Character chainID1Chain identifier. 23 - 26 IntegerresSeq1 Residue sequence number. 27 AChar iCode1 Insertion code. 43 - 46 Atom name2 Atom name. 47 Character altLoc2 Alternate location indicator. 48 - 50 Residue name resName2Residue name. 52 Character chainID2Chain identifier. 53 - 56 IntegerresSeq2 Residue sequence number. 57 AChar iCode2 Insertion code. 60 - 65 SymOP sym1Symmetry operator atom 1. 67 - 72 SymOP sym2Symmetry operator atom 2. 74 - 78 Real(5.2) Length Link distance ·· -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Advice on display of cyclic DNA: more ...
Hi Henry Nice molecule! I had only known cyclic DNA molecules as in "circular" DNA, e.g. procariotic DNA and plasmids. Chemicaly there is not much difference. I don't know the exact code being used fior calculating and rendering cartoons et al., but I guess it is based on phosphorus IDs and residue numbering. Since in your example the missing link is between residues 1 and 8, Jmol is not guessing that (what criterion should it use, distance? probably that will give trouble in more than one molecule because of proximity). This needs some thinking. Just for info, RasMol and Accelrys DS Visualizer don't link the ends either. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How to translate by angstroms
Hi Eran Translation should be possible using "move", if I remember correctly. Not sure about zoom; I think it only works in percent. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Reset the view ?
> Thank you for the tip, but I noticed that "write state" doesn't support > in the Applet version? Yes, as everything that writes to disk, it is not available for the unsigned applet. You can use application or signed applet for that. Or just save to memory in a Jmol user variable to wich the output of show is sent. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Reset the view ?
Hi Umanga When you have the initial view as you want it, use show state and store that script (in an internal variable* or saved to a file, "write state"), then later restore it either calling that script or loading the script file. *) may be using Java, o Javascript, or even a Jmol user variable; it depends on how you setup your app. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] VRML support and file extensions
Today I am playing with VRML export. Models export very nicely (restricted to atoms and bonds, it seems; not a complain, I knew that features were limited). Jmol offers by default the .vrml extension for files. To see the vrml files, I have installed Flux Player (application and browser plug-in), but it only accepts files with .wrl extension. I am not used to vrml, so would like to get some feedback from savvy users about which is the most common extension. Depending on that feedback, maybe the default for Jmol could be changed to wrl? BTW, I have just added info about VRML, Maya and POV-Ray export in the Wiki for future reference. Contributions are welcome. http://wiki.jmol.org/index.php/File_formats -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Using the sync command for 3D/stereographic visualization (on a GeoWall)
A paper that may be worth reading in this respect: * (2008) Adapting a single-user, single-display molecular visualization application for use in a multi-user, multi-display environment. http://www.cliftonforlines.com/papers/2008_forlines_molvis.pdf (now linked from MultiUser_Jmol and Jmol_Literature pages in the Wiki) El 21 Nov 2008 a las 22:15, Dean Johnston escribió: > > Jmol users, > > I've had a request to make my Jmol pages work with a GeoWall-type > setup. (If you're not familiar with GeoWall (www.geowall.org), it's > a low-cost stereo projection system. You setup a computer with a > dual-head video card, two projectors with polarizing filters, and > align the two projectors on the same screen. You can then use a > variety of software (including Jmol) to project two orientations, one > to each projector -- if you're wearing properly polarized glasses you > get a very nice 3D effect.) [snip] -- Check out the new SourceForge.net Marketplace. It is the best place to buy or sell services for just about anything Open Source. http://p.sf.net/sfu/Xq1LFB ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question about moveto
Hi Eran
> moveto timeSeconds {x y z} degrees zoomPercent transX transY {x y z}
> rotationRadius navigationCenter navTransX navTransY navDepth
> Can anyone offer some help as to what "{ 102 -219 -970 176.64}"
I'd say the 176.64 matches the "degrees" parameter. The braces are
ignored, just there for readability, AFAIK
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Re: [Jmol-users] Help
Hi Phan I agree with Duan. It may be a problem with the file path. Open the Java console and copy the exact error, and post it here. For a safest test, put the pdb file and the Jmol.jar file in the same folder, then open the script console and type load yourfile.pdb (do not use the top menu, File > Open, as that may insert the path) If that works, it's most likely a path problem. Java has problems with folder names that contain spaces or non-English characters; it converts those characters to Unicode but then either Jmol or the OS do not interpret them correctly. (At least in my Spanish Windows setup.) -- Check out the new SourceForge.net Marketplace. It is the best place to buy or sell services for just about anything Open Source. http://p.sf.net/sfu/Xq1LFB ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and Google Web Toolkit
El 15 Dec 2008 a las 11:46, Raphael André Bauer escribió: > it seems that your observation is right and using the jmol.js breaks > the GWT. However it is easily possible to use jmol without jmol.js and > thus avoiding this problem. An idea is to use the Firebug plugin for > Firefox that gives you the "real" html generated by jmol.js. A simple > copy and paste into the GWT application solves that issue and GWT and > Jmol work nicely together... It will likely work without any trouble, but note that Jmol.js renders different code depending on the browser (at least for insertion of the applet). So it's not that simple. That's one of the reasons why using Jmol.js is the recommended method. The best would be to find the exact confilct between GWT code and Jmol.js code. -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and Google Web Toolkit
El 15 Dec 2008 a las 11:46, Raphael André Bauer escribió: > it seems that your observation is right and using the jmol.js breaks > the GWT. However it is easily possible to use jmol without jmol.js and > thus avoiding this problem. An idea is to use the Firebug plugin for > Firefox that gives you the "real" html generated by jmol.js. A simple > copy and paste into the GWT application solves that issue and GWT and > Jmol work nicely together... It will likely work without any trouble, but note that Jmol.js renders different code depending on the browser (at least for insertion of the applet). So it's not that simple. That's one of the reasons why using Jmol.js is the recommended method. The best would be to find the exact confilct between GWT code and Jmol.js code. -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] one Label for a group of residues
Hi Umanga
Yes, that's the behaviour.
If you want a single label you must select a single atom -- or a
single coordinate, maybe at the center of the atom set. But that is
not done with "label", because labels are objects attached to atoms.
