[Jmol-users] (no subject)
car...@cerm.unifi.it -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] JSmol and jquery.simplemodal.1.4.4.min.js
Hi to everyone !! I tried to realize a kind of dialog window using Jquery Simplemodal in which I would like to create a simple Jmol interface showing the proteins and with some buttons for different actions. It is not the first time that I implement an interface using Jmol/JSmol and everything was always working fine. But now I have problem with Jquery Simplemodal ! Since I'm already using Jquery, I decide to use JSmol.min.nojq.js (that doesn't make use of Jquery) but the only result I achieved was the visualization of the protein inside the frame and no buttons !! I don't know if this can be considered a bug ! We spent all the day to work around this problem without any success ! Can somebody help us ? Thank you in advance to everybody ! /azzurra -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] window.location=some URL breaks Jmol viewer
Dear all, I am experiencing a strange problem with JSmol. I have a JSmol applet on my page and a link to download the PDB file. The link works by setting window.location to a php page that forces the download of the PDB file (via headers like Content-Disposition: attachment; filename=...) without actually leaving the papge where the Jmol applet is. The problem is that the Jmol applet works perfectly before I click on the link, and when I click there the browser dowloads the file but then the Jmol applet freezes. I had a look at the Javascript console and it turns out that if I try to do anything with Jmol after clicking on the link to download the PDB file I get a long list of errors: Uncaught TypeError: Cannot read property 'viewer' of null JSmol.min.nojq.js:80 g._processEvent JSmol.min.nojq.js:80 (anonymous function) JSmol.min.nojq.js:55 p.event.special.(anonymous function).handle jquery-1.8.2.min.js:2 p.event.dispatch jquery-1.8.2.min.js:2 g.handle.h Any ides of why it is so? Am I doing something wrong? Let me know. Best, Roberto Roberto Mosca, Ph.D. Structural Bioinformatics and Network Biology Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona C/ Baldiri Reixac 10 08028 Barcelona - Spain Email: roberto.mo...@irbbarcelona.org Tel: +34 93 40 39689 Web: http://sbnb.irbbarcelona.org/people/roberto_mosca -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] window.location=some URL breaks Jmol viewer
Ok, sorry, I could fix the problem by using window.open() instead of setting window.location. In any case, anyone can help me in understanding what happens? Thanks in advance! :) Roberto On Fri, Jan 24, 2014 at 6:01 PM, Roberto Mosca robmo...@gmail.com wrote: Dear all, I am experiencing a strange problem with JSmol. I have a JSmol applet on my page and a link to download the PDB file. The link works by setting window.location to a php page that forces the download of the PDB file (via headers like Content-Disposition: attachment; filename=...) without actually leaving the papge where the Jmol applet is. The problem is that the Jmol applet works perfectly before I click on the link, and when I click there the browser dowloads the file but then the Jmol applet freezes. I had a look at the Javascript console and it turns out that if I try to do anything with Jmol after clicking on the link to download the PDB file I get a long list of errors: Uncaught TypeError: Cannot read property 'viewer' of null JSmol.min.nojq.js:80 g._processEvent JSmol.min.nojq.js:80 (anonymous function) JSmol.min.nojq.js:55 p.event.special.(anonymous function).handle jquery-1.8.2.min.js:2 p.event.dispatch jquery-1.8.2.min.js:2 g.handle.h Any ides of why it is so? Am I doing something wrong? Let me know. Best, Roberto Roberto Mosca, Ph.D. Structural Bioinformatics and Network Biology Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona C/ Baldiri Reixac 10 08028 Barcelona - Spain Email: roberto.mo...@irbbarcelona.org Tel: +34 93 40 39689 Web: http://sbnb.irbbarcelona.org/people/roberto_mosca -- La chiocciol@ http://lachiocciola.tumblr.com/ -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] select specified chain
Using Jmol 14.0.4 and 4kjg.pdb; trying to select all the atoms in chain a (or b); 0 atoms are displayed I've tried: Select *a Select *:a Select chain='a' Select chain=a I have no problems selecting in other pdb files... Any suggestions? Margaret Franzen -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] select specified chain
Must have been a fluke; it works when I run a script. Margaret From: Franzen, Margaret Sent: Friday, January 24, 2014 1:40 PM To: 'jmol-users@lists.sourceforge.net' Subject: select specified chain Using Jmol 14.0.4 and 4kjg.pdb; trying to select all the atoms in chain a (or b); 0 atoms are displayed I've tried: Select *a Select *:a Select chain='a' Select chain=a I have no problems selecting in other pdb files... Any suggestions? Margaret Franzen -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] select specified chain
Hi Margaret It's working correctly for me in 13.28 14.0.7 14.1.6 May be your pdb file be altered? Try with direct retrieval from the PDB: load =4kjg.pdb; Select *:a; -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Java exception site list and local files
