Re: [Jmol-users] installing JSmol extension

Yes. And the surface looks great. Note: if you want to avoid the simplified rendering of the surface while rotating the model, you may add 8 to the block. This sets platformSpeed as defined at https://chemapps.stolaf.edu/jmol/docs/#set_platformspeed Jaim > On 25 Jul 2017, at 20:23, Angel Her

Re: [Jmol-users] installing JSmol extension

Dear Angel, Please see below what I wrote Henry. Somehow JSmol sometimes fails reading the JVXL file. From the existing files in jsmol/j2s/J/jvxl/readers/, I guess that the software finds out the format of the file to read, and call the matching reader. i.e PolygonFileReader.js for PoligonFile

Re: [Jmol-users] JSmol labels on zoom

Thank you Angel! > On 24 Apr 2017, at 13:21, Angel Herráez wrote: > > Hi Jaime > > It's always been like that by default, but I think there is an option: > set fontscaling on > although it is a little tricky to get it working when there is zoom between > two > applications of labels. > See

[Jmol-users] JSmol labels on zoom

There’s not a proportional change of size of Labels when zooming a model on JSmol 14.9.1 (and maybe on other versions), both on zooming initiated by script and by interactive mouse driven. Labels remain with the original font size despite the change in size of the model. Is there a way to contr

Re: [Jmol-users] Fwd: SourceForge Project of the Week March 27th, 2017

Congratulations!! On 23 Mar 2017, at 16:22, Robert Hanson mailto:hans...@stolaf.edu>> wrote: FYI -- Forwarded message -- Subject: SourceForge Project of the Week March 27th, 2017 Hi, If you’re receiving this email it is because you are listed as an admin on our next Projects

Re: [Jmol-users] Jsmol mutate behaviour

Angel suggested yesterday the minimizing solution which works. Thank you both! Jaim Here’s Angel complete solution: mutate 148 SER; select [SER]148:A; color CPK; wireframe 0.2; color opaque; minimize (selected and sidechain); // alternative: minimize fix (not (selected and sidechain));

Re: [Jmol-users] Jsmol mutate behaviour

On 29 Jan 2017, at 2:39 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: Might be just the carbon atoms. Can you please be more explicit? What I’m doing wrong? Is there a way to apply the mutate command and get the correct rendering? [cid:858B8B02-0D68-4323-84FC-E861DF60A73B@weizmann.ac.il

[Jmol-users] Jsmol mutate behaviour

Something funny on the results I get from the mutate command. By mutating a residue into the same residue, I was expecting no conformational change. What I’m doing wrong? Same results with jsmol_14.6.1_2016.08.11 and jsmol_14.7.5_2016.12.02 Please see the attached image. The same structure 5E

Re: [Jmol-users] "Augmented Reality": https://github.com/es605/HTMoLar

I would say that Molecular Playground http://molecularplayground.org/ http://proteopedia.org/w/Molecular_Playground qualifies for an effective 'Use of Jmol on augmented reality'. Jaim On 15 Aug 2016, at 18:58, Angel Herráez mailto:angel.herr...@uah.es>> wrote: I have had a little practice usi

Re: [Jmol-users] Capture PNGJ file as a variable

This should be the same as using preloaded images with javascript. Jaim > On 15 Jul 2016, at 11:51 AM, Angel Herráez wrote: > > El 14 Jul 2016 a las 12:13, Robert Hanson escribió: >> Note that by putting a PNGJ file into a variable you can >> >> -- extract or exchange the image > > So a questi

Re: [Jmol-users] incomplete cartoons in Calpha-only files

Jmol is unable to extract and render Sheet information from the new PDBe generated cif files, with chain IDs in sheet records are specified as A-2, A-3 , see http://www.ebi.ac.uk/pdbe/coordinates/1stp/assembly?id=1 On 8 Jul 2016, at 5:09 PM, Herráez Sánchez Ángel mailto:angel.herr...@uah.es>>

[Jmol-users] Jmol 14.6.0_2016.06..22 Saved State

Differences found on saved state from Jmol version 14.6.0_2016.06.22 SelectionHalos OFF; is not longer present in _setSelectionState() . Will this come back on a next release? There’s a new set cartoonsfancy false; (notice the plural) in addition to the previous set cartoonfancy false;. set

Re: [Jmol-users] JmolData.jar jmol-14.6.0_2016.05.24

On 14 Jun 2016, at 3:45 AM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: I don't think capture should work from JmolData. Try Jmol.jar Thank you, Jaim -- What NetFlow Analyzer can do for you? Monitors network bandwid