So you may either:
a) choose one of the atoms (manually chosen), select it and label it
b) use "echo", which can be located at any coordinate:
select :a and (resno>10 and resno<50);
set echo myLabel {selected};
label "Selection";
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Re: [Jmol-users] Jmol mediawiki extension
El 10 Dec 2008 a las 18:34, Robert Hanson escribió: > Something's not right. > > mayscript = false in no way prevents jmolButton from being created, > and with mayscript=false, the jmolButton still works fine. > > Something else is going on there. I though it weird, but that is tested on an independent page I made for the purpose (no wiki), and that's what I see in several browsers. And no javascript error raised. BTW, I think we are not making mayscript = false, we are removing the mayscript tag and adding a maynotscript tag (haven't actually checked this). So, the browser will behave as if no mayscript tag is defined. Under this condition, the page I mentioned says that Firefox 2 will do Javascript to Java and not Java to Javascript, while other browsers will do both. But in Ff3 I see that both work. My Ff2 (portable version) works as they say. -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
> All -- I'm pretty sure that if you invoke _jmol.noEval = true in your
> wiki code, you will completely shut down any JavaScript functionality
> of Jmol except callbacks. This setting cannot be changed within Jmol
> -- it is checked upon applet creation and cannot be changed within the
> applet. So it does not matter what you do after that. The
> functionalities that employ JavaScript in Jmol include:
>
> script "javascript:"
> javascript ".."
> x = javascript(".")
> isosurface FUNCTIONXY
> callback methods
Right, it seems to be working although I haven't tested all those
possibilites yet.
> But, really, it's simpler than that if you want to disallow all
> callbacks and every last bit of JavaScript capability of the applet --
>
> just don't have "mayscript" in the applet tag.
Oh, great! Will that be obeyed by all browsers? I think to recall
reading that support of the "mayscript" parameters is uneven across
browsers.
I will test that too.
Thanks, Bob. We are taking big setps towards safe integration in
wikis.
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Re: [Jmol-users] Select relative residue numbers in a chain
Hello Umanga Jmol will always use the residue numbers that are written in the pdb file (not the order in the chain or in the file). So, your problem seems to be in the exact data you have in your pdb file. That said, there may be a way for Jmol to find out the length of chain A and add it to the actual residue nr. in B. But I would say that is a non trustable solution for other models (even for this, see below). More things: 1. There is some error in the numbering of your first example: it cannot go from 98 to 97. a look at 1uj3.pdb gives this: chain A goes from residues 1 to 214 chain B goes from residues 301 to 517 So your offset of 215 is not valid either. 2. Your commands are OK, but you can use simpler notation for residue numbers: select :a and (resno > 97 and resno < 106); color red is the same as select :a and 98-105; color red or even select 98-105:a; color red -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
El 9 Dec 2008 a las 14:03, Nicolas Vervelle escribió: > For example, I think you can stillrun Javascriptwithscripts > calling other scripts: > * Create a wiki page with contents corresponding to a Jmol script with > Javascript in it. > * Add a tag in a page with a script calling the other script Aha, that's the sort of idea I wanted to hear (but had not imagined). Then maybe we should block the use of the "script" command too. After all, we shouldn't need too much Jmol scripting flexibility inside a Wiki; just basic display options that can be pasted in the page, not in independent files. I will test it this evening. -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
I'd like to keep this discussion going, so here is a little bit more, picking up on the possibilities to have Jmol supported in Wikipedia and other Wikis: On 30 Nov 2008 22:53, Nicolas Vervelle wrote: > > On the matter of security issues, there are at least 2 things to do : > * Being able to entirely deactivate the possibility to let arbitrary > Javascript being called by Jmol. I don't know if there's a way in > Jmol to disable this. There's a need to completely disable the > 'javascript' command in Jmol scripts. The problem is demonstrated by > http://wiki.jmol.org:81/index.php/User:Ilmari_Karonen/JS_injection_dem > o Do we still need this? (see below) > * Ensuring that the extension doesn't allow for true Javascript > injection (whatever text is entered by someone in the tags, > this only creates Jmol applet and Jmol scripts, nothing else). I > think this means ensuring that in the generated page, the text is > always correctly escaped to prevent Javascript injection. This is implemented in the last update. > The second problem nees to be treated in the extension. My knowledge > on PHP and the security issues is limited (and I don't have much time > avaiable), so some help from someone knowing how to deal with the > script injection would be very useful. The way I've implemented it, any script passed to the Extension (inside the extension's
Re: [Jmol-users] Out of Memory Error Handling
I understood that there was a mechanism (setting) to prevent error messages from being translated. From the recent discussion, I am not clear as whether that is not working as I thought it would. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol mediawiki extension
Hi Gerard Thanks for the suggestions. Jmol is already fully internationalized and localized, over 10 languages: http://wiki.jmol.org:81/index.php/Internationalisation/Current_Status I'm not sure if the MediaWiki extension would need any further localization. Does the testing environment that you mention need a web Wiki setup, or can it be tested locally? I would be interested on it, but haven't got a Wiki to implement it --nor the time to involvemyself into such a task--. El 1 Dec 2008 a las 11:24, Brian Salter-Duke escribió: > Hi folks, > > Gerard Meijssen <[EMAIL PROTECTED]> has asked me to pass this on > to the Jmol list. I responded to this discussion on the Commons-l list:- > > [Commons-l] Support for Chemical Markup Language - followup > > -- > Hoi, > > If you want to get the JMOL software internationalised and localised, > you may want to consider talking to the Betawiki people. We do the > localisation of MediaWiki and we do the localisation of many of its > extensions. We would be interested in working on JMOL as it is a lively > and relevant software / community. > > I am also involved in a testing envirionment for MediaWiki extensions, > if you are interested in using this environment, let me know.. I take it > that you will convey my message to the JMOL mailing list ? Thanks, > Gerard - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] script to move echo
Brilliant, Frieda! How about putting an animated gif as background image in Jmol? I think we can put images as background, of course I don't know about animated ones. Or try the weird transparency trick that was recently discovered and put the animgif as an image in the webpage behind the transparent applet. (Just a couple crazy ideas). - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmol doesn't work with openjdk in Debian
