[Jmol-users] --nodisplay

Hello, I need to convert tens of thousands of cube files to jvxl files. I am able to do this on my mac by running a command like: java -jar Jmol.jar -ionx HOMO.cube script where script contains: isosurface SIGN color red blue cutoff 0.02 HOMO.cube; write myfile.jvxl This all works well. The

[Jmol-users] Firefox 4.0 beta 10

Still broken. J. Philip Bays Professor of Chemistry Department of Chemistry and Physics Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD

Re: [Jmol-users] --nodisplay

No graphics on that Linux. Try JmolData.jar instead of Jmol.jar On Tue, Jan 25, 2011 at 12:43 PM, Swank, Craig craig.sw...@nrel.gov wrote: Hello, I need to convert tens of thousands of cube files to jvxl files. I am able to do this on my mac by running a command like: java -jar Jmol.jar

Re: [Jmol-users] --nodisplay

Hello, Even without displaying anything, Java requires a display for some graphical operations (image and font management, ...) I think this is due to Java design. I had the same kind of problems for an application, and I solved it by using a virtual display (search for program named xvfb). With

Re: [Jmol-users] --nodisplay

Thanks for the suggestion. I tried it and got this: [cswank@scctest convert_test]$ java -jar /app/www/auto_opv/src/opv/opv/views/static/applets/jmol-12.0.19/JmolData.jar x.mol -n -s mo.spt Exception in thread main java.lang.NullPointerException at org.jmol.viewer.Viewer.initialize(Unknown

Re: [Jmol-users] --nodisplay

Ok, I got the Vxrb thing working. I have a python script that imports my data into a db. At the beginning of the script I start Xvrb in the background like this: from subprocess import Popen, PIPE vxfb = Popen(['Xvfb', ':4', '-screen', '0', '800x600x24'], stdout = PIPE) When the script is

Re: [Jmol-users] --nodisplay

Forgot one important thing. In my ~/.bashrc script I have: export DISPLAY=:4.0 The solution below won't work without that. Craig On Jan 25, 2011, at 1:22 PM, Swank, Craig wrote: Ok, I got the Vxrb thing working. I have a python script that imports my data into a db. At the beginning

Re: [Jmol-users] --nodisplay

however, JmolData is set up to be entirely graphic-less for this sort of operation. At least I'd like you to try that. On Tue, Jan 25, 2011 at 2:10 PM, Nicolas Vervelle nverve...@gmail.comwrote: Hello, Even without displaying anything, Java requires a display for some graphical operations

[Jmol-users] extract min and max resNo to javascript

Hello all This must be trivial, but I'm stuck I need to extract the minimum and maximum residue nurmber from a one-chain pdb file into a Javascript variable. The Jmol commands are m1 = {*}.resno.min m2 = {*}.resno.max but I don't know how to pass those to a javascript variable (I need to

Re: [Jmol-users] extract min and max resNo to javascript

Hi, I think you can build on this: jmolScriptWait('var foo = bar;'); var msg = jmolEvaluate( script('echo @foo'); ); Alex Am 26.01.2011 um 01:05 schrieb Angel Herráez: Hello all This must be trivial, but I'm stuck I need to extract the minimum and maximum residue nurmber from a

Re: [Jmol-users] extract min and max resNo to javascript

Great, Alex, thanks I had forgotten about jmolEvaluate() This does the trick: alert( jmolEvaluate( {*}.resno.min; ) ); -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a

Re: [Jmol-users] extract min and max resNo to javascript

var x = eval(jmolEvaluate([ + {*}.resno.min + , + {*}.resno.max + ])) would get you both of them at once. 2011/1/25 Angel Herráez angel.herr...@uah.es Hello all This must be trivial, but I'm stuck I need to extract the minimum and maximum residue nurmber from a one-chain pdb file into a

Re: [Jmol-users] extract min and max resNo to javascript

Alex and Angel, I think Alex's response is the textbook approach, but I've had real problems with jmolScriptWait. I don't think it's a bug. I just think it's susceptible to fussy waiting forever (hangs). As an alternative, I find that a call back works nicely. In the call back function below,

Re: [Jmol-users] extract min and max resNo to javascript

Bob, That's interesting. Does this mean that you do not have to use the WAIT? Otis var x = eval(jmolEvaluate([ + {*}.resno.min + , + {*}.resno.max + ])) would get you both of them at once. 2011/1/25 Angel Herráez angel.herr...@uah.es Hello all This must be trivial, but I'm stuck I need to

Re: [Jmol-users] extract min and max resNo to javascript

Son of a gun. The following works without any WAIT function: var jmolSmiles = jmolEvaluate({*}.find('SMILES')) Unless it's in jmol.js and I don't see it? Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org

Re: [Jmol-users] extract min and max resNo to javascript

Note that jmolEvaluate() does not use the same mechanism as jmolScriptWait(). It bypasses that and totally independently evaluates an expression just like you had executed a PRINT command. Any other scripts may be executing; this execution is independent of that. On Tue, Jan 25, 2011 at 6:33 PM,

[Jmol-users] anim and spin issue

Hi All, I am seeing some strange behaviors with animating a 10-model pdb file when I turn on spin. At best, very jerky, then stops; at worst, strange distortion of molecule. I see that there was an issue with this in 2009 but it was fixed. Wondering if anyone else is seeing problems with

Re: [Jmol-users] anim and spin issue

Seems that reducing the hermite level to zero improves this considerably, which makes sense. However it is still not a smooth animation when spinning, as it is for example here: http://proteopedia.org/wiki/index.php/Mechanosensitive_channels:_opening_and_closing Frieda On Jan 26, 2011, at