[Jmol-users] JmolData.jar jmol-14.6.0_2016.05.24

Could it be that command ‘capture’ fails on JmolData.jar from jmol-14.6.0_2016.05.24 ? After loading a model, ‘ capture “file.gif” Y 30 ’ generates a file with only GIF89a?? on it. On the other side, ‘ write IMAGE 500 500 GIF “file.gif” ‘ works Ok. Jaim -

Re: [Jmol-users] JmolApplet.jar

Agreed. Signed Java can become handy in the distribution. Files not needed for a functional JSmol, like examples, scripts, etc, can be on a separated download. Jaim > On 18 May 2016, at 12:38 PM, Angel Herráez wrote: > > I certainly would prefer to have Java available in the distribution. For

[Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

It seems that JSmol gets unloaded when a page gets out of focus, by flipping between pages, on Safari Mac Version 9.0.3 (11601.4.4). 1. Open any page on Safari Mac (tested on Version 9.0.3) 2. Now open a page with JSMol on it, i.e. http://proteopedia.org/w/1dnn 3. Go to the previous page: Hist

Re: [Jmol-users] JmolVersion="14.4.1_2016.01.04"

Thank you! This release fixes the problem with scenes depending on default values. Jaim __ On 5 Jan 2016, at 5:58 AM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: Download Jmol-14.4.1_2016.01.04-binary.zip (18.2 MB)

Re: [Jmol-users] JSmol defaults for label ?

;> wrote: Please give me a script I can test. On Sun, Jan 3, 2016 at 9:57 AM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: Can you please implement defaults again? Jaim On 3 Jan 2016, at 3:33 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: Yes, that'

Re: [Jmol-users] JSmol defaults for label ?

Can you please implement defaults again? Jaim On 3 Jan 2016, at 3:33 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: Yes, that's something I changed. Darn. When does it happen? On Sun, Jan 3, 2016 at 6:18 AM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wro

[Jmol-users] JSmol defaults for label ?

JS.ScriptQueueThread.runNextScript() 6 JS.ScriptQueueThread.run1(a) args[0]=0 7 J.thread.JmolThread.run() 8 start() 9 function () __ Dr Jaime Prilusky R&D Bioinformatics and Data Management Skype: jaime.prilusky.wis mail: jaime.prilu...@weizmann.ac.il<mailto:jaime.prilu...@weizmann.ac.i

Re: [Jmol-users] Jmol-14.4.1_2015.12.21

Please check the build. There’s inside jsmol.zip two folders, jsmol and jsmol2 On 22 Dec 2015, at 6:21 AM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: Jmol-14.4.1_2015.12.21-binary.zip

Re: [Jmol-users] test please

__ Dr Jaime Prilusky R&D Bioinformatics and Data Management mail: jaime.prilu...@weizmann.ac.il<mailto:jaime.prilu...@weizmann.ac.il> OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On 21 Dec 2

Re: [Jmol-users] Jmol -- testing requested

Thank you. This new version fixed the "Errors on missing Isosurface file": electrostatics2, 3BSN_3BSO, hupa_LC, HupA_2 and HupA_3 The rest stays: The error of PyMOL reader not reading "H69" as "helix" (RGS-Ga_8pdb_structures_aligned_S90_20.5.15.pse) persists. The generated JPNGJ contains two

Re: [Jmol-users] Load multiple models

frame all; will help > On Jul 27, 2015, at 9:35 PM, Thomas Hrabe wrote: > > Hi there, > > I have problems with loading multiple pdbs into one view: > > > Jmol.script(applet,'load FILES > "http://fatcat.burnham.org/fsn-data/chains.superimposed/1pzuB.1a02N.pdb"; > "http://fatcat.burnham.org/

Re: [Jmol-users] Chemical elements and counts

> On Jul 15, 2015, at 11:46 PM, Robert Hanson wrote: > Most recent Jmol version allows > X = Jmol.evaluateVar(jmolApplet0, {*}.element.pivot > > $ load =1crn > $ print {*}.element.pivot > { > "C" : 1017 > "H" : 532 > "N" : 268 > "O" : 375 > "S" : 10 > } What exactly happens

[Jmol-users] Jmol 14.3.13_2015.05.19 viewer.getBoolean(navigateSurface)

Executing headless JmolData.jar (see below the command line executed) from Jmol 14.3.13_2015.05.19 reports three times viewer.getBoolean(navigateSurface) - not listed while this message is not present on the same operation on older versions of Jmol, i.e. 14.1.8_dev_2014.01.23 /usr/bin/java -D

Re: [Jmol-users] Add hydrogens to PDBs after they are loaded

Brenton, On the script you currently use, you should be able to add pdbAddHydrogens before loading, as here: set pdbAddHydrogens true; load= 2ace; Regards, Jaim > On Apr 21, 2015, at 8:56 AM, Brenton Horne wrote: > > Hi, > > I have been using the JSmol extension for MediaWiki and I'd like