El 20 Nov 2008 a las 22:09, Ondrej Certik escribió: > Wow, all those applets work perfectly in my browser. So the problem > seems related to some communication between the applet and javascript, > right? Yes, that confirms it. These pages do not use Jmol.js (in fact, they are rather old are were semi-lost, I dug them out from the webpages some time ago, but they are not the recommended method for writing pages. The Jmol.js inserts the applet using a much more cross-browser code.) But then you are quite limited to ways of interacting with the applet from buttons, links etc. Or at least they are harder to code than using Jmol.js. Your former reports clearly pointed to a Java-Javascript communication problem. > I haven't yet tried a different browser. That is VERY important. You need to know if it's the Java VM or the browser implementation. > So I'll report using the jmol demo pages as an example that doesn't > work. But if they say that it is a problem in your applets, I'll get > stuck again. :) No, The applet is the same. It's the javascript interface that varies. Are you saying that the links at the end of "Basic Scripting" work in your system, or just the applets? Hmmm... - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] problem with pop-up in Java 6u10
Dear Jmol users: -- For your information -- I have found a Java bug repainting Jmol's pop-up menu when the latest Java (6u10) is installed. It seems to be related to the display driver/graphics card. I see it in Windows XP with any browser, only in my notebook but not in my desktop PC. It is absent in 6u7. It affects both applet and application (as well as other non-Jmol app & applets like JChemPaint). I've reported it to Sun Java and it is described here: http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6773336 They shall be working on it. If you have a similar problem (the pop-up menu has white patches while you hover the mouse pointer over it), you may want to follow that bug tracking or even to report details about your system. Some screenshots are available at http://www31.websamba.com/jpeg62/javaproblem/ - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmol doesn't work with openjdk in Debian
El 18 Nov 2008 a las 14:29, Ondrej Certik escribió: > do I need to install some files as well? I thought it will work out of the > box. Right. Working with the demo pages is the safest way to assure that your system works. Nothing to set up on your side. > > http://www.javasonics.com/support/check_liveconnect.php > I tried that page, and unfortunately, the java -> javascript > communication is not working for me (I tried all 4 options). That's quite clear: the communication is not working in your system. That will likely explain all your errors. > Does this > mean an error in openjdk in Debian? I'd say so, but... have you tried another browser in the same system? It might be Iceweasel's implementation of the JVM. Is Iceweasel a Mozilla/Gecko based browser? > exactly the problem is? If not, I'll report it again as a bug in the > openjdk package -- but I am really new to these things, so the bug may > be somewhere else. If you reported the problem using http://developer.apple.com/internet/safari/samples/ColorBlockApplet.ht ml and they replied it has not a tag, you should report with a site that has the mayscript tag, as Jmol demo pages do. However, that may be not the simplest example to offer to third parties (since it is inserted by the Jmol.js library, not directly). In addition, don't be confused, if you get the Jmol window with the timer going on for ever, that means Jmol applet has not really finished loading. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] installation
Hi Kris I'm no expert in Linux, but it seems that your system doesn't know how to open jar files. So, you must invoke Java for that file: java -jar Jmol.jar adding the proper paths to java and Jmol.jar, if needed Another option is to try the script file included in the distribution, which for your system should be jmol or jmol.sh that is supposed to have the proper parameters, but you probably have to tweak it a bit Let us know if you find the solution (or not) - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmol problems on IIS windows server 2003
Hi SC You need to give details about the errors you get in the Java console, or the URL for testing, so that some of us can see where is the problem. (If you don't know how to find the Java console, see here http://wiki.jmol.org/index.php/Solving_Java_Problems - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Deleting connections
Maybe that is being affected by the setting (and / or) of set bondMode - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Scripting documentation mirror
El 13 Nov 2008 a las 16:45, Rolf Huehne escribió: > This copy doesn't seem to be fully functional. The version selection > doesn't work and also the examples. Passing parameters to the HTML file > doesn't seem to be allowed. Thanks for checking Rolf. I just viewed the main page and didn't test it. I'm not very surprised that it doesn't work, because it lives in the SVN browse system, so maybe the javascript doesn't get loaded. I should have verified that. So I will remove the link. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Scripting documentation mirror
Thanks for raising this, Rolf To me it sounds as a very interesting suggestion. From here in Spain, the page load time from the StOlaf server is regularly rather long. An alternative server would hence be of help. Of course, I'm not sure of how difficult it may be to maintain an up- to-date copy (automatically?) > In the Wiki there could be created a page where anyone who maintains a > mirror site could register it. ((forget this I don't quite understand what you mean by "register". Uploads of files to the Wiki are difficult (I can't even upload images lately). But Nico can comment on that as he knows the intricacies of the Wiki server. )) Oh, I see now: you mean whoever keeps the mirror site adds a link in the Wiki, right? That's OK Then the main issue is that Bob should remember to pack the pages periodically? - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MEP isosurface coloring
Frieda, I'd say that you can set a custom range for charges, then the color range effectively used will be widened. (I don't remember the syntax right now.) - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Protein Hydrogen Bonds again
David, a very quick response; I'll need some more time to check details: > would like Jmol to be able to display H-bonds between amino acid side > chains and main-chain atoms I agree that this would be very interesting, but it seems hard from the coding side (or we need a volunteer programmer) > Question 1: Jmol will display main- > chain main-chain H-bonds in proteins read from pdb files in which > this information (or implied info as secondary structure) does not > appear to be present. Am I right in thinking that Jmol calculates > these, presumably while it is calculating secondary structure? Bob can tell you more precisely, buit I guess if draws Hbonds based on atom names (O for carbonyl oxygen, H for peptide amino) and some simple criterion of distance and/or angle. Not really a stringent calculation. > Question 2: It was suggested to me that as I have the side-chain H- > bond info in a relational database (from the HBplus program) I could > add this to a pdb file, specifying CONECTS, and Jmol would interpret > this. The records are CONECT yes, Jmol would read those and draw solid covalent bonds, which you don't really want. The way to go is to use Jmol script "connect" which allows to specify them as Hbonds. You should set up a script that is run after pdb loading. > rather than H-bonding. What I want is to be able to turn this on and > off in the same way that I can script the current bonds. Anyone shed > some light on this? On and off can be done, but will need the whole list of atoms involved every time. Well, you can define an atom set and then use a simple distance filter. > Question 3: If the route suggested in 2 is not really an option, what > is the team's attitude to adding code to Jmol. A colleague has just > found some C code a student wrote many years ago that calculates side- > chain H-bonds. The advantage of this is that we have the source and > porting from C to Java would be less difficult than porting from some > other languages (e.g. Fortran). If I proposed it as a 15-week project > for a Masters student in Computing Science or IT, would this seem > feasible and would it be welcomed by the team? I see that as a wonderful option Jmol is highly modular, I'm sure that could be easily integrated. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] struggle with if statement to toggle background color