I've had no problem with local files on a Windows PC using Firefox or Chrome with appropriate settings. You can just set your security settings back to Medium to be able to use older applets if you need to. No need to change any security settings for the newer applets. On Thu, Jan 23, 2014 at 7:46 AM, Richard Steane richard.ste...@ntlworld.com wrote: Hello All Having 'upgraded' to Java version 7 update 51, I have added my old Java section to the exception site list and have had much easier access to my pages on the WWW. This was accessed from Windows control panel, search for Java, double click Java icon to get to Java control panel, then security tab and edit site list ... adding: http://www.biotopics.co.uk/JmolApplet/ to the exception site list. Now I want to add my local files directory to that as well so as to interact with the files directly. I have not been able to do this successfully. I'm not sure of the format (especially the header) file:C/blabla/ ../JmolApplet/ ? Or should I be using \ as it appears in the browser's local files URI ? Any help will be appreciated. Richard Steane -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol and jquery.simplemodal.1.4.4.min.js
I'd say congratulations are in order for just getting the protein there! :) My guess is that you will see some sort of JavaScript error in the JavaScript console. What happens when you debug this with the developer console open or with the debugger running? Debugging jQuery can be a real challenge. The good thing is that it is all JavaScript. You can help yourself by substituting jsmol/js/JSmol.full.nojq.js for jsmol/JSmol.min.nojq.js. That at least is readable, editable, and debuggable. Same goes for jQuery. Are you using the uncompressed version, at least for now? Same problem when you use Jsmol.min.js? Or could it be a version problem? JSmol will need at least jQuery 1.9. On Fri, Jan 24, 2014 at 10:50 AM, car...@cerm.unifi.it wrote: Hi to everyone !! I tried to realize a kind of dialog window using Jquery Simplemodal in which I would like to create a simple Jmol interface showing the proteins and with some buttons for different actions. It is not the first time that I implement an interface using Jmol/JSmol and everything was always working fine. But now I have problem with Jquery Simplemodal ! Since I'm already using Jquery, I decide to use JSmol.min.nojq.js (that doesn't make use of Jquery) but the only result I achieved was the visualization of the protein inside the frame and no buttons !! I don't know if this can be considered a bug ! We spent all the day to work around this problem without any success ! Can somebody help us ? Thank you in advance to everybody ! /azzurra -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Audio?
I would just use the javascript command to introduce your own audio components. On Wed, Jan 22, 2014 at 1:27 PM, Ron Mignery remign...@gmail.com wrote: Could a play audio.file command similar to the Java play function be added to scripting? This would allow clicks and beeps or even entire narrations to be added to Jmol animations. Hopefully it would run in a separate thread. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] ModelKit add atom kills side-chain atomNames in polypeptides?
Makes sense. There's no way to know the atom name. On Wed, Jan 22, 2014 at 1:06 PM, Ron Mignery remign...@gmail.com wrote: The atomName of all polypeptide side-chain atoms is reduced to just the element name when an atom is added anywhere with the model kit in Jmol 14.0.4. *example:*CB=C -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Some commands inside user function fail only when the function is called for its return value
Yes, that is correct. When a function is being used in a math expression,
all delays are disabled. Otherwise the script would hang in the middle of a
mathematics expression, and while that might be possible in Java, that
would be totally impossible to recover from in the asynchronous environment
of JavaScript. Sorry if that is not documented.
You'll have to consider that a feature.
Bob
On Wed, Jan 22, 2014 at 1:03 PM, Ron Mignery remign...@gmail.com wrote:
Is calling a user function for a return value broken in Jmol application
14.0.4?
Delay, rotateSelected etc. seem to fail in the function only when called
for the return value
function xyz {
print now(xxx)
delay 1
print now(xxx)
return true
}
function test {
xxx=now()
xyz
z=xyz
}
test
0\ ~1 sec = ok
1047 /
1047 \ ~0 sec = not ok
1112 /
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http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [Jmol-users] Bug in break command in the Jmol application 14.0.4?
stranger than that... will fix
On Wed, Jan 22, 2014 at 12:58 PM, Ron Mignery remign...@gmail.com wrote:
Is break n broken in Jmol 14.0.4?
function xxx {
for (i=0;i4;i++) {
for (j=0;j4;j++) {
print i
break 0
}
}
}
xxx
0 \
1 \ ok
2 /
3 /
function xxx {
for (var i=0;i4;i++) {
for (var j=0;j4;j++) {
print i
break 1
}
}
}
xxx
0 \ not ok, function called twice?