Re: [Jmol-users] MediaWiki Jmol Extension

://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-extensions/ and follow the few steps from the readme.txt file. Please let me know if you encounter any problem. Jaim -- Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of Biological Services Weizmann Institut

Re: [Jmol-users] Safari reloading JSmol over and over

Had similar problems on Mac OS X 10.9.5 Safari 7.1 while testing FirstGlance 2.2 I would say that's the results of running JSmol with loaded portions from different versions. The problem disappeared after clearing cache and reseting Safari a couple of times. Jaim On Sep 30, 2014, at 1:37 AM,

Re: [Jmol-users] visible vs. restrict

On Sep 18, 2014, at 8:18 AM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.17.zip bug fix: spin broken in WebGL (Jaime) spin still broken on Mac, Safari, FFox and Chrome. set antialiasDisplay ON/OFF also broken. Menu->About->Jmol repo

[Jmol-users] spin on WebGL

Tested on JmolVersion=“14.3.7_2014.09.16” on Mac Safari 7.0.6 and FFox 32.0.1 WebGL looks Ok. Mouse interacts Ok with the structure in the applet. spin ON/OFF, is broken while on WebGL, both issued from the console and from a button script. moveto and zoomto while on WebGL are able to initiate

Re: [Jmol-users] quality of the model

set antialiasDisplay ON http://chemapps.stolaf.edu/jmol/docs/#setantialiasing Jaim On Sep 16, 2014, at 3:54 PM, GABRIEL PONS IRAZAZABAL mailto:gp...@ub.edu>> wrote: My question is: In first Glance Jmol, from Eric Martz, there is an option to improve the quality of the display. Could you tell

Re: [Jmol-users] jmol-14.3.7_2014.09.07c

files at St. Olaf have had updated Jmol.jar versions but not JSmol.zip. My goodness. OK. Make that: http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.08.zip On Sun, Sep 7, 2014 at 10:52 PM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: On the file I downloaded,

Re: [Jmol-users] jmol-14.3.7_2014.09.07c

On the file I downloaded, the file j2s/Jmol.properties reports old version: ___JmolDate="$Date: 2014-08-14 15:07:40 -0500 (Thu, 14 Aug 2014) $" ___fullJmolProperties="src/org/jmol/viewer/Jmol.properties" ___JmolVersion="14.3.6_2014.08.14" On WebGL Mac Firefox and Safari: spin is not working and m

Re: [Jmol-users] The world of Jmol - an update: crystallography

Wow!! Thank you for the update and the glimpse into a busy present and a promising future. (‘The world of Jmol’, nice title for an ongoing story) Jaim On Sep 4, 2014, at 2:53 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: [Sorry for the blog-like nature of this message. I'm not ready to b

Re: [Jmol-users] inactive mouse with WebGL

On Sep 3, 2014, at 3:37 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: Thanks -- I will check this before the next release. It is broken on chemapps, but it is not broken on my local site, suggesting that I just need to update the files on chemapps. Check http://chemapps.stolaf.edu/jmol/z

Re: [Jmol-users] JSmol - Unable to load PDB file appears to think it is binary

On Sep 3, 2014, at 12:49 PM, Mark Wass mailto:m.n.w...@kent.ac.uk>> wrote: Thanks for the suggestion Jaim. It works properly in firefox but not in Safari. Is there a fix to get it working in Chrome and Safari? I’m also looking for a solution :-) I remember for this or a related problem being me

Re: [Jmol-users] JSmol - Unable to load PDB file appears to think it is binary

This seems to be a Chrome problem. Try with Firefox or Safari before trying to fix your server. Jaim On Sep 3, 2014, at 12:33 PM, Mark Wass mailto:m.n.w...@kent.ac.uk>> wrote: Hi, I am currently trying to get Jsmol to work on my server. I have used Jsmol successfully on other servers but this

[Jmol-users] inactive mouse with WebGL

Can you please verify if mouse interaction is broken for WebGL? Tested Firefox and Safari on Mac 10.9.4 Applet renders structure Ok, but mouse can’t interact (rotate, zoom, open menu, etc). Interaction from page works Ok (links, buttons, pulldown, etc). See either http://chemapps.stolaf.edu/jmo

Re: [Jmol-users] support needed -- XHR -- asynchronous vs synchronous

Bob, Can you please provide a template letter? Jaim On Aug 31, 2014, at 1:45 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: Folks, I would appreciate some letter-writing support in relation to http://lists.w3.org/Archives/Public/public-webapps/2014JulSep/0084.html http://lists.w3.org/Ar

Re: [Jmol-users] jmol-14.3.7_2014.08.25.zip

@stolaf.edu>> wrote: I'm guessing that is a caching problem? On Tue, Aug 26, 2014 at 2:24 AM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: JSmol.min.js reports TypeError: 'undefined' is not an object (evaluating 'a._checkDeferred’) when sending script