Hi Paul I'll bet that the variable you need to read is not called "background" 1.- Ask for the state and look for the real name. 2.- Better use "color background xxx", as "background xxx" is deprecated. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Atom color in .mol2 files
El 30 Oct 2008 a las 13:44, FyD escribió: > Why not simply taking the column of the FF atom types available in the > Tripos mol2 file format & display it "as it is" ? I think it's not a question of just "displaying" them, because they must be converted (mapped) to element names, or you'll get the pink color problem. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Atom color in .mol2 files
OK, I've got it Jmol is not using the atom name for element identification; mol2 has an "atom type" field which seems to be both the cause and the cure. http://www.tripos.com/data/support/mol2.pdf In your DMSO file, the atom type for the offending atoms is CT and H1. This is not supported by mol2 spec. See http://www.tripos.com/mol2/atom_types.html http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html If you cahnge that to just C and H, Jmol behaves. You should maybe use the proper types, which seem to be C.3, H, S.o, O.2 They also work in Jmol. > > I guess it is because the name of > > the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23 As I said, not that name, but the type at column 50. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Atom color in .mol2 files
FyD wrote: > At http://q4md-forcefieldtools.org/RED/index-test.php, one can see the > DMSO molecule (Tripos mol2 file format loaded). > > I am surprised by the color of the carbons/hydrogens is pink That's Jmol color for non-identified elements. > I guess it is because the name of > the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23 It's usually an issue with misaligned atom names (at least in pdb format, I'm not used to mol2). Check the mol2 format specification. > Does it mean that only the chemical symbols are recognized as atom names ? > So what about atom names in amino-acids such as CA, CB etc... Absolutely not. CA are read as "carbon, type CA i.e. alpha carbon of proteins". But in PDB, there is a space before the C; if you shift it one character to the left, it would be read as calcium. In addition, pdb has a field specific for the element symbol (close to column 79) which will be used in preference to that dedcue form the atom name. mol2 may have one too. 1. Check your mol2 format and whatever program is generating it. 2. Open the file in another viewer and see how it reads it, or even export it again to mol2 3. Edit the mol2 file and insert/delete a blank column where appropriate - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Label for Atomic charges
FyD wrote: > Quoting Angel Herráez <[EMAIL PROTECTED]>: > > Thanks a lot Angel... > > >> http://q4md-forcefieldtools.org/REDDB/ Today I see the models in this page correctly. Behaviour of the "spin" checkboxes is disconcerting, though. The models keep rotating and changing even with the checkbox off. > Which browser/OS do you use ? Mostly Firefox 3, under WinXP. I have no experience in Linux, sorry. Less in 64 bits. > - With konqueror, or opera/firefox under linux 32-bits, I load the > applet and right click to display the "Java Applet Window". Is that the script console? > windows the position of this Java Applet Window is correct; under > linux it goes on an extreme side (left or right) of the screen. Any > idea why ? That should be OS-specific, or Java-specific. I've read about having two monitors were either the console or the pop-up opens in the other one... > Thanks. Concerning the CML file format, is it possible to add a > description of the FF atom types in this file format ? That would depend on the official specification of the CML format. Jmol can be adapted to read anything the file contains, but it must be defined as an official format spec. Good luck - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem running Jmol
Hello, Max > I tried to run Jmol on Linux/Fedora but just after I type ./jmol I only > get a blank screen with only one icon menu(open a file). > Could anyone help me? Do you get a Jmol window? with black background? Is there a menu at the top? Try running it with java -jar Jmol.jar Give more details of what files you have. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] unloading molecule
Hi Zeyar 1. The "zap" command is what will clear the display. 2. Whenever you load a new molecule, the old one will be removed; no need to zap it. 3. I'm not sure if you can quit Jmol application from a script. I'll try to find out. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] isosurface command
Frieda, how about
{*}.partialcharge = {*}.property_temperature.all
?
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Re: [Jmol-users] AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files
El 9 Oct 2008 a las 18:12, Robert Hanson escribió: > Very slick, Angel! Files loaded for me in about 5 seconds. I forgot > that you could zip up the data files. Of course! In fact, they had been gzipped from the beginning; my friend doing this has some disk space constraints (he's running rather huge molecules and dynamics) and he's got used to gzip always. When he asked we should ungzip them, I said Jmol should cope with it, and it did indeed :-) He's given me permission to use and distribute the files, so if you think it necessary we can add them to the collection of test files, or to your doc/demo pages. > Is there some way to differentiate "a water molecule" from the "water > box" ? In this particular case, that water molecule has a residue name of [CAT], so Jmol doesn`t see it as water which is only [WAT] in the FILTER switch. (I think it's the water molecule involved in the catalytic mechanism, so rather importat among the others, and probably somehow restrained in the MD) BTW, until I tried and then read the doc, I was expecting I could use normal atomic expressions in FILTER, like "not water". Only atom and residue IDs, it seems. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Realistic Probe radii for cavity search?
El 6 Oct 2008 a las 6:46, Robert Hanson escribió: > I recommend leaving the envelope radius at 10. It is used to define > the outer limits of the molecule, thus defining what the openings of > the cavities look like. Feel free to try different settings, though. In my very short experience with cavities, I was finding some "cavities" on the surface of the protein until I cut down the envelope value. I got the feeling that the adequate value will depend on the protein overall size. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 11.6 release -- delayed
My problem with
{selected}.y = 0
has been solved too in RC18
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[Jmol-users] moving draw objects produces duplicates
I am with 11.6.RC18 doing something I've done before, but I am
finding a strange effect.
If it makes any sense, I will investigate further and report details.