0 /
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Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [Jmol-users] window.location=some URL breaks Jmol viewer
Where is the need for window.open() or window.location coming from in the first place? Jmol has a WRITE command that would let you do that, I think. Why not just use write file xxx.pdb That's much cleaner. On Fri, Jan 24, 2014 at 12:13 PM, Roberto Mosca robmo...@gmail.com wrote: Ok, sorry, I could fix the problem by using window.open() instead of setting window.location. In any case, anyone can help me in understanding what happens? Thanks in advance! :) Roberto On Fri, Jan 24, 2014 at 6:01 PM, Roberto Mosca robmo...@gmail.com wrote: Dear all, I am experiencing a strange problem with JSmol. I have a JSmol applet on my page and a link to download the PDB file. The link works by setting window.location to a php page that forces the download of the PDB file (via headers like Content-Disposition: attachment; filename=...) without actually leaving the papge where the Jmol applet is. The problem is that the Jmol applet works perfectly before I click on the link, and when I click there the browser dowloads the file but then the Jmol applet freezes. I had a look at the Javascript console and it turns out that if I try to do anything with Jmol after clicking on the link to download the PDB file I get a long list of errors: Uncaught TypeError: Cannot read property 'viewer' of null JSmol.min.nojq.js:80 g._processEvent JSmol.min.nojq.js:80 (anonymous function) JSmol.min.nojq.js:55 p.event.special.(anonymous function).handle jquery-1.8.2.min.js:2 p.event.dispatch jquery-1.8.2.min.js:2 g.handle.h Any ides of why it is so? Am I doing something wrong? Let me know. Best, Roberto Roberto Mosca, Ph.D. Structural Bioinformatics and Network Biology Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona C/ Baldiri Reixac 10 08028 Barcelona - Spain Email: roberto.mo...@irbbarcelona.org Tel: +34 93 40 39689 Web: http://sbnb.irbbarcelona.org/people/roberto_mosca -- La chiocciol@ http://lachiocciola.tumblr.com/ -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bug in break command in the Jmol application 14.0.4?
This is fixed. May get a release today; more likely tomorrow.
On Fri, Jan 24, 2014 at 5:21 PM, Robert Hanson hans...@stolaf.edu wrote:
stranger than that... will fix
On Wed, Jan 22, 2014 at 12:58 PM, Ron Mignery remign...@gmail.com wrote:
Is break n broken in Jmol 14.0.4?
function xxx {
for (i=0;i4;i++) {
for (j=0;j4;j++) {
print i
break 0
}
}
}
xxx
0 \
1 \ ok
2 /
3 /
function xxx {
for (var i=0;i4;i++) {
for (var j=0;j4;j++) {
print i
break 1
}
}
}
xxx
0 \ not ok, function called twice?
0 /
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Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Critical Workloads, Development Environments Everything In Between.
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Re: [Jmol-users] Where's my ATP?
select hetero ? On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Thank you Angel for the explanation. Still looking for a solution. Jaim On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.es wrote: I'm guessing, but ATP may be recognized as nucleic by Jmol algorithm and hence excluded from the ligand set, which is not protein, not nucleic, not solvent if I remember correctly Sorry, ligand used to be hetero and not solvent, but the problem may be along those lines. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Where's my ATP?
definitely: boolean isHetero = line.startsWith(HETATM); On Fri, Jan 24, 2014 at 6:16 PM, Robert Hanson hans...@stolaf.edu wrote: select hetero ? On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Thank you Angel for the explanation. Still looking for a solution. Jaim On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.es wrote: I'm guessing, but ATP may be recognized as nucleic by Jmol algorithm and hence excluded from the ligand set, which is not protein, not nucleic, not solvent if I remember correctly Sorry, ligand used to be hetero and not solvent, but the problem may be along those lines. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] type docu list access inconsistency
I agree completely. Good catch!
$ show @{ ([3,4,5])[1][1] }
[3]
is correct. array[i][j] should always return an array, provided i = the
length of the array.
This behavior is suggested by the documentation, and that it would return
just the number 3 is
unexpected.
Fixed for Jmol 14.0/1.8
Bob
On Wed, Jan 22, 2014 at 5:20 AM, Alexander Rose alexander.r...@weirdbyte.de
wrote:
Hi,
- the hash type is missing in the description of the type method under the
heading general .xxx functions
I do not know if this is intentional. Range selecting from lists returns a
list when there is more then one item in the list but only the item for
single item lists (and not a single item list)
var l = [0]; l=l[1][50]; show l;
= l = 0
var l = [0,1]; l=l[1][50]; show l;
= l = [0,1]
I had some code where I expected a list after range selecting from a list.
Took me a while to find out what was the cause. For now I wrap it in a
listify function (see below) but one gets into trouble with lists of lists.