1. I draw a small sphere using
draw pru diameter 0.3 {3.6 -1.35 1.4}
2. Then I activate
set picking draw
3. and move the object using Alt+drag. Instead of moving, the sphere
duplicates, that is, the original one stays there while I move the
new one.
4. If I request the info with
show draw
I get this:
draw ID "pru" diameter 0.3 [ 0 {3.6 -1.35 1.4} ] [ 1 {3.6 -1.35 1.4}
] [ 2 {3.6 -1.35 1.4} ] [ 3 {3.1282716 -1.4552727 1.9073887} ] ;
draw ID "pru" fill noMesh noDots notFrontOnly fullylit;
Is this intended, or meaningful, or just a byproduct or bug?
It was not happening with 11.5.x versions
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Re: [Jmol-users] final testing appreciated
Using 11.6.RC17 I get this error:
eval ERROR: el argumento no es válido
line 1 command 64 of file null:
{ selected } . >> y << = 0
The offending script is
select 2.0; spacefill off; wireframe 0.04; color [xFF00FF];
{selected}.y = 0;
It worked in 11.5.41 at least
(I seem to recall having problems with this before)
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Re: [Jmol-users] jmol demo on sourceforge
Hi Jennifer Thanks for reporting this. However, I am seeing no problem. Please, 1.- Clear your Java cache (procedure described at http://wiki.jmol.org:81/index.php/Solving_Java_Problems#Java_cache 2. Clear your browser cache. Quit your browser and reopen it 3. Try the page. If the problem still persists, please report details: your browser, OS and Java versions, and any messages in the Java console. I assume that you mean the Jmol applet in the front page, not in the "demo" sections, right? - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] volume of cavities inside proteins?
Small additions to Bob's reply: > The cavities are totally created within Jmol. No additional program. The command is "isosurface", with "cavity" keyword > Animations. 100 PDB files is not a problem. You can either load them > as one file Or load them one file at a time, using "load append". The filenames can probably be fed using a loop in Javascript or in JmolScript, if they are something like protein1.pdb, protein2.pdb, protein3.pdb etc - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] final testing appreciated
I've added some information about clearing Java cache and other Java- related stuff into the Wiki: main page > Running Jmol > Solving Java Problems Also linked from Running Jmol Application and Running Jmol Applet Any confirmation or correction of that info from the Mac or Linux users will be welcome --I cannot test those systems. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] final testing appreciated
Just found this (well, not me, Google of course): Clearing Java cache on Linux, Mac, Windows: http://www.uwplatt.edu/oit/howto/java-cache.html - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Browser Crahes While Loading Jmol
Vinu manikandan wrote:
> Sir I restructured the program in such away that the different values
> are provided in the same page for example
> 1)1-55,
> 2)100- 120,
> 3)130-140 and
> I want to select these regions in the Jmol with out loading the
> protein structure again and again on the PDB Structure 1UW5.pdb one
> by one by providing a hyperlink to each of these values.
> When I had given the simple hyperlink
> 1-10
Yes, if you use the hyperlink in that way you reload the page. You
just need to send Jmol a script from within the page.
Using a link it would be something like:
(I assume that you are using Jmol.js)
jmolLink("select 1-10; color cyan; ", "1-10")
jmolLink("select 1-55; color cyan; ", "1-55")
jmolLink("select 10-120; color cyan; ", "100-120")
The first argument is the script, teh second is the text displayed as
hyperlink (may be anything you want).
The "color cyan" is just an example of a way to act on the selected
residues. Dots or halos are other good choices for highlighting.
You can also use buttons or a drop-down menu instead of the hyperlink
--just cosmetic, it depends on which look you prefer; it will work
the same.
> Sir, can you provide me an alternative way such that the Loading of
> the Protein happens a single time and mapping can be done multiple
> times.
See above
> Sir,I am using the new Mozilla Fire fox 3.0.2 and the Java jre6. I
> had checked this with other Browsers such as IE6, Safari and New
> Google Browser Chrome.
Good, the purpose of my question was whether you are also
experiencing crahses with the other browsers (in which case the
problem may be in the page code) or only in Firefox (then it's a
browser-specific problem).
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Re: [Jmol-users] Browser Crahes While Loading Jmol
Hi Vinu
El 25 Sep 2008 a las 12:31, vinu manikandan escribió:
> I had mailed the Jmol users blog couple of times, may be i was not
> clear in my question that's why ididn'tget any answers.
Maybe. Anyway, the list is so active that sometimes messages just
drop down too quickly. Don't hesitate to insist.
> Sir this is the code i used in my CGI script.
>
>
> jmolInitialize("jmol")
>
Re: [Jmol-users] final testing appreciated
Re: draggable applet
Here is a partial copy of my previous post (4 Sep.)
--- Forwarded message follows ---
[...]
I've tested it and it works. The applet detaches (Firefox 3 and
Chrome) and stays as a borderless window with a tiny close button
(that returns it to the browser), no way to resize. Maybe useless,
but cool!
This is the code I've used:
jmolInitialize("./", "JmolApplet.jar")
jmolSetDocument(0)
var s= jmolApplet(400)
s = jmolAppletAddParam(s,"draggable", "true")
document.write(s)
jmolSetDocument(document)
--- End of forwarded message ---
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Re: [Jmol-users] final testing appreciated
El 24 Sep 2008 a las 17:35, Thomas Stout escribió: > Oh, I restarted everything - including the computer and re-downloaded My experience with Firefox (Win) is that on some occasions it caches the applet and insists on using the cached copy even after restart and even if a new applet version is being tried. Apart from trying hard reload of page, closing and reopening Firefox, you may need to clear Firefox and/or Java caches. That would explain Tom's problem, since only the unsigned RC14 applet would have been cached and the signed one would eb recognized as a different one. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] final testing appreciated
El 24 Sep 2008 a las 16:06, Robert Hanson escribió: > OH, OK, I'm glad that worked. I had heard about that and was > wondering about it. Is that what then allows one to drag the applet > out of the window and onto the desktop? As I understand, the "draggable" is a feature of applets in the new Java 6u10 (still in RC, or beta). I've tried it and it works with Jmol and JChemPaint (if seems to be a general feature) but I think it has to be activated when inserting the applet; I'll chase my test code and post it here if anyone is interested --frankly I don't see the utility. As for the Firefox/Mac Java fix, it was an old issue with Apple Java versions and Firefox, but In had understood that is was soulve din recent versions of Java and/or Firefox. It seems not the case. This is documented at http://wiki.jmol.org:81/index.php/Support/Osx - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] frame [array of models]?
(following my previous post) Rob, You could also try to **delete** the unwanted frames (I think it's done with a variant of ZAP) then play the animation - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] frame [array of models]?
El 24 Sep 2008 a las 21:17, rob yang escribió: > Hmm, that does the trick. What if I want to animate only selected > models too? I'm quite sure that there are options for choosing the frame range involved in animation. Check the doc. But maybe not possible for non- contiguous frames. > including ones that are not "displayed" which results in blackout period. Yes, that sounds likely the way it is. How many frames do you have? You could fake the animation by scripting them one at a time and using a loop. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] help needed -- bonding radii of anions
In case it is of help, I found in our library a 56th edition (1975- 76) and a 77th edition (1996-97) of the CRC Handbook of Chemistry and Physics. Both have tables entitled "CRYSTAL IONIC RADII OF THE ELEMENTS" (pages F209 to F210 and 12-14 to 12-15 respectively) with these values: > > (8 << 4) + (-2 + 4), 1320, // "O-2" 1.32 (56th) 1.36 for CN 3 (coordination number, 77th) 1.40 for CN 6 > > (8 << 4) + (-1 + 4), 1760, // "O-1" // WAY too large? 1.76 (56th) 1.37 for "OH(-1)", CN 6 (77th) > > (14 << 4) + (-4 + 4), 2710, // "Si-4" 2.71 (56th) no entry (77th) > > (14 << 4) + (-1 + 4), 3840, // "Si-1" // same problem here? 3.84 (56th) no entry (77th) > > (34 << 4) + (-2 + 4), 1910, // "Se-2" 1.91 (56th) 1.98 CN 6 (77th) > > (34 << 4) + (-1 + 4), 2320, // "Se-1" // same problem here? 2.32 (56th) no entry (77th) - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] synchronizing "select commands" in multiple jmolcheckbox(es)
Avehna,
It appears to me that your solution is to have each checkbox call
only the part of script specific to the relevant piece of protein.
So, all your problem is a scripting one.
> They are several segments, so I will need several
> combinations if I'm using just jmol commands.
No, you shouldn't need combinations. Each checkbox should call code
that only affects its relevant portion of protein.
> the end define the whole jmol command once in dependence on which
> checkbox was picked before.
That is possible, but I think you can avoid that complex solution.
> "jmolSetCheckboxGroup(chkMaster, chkBoxes)"
I don't think this is suitable for your needs.
> problem using this function, I dont know why it seems to me a little
> complicated.
It is, a little bit.
Let's say you want this:
* protein segment 1 is residues 3 to 20
* protein segment 2 is residues 30 to 50
* checkbox 1 will color segment 1 in blue
* checkbox 2 will color segment 2 in red
* unchecked will color in default CPK
This is what you need:
In the loading script, include:
define segment1 3-20; define segment2 30-50;
And for the checkboxes, this:
jmolCheckbox("define temp selected; select segment1; color blue;
select temp;", "define temp selected; select segment1; color cpk;
select temp;", "segment 1")
jmolCheckbox("define temp selected; select segment2; color red;
select temp;", "define temp selected; select segment2; color cpk;
select temp;", "segment 2")
(You can also avoid the initial definition and integrate them in the
script, like
jmolCheckbox("define temp selected; select 3-20; color blue; select
temp;", "define temp selected; select 3-20; color cpk; select
temp;", "segment 1")
)
OK?
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Re: [Jmol-users] identifying proteins in mol2 files
Dear Frieda I've never tried that. From the doc http://www.tripos.com/data/support/mol2.pdf it seems that atoms can have IDs and residue IDs; they quote an example: 1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000 BACKBONE|DICT|DIRECT 1 CA -0.149 0.299 0.000 C.3 [...] the atom is named CA and is [...] It belongs to the substructure with ID 1 which is named ALA1. So, Jmol should be able to interpret that, but maybe the file reader has not been set for that. As far as I know, the "protein" is determined based on bonding and key atom names (N, CA, C) within the same residue. Similarly for residue names. A quick test with a pdb file read into Accelrys DS Viewer 1.7 and saved into mol2 shows that the atom IDs are read in Jmol (example: select *.CA works), but not recognized as protein. "select ala" doesn't work either. So maybe it's just the residue ID part that is not being interpreted. Notably, that goes after the coordinates, rather than before them as in pdb. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Tutorial-Authoring Template Released
El 10 Sep 2008 a las 5:13, Robert Hanson escribió: > http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/contents > /contents.htm > Jmol Version 11.3.13 2007-08-28 16:07 > > really? I'm quite sure that tutorial was written some time ago, and does not use Eric's newest JTAT. So it's probably so, really. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] beyond a limitation of JMOL: TiBS article on publication-integrated 3D models in PDFs
just a record for the future... > fascinating. So one would simply need to write a U3D file format > exporter. Very good project for someone. http://sourceforge.net/projects/u3d Universal 3D Sample Software Set of libraries to write, read, extend, render and interact with U3D- formatted data, as defined by standard ECMA-363. Intended as starting point for tools and applications to support U3D (exporters, importers, authoring packages and interactive viewers) Apache License V2.0 Programming Language : C++ Registered : 2005-03-05 Last Update: Jan 16 2007 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] beyond a limitation of JMOL: TiBS article on publication-integrated 3D models in PDFs
Amazing! Thanks for pointing this out, Wayne. I have missed the last two email ToC for TIBS, which I regularly review. Movement of the model is very smooth. The quality of the renderings is not so good -- must be related to file size, since PyMol can have a very good quality. El 5 Sep 2008 a las 0:20, Wayne Decatur escribió: > > [Jmol-users] beyond a limitation of JMOL: TiBS article on publication- > integrated 3D models in PDFs > From: Wayne Decatur <[EMAIL PROTECTED]> - 2008-09-04 21:58 > Thought people might be interested in a new article in Trends in > Biochemical Sciences by Pravin Kumar, Alexander Ziegler, Julian > Ziegler, Barbara Uchanska-Ziegler, > and Andreas Ziegler entitled "Grasping molecular structures through > publication-integrated 3D models". They detail using Pymol and Adobe > Acrobat 3D toolkit to "describe how an interactive 3D model of a > molecular complex can be embedded > directly into a PDF, thus providing readers with important and > educational > visual information that would otherwise be more difficult to > disseminate." > > Article can be accessed at: > http://www.sciencedirect.com/science/journal/09680004 > - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Load command and NMR structures