Best
Alexander
function listify( x ){
if( x.type==array ){
return x;
}else{
return [ x ];
}
}
--
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St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [Jmol-users] Jmol 14.0.6 released
Documentation for SMILES and SMARTS and Jmol bioSMILES/bioSMARTS are at http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/smiles/package.html I'll be the first to admit that is obscure! And I see the change of code location in SourceForge broke that link in the documentation. On Wed, Jan 22, 2014 at 4:16 AM, Mike Casey mike.ca...@ucd.ie wrote: The SMILES/SMARTS comparison in Jmol is great! As Bob says, you don’t have to worry about the origin of the SMILES strings (as long as they are valid, of course), Jmol will get the comparison right every time. One useful additional feature that is not mentioned in the interactive scripting documentation page, is that Jmol can ignore stereochemical information present in the strings using the /nostereo/ option, e.g. var result = Jmol.evaluate(myJSmol, '' + studentSMILES + '.find(SMILES,/nostereo/' + correctSMILES + ')'); where ‘studentSMILES’ and ‘correctSMILES’ are variables containing SMILES strings. The /nostereo/ option must be documented in one of Bob’s other demonstration pages, I can’t remember which one. It can be very useful because users sometimes use dashed/wedged bonds where they are not needed. Mike *From:* Robert Hanson [mailto:hans...@stolaf.edu] *Sent:* 22 January 2014 03:10 *To:* jmol-users@lists.sourceforge.net *Subject:* Re: [Jmol-users] Jmol 14.0.6 released The nice thing about Jmol's SMILES comparisons is that it is totally independent of what program was used to make the SMILES string in the first place. There is no need for a canonical string for our purposes (as there might be for database look-ups). Thus, it matches any matching structure, regardless of method of construction. And it can detect isomerism. So it's really a very convenient solution to this problem of checking answers. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Tinker xyz files as Jmol input
Definitely not PDB format. Why do people do this? -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] (no subject)
I use the application, not the applet. Can I use the javascipt command there? The documentation describes the javascript command as applet only. On Fri, 24 Jan 2014 at 5:08 PM, Robert Hanson hans...@stolaf.edu wrote I would just use the javascript command to introduce your own audio components. On Wed, Jan 22, 2014 at 1:27 PM, Ron Mignery remign...@gmail.com wrote: Could a play audio.file command similar to the Java play function be added to scripting? This would allow clicks and beeps or even entire narrations to be added to Jmol animations. Hopefully it would run in a separate thread. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Model Kit add atom kills ALL sidechain atomNames
It is not the name of the added atom that is reduced. ALL side chain atoms in all chains are reduced. For example, load 1PQA in the application, add a single hydrogen to a water anywhere, exit the model kit and hover on any sidechain atom anywhere. What was CB is now C, OG is now O, etc. On Fri, 24 Jan 2014 at 5:09 PM, Robert Hanson hans...@stolaf.edu wrote: Makes sense. There's no way to know the atom name. On Wed, Jan 22, 2014 at 1:06 PM, Ron Mignery remign...@gmail.com wrote: The atomName of all polypeptide side-chain atoms is reduced to just the element name when an atom is added anywhere with the model kit in Jmol 14.0.4. *example:*CB=C -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] (no subject)
I don't see the Jmol application as much more than a development tool. The target environment for Jmol is a web page. On Fri, Jan 24, 2014 at 11:18 PM, Ron Mignery remign...@gmail.com wrote: I use the application, not the applet. Can I use the javascipt command there? The documentation describes the javascript command as applet only. On Fri, 24 Jan 2014 at 5:08 PM, Robert Hanson hans...@stolaf.edu wrote I would just use the javascript command to introduce your own audio components. On Wed, Jan 22, 2014 at 1:27 PM, Ron Mignery remign...@gmail.com wrote: Could a play audio.file command similar to the Java play function be added to scripting? This would allow clicks and beeps or even entire narrations to be added to Jmol animations. Hopefully it would run in a separate thread. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jmol-14.1.8_2014.01.24
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.8_2014.01.24.zip bug fix: y = ([3])[1][1] should be [3] not 3 bug fix: break n nonfunctional bug fix: format() and label() functions limited to 4 arguments; should be unlimited bug fix: errors in paths to js code in web export templates. currently uploading. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Where's my ATP?
I'm looking for the equivalent to getProperty ligandInfo that will return the complete list of names in HET or HETAM definitely: boolean isHetero = line.startsWith(HETATM); On Fri, Jan 24, 2014 at 6:16 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: select hetero ? On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Thank you Angel for the explanation. Still looking for a solution. Jaim On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.esmailto:angel.herr...@uah.es wrote: I'm guessing, but ATP may be recognized as nucleic by Jmol algorithm and hence excluded from the ligand set, which is not protein, not nucleic, not solvent if I remember correctly Sorry, ligand used to be hetero and not solvent, but the problem may be along those lines. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