Chris Weichenberger escribió: > It also seems to be > inconsistent since the 'load' command asks for consecutive integers > starting with 1 whereas the 'frame'/'model' command requires the PDB model > number. I've checked the doc and it's correct, "frame" and "model" will use the PDB MODEL number if available. "In the case of the loading of a single PDB file containing MODEL records, the integer used here corresponds to the number in that record." I guess that for sequential numbers we now have the n.m syntax, that is, "frame 1.0" will display the first model, irrespective of its internally-assigned number --or won't it? No! It's "frame 1.1" The key issue is that only pdb files have model numbers, so Jmol is taking a general solution for "load". > May I ask the Jmol developers to extend the 'load' command such that it > can cope with model numbers contained in the PDB file? To assist you, I > have included pathologic cases I found when scanning our database for this > problem. That should be some kind of switch or new parameter, maybe? How about "load model " ? for backward-compatibility - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] screenshot generation from Jmol
[ Was: Re: [Jmol-users] At request of AHerraez, discussion of feature request moved to this list ] sorry for the mess of postings :-) Second part of reply, regarding the generation of images. David Halitsky wrote: > If (1-4) are possible as specified above, the next question is > whether there is a way to capture the two views that the user creates > in Frame A and Frame B so that they can be produced in a document of > the type that appears in each "case" in the StrucClues Case Library Yes, the views can be captured to the user's computer, in a web page (e.g. popup window) from where the user can copy or save them to disk, using the browser's capabilities. If you need to "capture" to the server, I cannot say *but see below. The discussion on how to make snapshots is quite long. There are several mesages in the list some time ago and there are several places that use this functionality; Bob has at least one, I dont0 remember exactly where right now, and I have a testpage/tutorial at http://biomodel.uah.es/Jmol/export-image/index.htm See if you can make it from that, then ask if you need help. > (As you can see, RasMol was used interactively to produce the views > in the case library, and screen shots of the RasMol views were then > saved to PowerPoint and the PowerPoint was then converted to jpeg or > gif.) >From the screenshot, displayed inside the browser, you can save directly to your disk in some browsers, or else copy-paste into any image editing program (I would not recommend Powerpoint, as the quality of saved images is poor). You get a jpeg file directly. Now that I think of it, in fact all the trouble was getting the server-generated image into the client browser, so there should be a way to store the image in the server maybe. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Pass Jmol start/end residue #'s as well as PDB/Chain ID's
(I'm bringing into this list the discussion started in the SF feature request site as this is more flexible. Although quite verbose, it may be of help to other users) > >Comment By: David Halitsky (davidhalitsky) > > Hi Angel - > > Thanks again for replying so promptly. > > I think I should have made the context clearer: input parameters on the > applet "command line". > As per discussion in this thread at SAP: > https://forums.sdn.sap.com/thread.jspa?threadID=972132&tstart=0 Sorry, the discussion there is quite confusing to me, with all the jargon about portals and so on. I tried to find specific Jmol-related comments there and I couldn't. > here's what we want to do: > > 1) we're in Frame1 of a portal that has two other frames in it: FrameA and > FrameB. > > 2) A query in Frame1 against a certain database brings back two sets of > specifications for Jmol, say: > > a 1hru, A, 123-145 > b) 2eqa, A, 144-167 > > 3) Via "client-side eventing" at the portal level , the portal passes the > parameters in (a) to JMol and Jmol runs in FrameA to display the "partial" > structure view requested (with rotate capability, same as in interactive > JMol; > > 4) At the same time , the portal passes the parameters in (b) to JMol and > Jmol runs in FrameB to display the "partial" structure view requested (with > rotate capability, same as in interactive JMol; > > Is this scenario currently possible as JMol is currently written? As long as you have already set the means to communicate with the Jmol applets in your portal system, I think it is indeed. This is what I'd pass to Jmol in FrameA: load "1hru.pdb"; display *:A and 123-145; and this to jmol in FrameB: load "2eqa.pdb"; display *:A and 144-167; (you will have to adjust the loading of the pdb file depending on where it is located) "display" is a better choice than the alternative, "restrict", for reason I won't discuss now (but we can separately, if you need it) Depending on your ways of inserting Jmol into your frames, there may be some details to solve, but on the Jmol scripting side that's all needed. > Or would I have to settle for the portal simply invoking Jmol in FrameB > and again in FrameC and letting the user manipulate settings in the > console, as you suggest. No, I won't suggest so, you can indeed preprogram what you want. > Thanks very much again for your time. A pleasure to help. > -- > > Comment By: Angel Herraez (aherraez) > Date: 2008-07-23 11:44 > > Message: > Logged In: YES > user_id=1065324 > Originator: NO > > Hi again > > I thought that your would be programming the selection in the page. Users > will also be able to do those as long as they can and know how to use the > console. All my comments will apply based on that assumption. > >select 12-14,45-60,123-165 > is something that you can already do > >select 12-14(A), 45-60(B), 123-165(B) > is not possible as such, only if converted to >select 12-14 and *:A, 45-60 and *:B, 123-165 and *:B > which, by the way, is the same as RasMol syntax, except that maybe the > comma is not allowed in RasMol and you need to use "or". > > > > -- > > Comment By: David Halitsky (davidhalitsky) > Date: 2008-07-23 11:23 > > Message: > Logged In: YES > user_id=2156323 > Originator: YES > > Hello aherraez - > > Thanks for taking the time to respond. > > As I mentioned in the request, Rolf Huehne of Jena thought that users > couldn't currently select residues. If users currently can select residues > the way you indicate, that's great. (I guess I should have looked at the > documentation first, before making the feature request. ) > > But as long as the feature request is open, it would be very nice to have > a standard "list" version of this parameter, e.g. instead of just 123-145, > you could have: > > 12-14,45-60,123-165 > > and also a version of this that crosses chains, e.g. > > 12-14(A), 45-60(B), 123-165(B) > > > Reason why this would be nice is that in certain cases documented at > StrucClues (http://strucclue.ornl.gov), non-contiguous areas of a chain are > of interest, and also non-contiguous areas across chains. (I mean > non-contiguous in the primary structure sequence, of course.) > > . I won't be offended. > >
Re: [Jmol-users] New Feature Request: input parm for start/end residue numbers
I am following this thread on the SF feature request system El 23 Jul 2008 a las 15:02, [EMAIL PROTECTED] escribió: > Rolf Huehne of JenaLib has told me that Jmol does not currently have [...] - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] using atom expressions in set labelgroup or set labelfront
Thanks, Bob.
It's not doing what I was imagining, though.
set labelGroup on {44-58};
So the atom expression says which atoms the label setting will be
applied to, and not which atoms the label will keep in front of?
(I am trying to label protein helices with a label that stays in
front on the helix stretch, not hidden by other residue in that same
stretch but hidden if another helix comes in front)
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Re: [Jmol-users] PDB question
To me, it looks like an error in the pdb data. Indeed, ALA 140 is the end of the chain, so a sheet from 137 cannot go farther. The position looks good to pair with the other strand, although quite wavy. As far as I know, the HELIX and SHEET records, if present, are put there by the authors to force definition of secondary structure elements. So, the method to determine them would be up to the authors. But they should have passed through validation as part of the PDB deposition process. Hmm... - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] using atom expressions in set labelgroup or set labelfront
The doc
http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#setlabels
says that you can put an atom expression, between braces, after
"set labelFront" or "set labelGroup"
I cannot get this to work in either 11.4.5 or 11.5.47, as I get a
syntax error:
set labelgroup {44-58}
·
ERROR en guión:el argumento no es válido
line 1 command 1 of file null:
set labelfront >> { << 44 - 58 }
Script completed
·
I've tried {} or {()}, and I've tried a user defined set or the above
expression, or a single residue number.
Can anyone advise if I'm getting it wrong, or there is a bug, or the
doc is not exact?
Thanks
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Re: [Jmol-users] Announcing introductory web tutorial on Jmol and making web pages...
Jonathan, this looks a very interesting idea. I will work through it and make suggestions later on. A Spanish traslation could be very useful too. I likely will work on both during August and come back to you. First and quick impressions: * The link on 2nd line, Jmol "Eport to Web..." Tutorial takes to this same page -- confusing-- And there is a missing "x" in export * The body-table-row has a scrollbar but the page has another, at least in Firefox. The outer one should not be needed; you can look for a fix in the source code of my resizable Jmol templates. Congratulations for the idea - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: Protein Explorer
El 17 Jul 2008 a las 10:24, Bob Hanson escribió: > Jmol Protein Explorer is ready for testing and may be considered in > "beta" state. Wow, Bob! I know a bit about PE internal complexity, so that must have been a huge effort. Congratulations! - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] gradient coloring isosurfaces
Thanks, Bob > I think that is intentional -- how you light the surface is not a > characteristic of the surface itself. > It's a property of the state. If that's so, then Ok; I'll just have to add the fullyLit parameter when loading from disk. But the jvxl file does include it on line nr.12: 1.4E-45 14112 9380 -1 0.0 0.0 0.0 0.0 rendering:isosurface mysurf fill noMesh noDots notFrontOnly fullylit that's the reason why I thought it was being saved. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Save/load state command
> Web: load /*file*/"http://chemapps.stolaf.edu/jmol/docs/examples-
> 11/data/quartz.cif" {1.0 1.0 1.0};
> DW:load /*file*/"file:/Volumes/nggroup/external/test/histidine.cif";
> (this is on Mac OS X)
> Both fixed paths.
Yes. I now remember seing this before, though I don't use state
often.
The question is that since the Jmol app can load files from anywhere
in the local file system, it adds the full path to the state script,
even if Jmol and the model are in the same folder. So you basically
end up editing the state script file always.
I think it would be more useful for general development if the saved
path was relative --at least when Jmol and the model are in the same
folder, or the model is in a subfolder below Jmol--. Of course, this
usefulness depends on what the developer has in mind, mainly moving
or publishing those files or just using them in the local computer
only.
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Re: [Jmol-users] Save/load state command
I also think that a fixed path is not good. However, from Nick's quote > > # Jmol state version 11.4.4 2007-12-20 06:37; > # fullName = "jmolApplet0[343951889313757]"; > # documentBase = "file:/Users/ngreeves/Sites/external/JmolPopup.htm"; > # codeBase = "file:/Users/ngreeves/Sites/external/"; The initial # will prevent Jmol from reading those lines, so that's really just a comment and will not have any effect on final behaviour of the state script. Check the line that starts with "load " and see which is the path there. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] gradient coloring isosurfaces
Bob Hanson wrote: > Newly available in Jmol 11.5.46 > (http://chemapps.stolaf.edu/jmol/docs/examples-11): > > You can now use the FUNCTIONXY keyword after the MAP keyword This is wonderful, Bob! It's working and great-looking. I found a bug (in 11.5.46, haven't tested other versions yet): loading an isosurface from disk (colored or not) ignores the "fullyLit" state, which was on when the surface was created and apparently is included in the saved jvxl I also noticed some inconsistencies or mistakes in the documentation of functionXY for returning string or array formats, between your last message and what is in the web doc. I will post the details later. - Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] gradient coloring isosurfaces
It seems that my question was not clear, so here I go again: I want to know if there is a way to (contour) color a surface without relaying on an external (cube) file that provides the color mapping. For example, to color based on the z coordinate of the surface's points, or by distance to a certain atom. Or, how can I generate a color mapping file without having Gaussian. - Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jvxl.jar file (was problem loading functionXY isosurface from file)
Thanks, Bob. Loading functionXY isosurfaces from disk is now working OK with 11.5.46_dev from your site A separate question: I see that there is a jvxl.jar file in your Jmol.zip Is this file needed for the applet? What's its purpose? I don't think I've read anything about it. - Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] gradient coloring isosurfaces
I am making an isosurface using a math function and would like to color it according to the z value. All examples of contouring and colormapping I find are based on an external (cube) file with the coloring data. Is there a way to color the surface without external data? Thanks - Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