Re: [Jmol-users] jmol-14.3.7_2014.08.25.zip

JSmol.min.js reports TypeError: 'undefined' is not an object (evaluating 'a._checkDeferred’) when sending scripts from a web page via JavaScript. Entering same commands on the JSmol applet Console works Ok. I assume that I’m testing the correct version. Expanding jmol-14.3.7_2014.08.25.zip, the

Re: [Jmol-users] applet with multiple isosurfaces

ob On Sat, Aug 16, 2014 at 1:25 PM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: On Aug 16, 2014, at 9:24 PM, Angel Herráez mailto:angel.herr...@uah.es>> wrote: > There is "isosurface list", which returns the IDs and some data, but not the > jvxl data >

Re: [Jmol-users] applet with multiple isosurfaces

On Aug 16, 2014, at 9:24 PM, Angel Herráez wrote: > There is "isosurface list", which returns the IDs and some data, but not the > jvxl data > You are giving an ID to each surface, right? > Otherwise only the last isosurface is accessed by most commands. Yes. I do have an ID for each isosurface.

[Jmol-users] applet with multiple isosurfaces

After creating multiple isosurfaces, how do I get the list of the IDs defined isosurfaces and their data in JVXL format? The following two commands seem to act on only one isosurface. They do return info and data of the latest isosurface defined getProperty isosurfaceInfo show isosurface The d

Re: [Jmol-users] Jmol select chains in large structures

P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z 0 1 2 Bob On Thu, Aug 14, 2014 at 3:11 AM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: How to select chains in large structures? Testing on Jmol.jar 14.2.4_2014.08.03 2014-08-03 08:56 We are

[Jmol-users] Jmol select chains in large structures

='AX' 1628 atoms selected $ select chain=‘AZ’ 526 atoms selected Could it be that the internal structure index is wrong? Suggestions? Jaim __ Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of Biological Services Weizmann Institute o

Re: [Jmol-users] bug fixes

On Aug 12, 2014, at 9:05 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: It was Chrome/Safari. http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.5_2014.08.12.zip please test -- I would like to release this Friday. Excellent. Testing on Mac OSX 10.9.4. Both parenthesis are Ok now. Is confusing t

Re: [Jmol-users] bug fixes

Jmol version 14.3.5_2014.08.09: unable to type open parenthesis '(' in JSmol Console. Closing parenthesis ‘)' is Ok. On Aug 10, 2014, at 6:43 AM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.5_2014.08.09.zip . bug fix: CIF reader broken for lo

Re: [Jmol-users] speedy testing requested

Testing now. j2s/Jmol.properties states ___JmolVersion="14.2.2_2014.06.29" so it's difficult to know if the new version was loaded. On quick test the loaded JSmol looks Ok. Jaim On Aug 2, 2014, at 5:45 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: I have just released Jmol 14.2.3 and

Re: [Jmol-users] jmol-14.3.3_2014.07.29.zip

You’re right. On a simple page ( http://proteopedia.org/wiki/tests/sync2.html ), ’sync * ON' works. I will try to find out what’s interfering with this function on the original page. Regards, Jaim On Jul 30, 2014, at 1:01 AM, Robert Hanson wrote: > Please send me a link to a nonfunctional pa

Re: [Jmol-users] jmol-14.3.3_2014.07.29.zip

;/a>;); Jmol.getApplet("jmolApplet2",Info0);Jmol.script(jmolApplet2,"load $c1c1;"); Jmol.getApplet("jmolApplet3",Info0);Jmol.script(jmolApplet3,"load $NC(C)C(O)=O;"); On Jul 29, 2014, at 12:47 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: I need mo

Re: [Jmol-users] jmol-14.3.3_2014.07.29.zip

On 14.3.3_2014.07.29, the following fails in my tests to sync multiple applets, both on JSmol and Java. jmolCheckbox('sync * ON','sync * OFF','check to sync',false); Other tested features are Ok. Jaim On Jul 24, 2014, at 9:10 AM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: http://chemap

Re: [Jmol-users] jmol-14.3.3_2014.07.24.zip

On 14.2.3, the following fails in my tests to sync multiple applets, both on JSmol and Java. jmolCheckbox('sync * ON','sync * OFF','check to sync',false); Other tested features are Ok. Jaim On Jul 24, 2014, at 9:10 AM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: http://chemapps.stolaf.e

Re: [Jmol-users] is there a way to undisplay Jmol_S on the applet?

Nameserver is unable to translate www.rsquarelabs.com into a valid IP address Can you provide the IP of the server? Jaim On Jun 18, 2014, at 1:53 PM, Ravi Raja Merugu mailto:raviraja.mer...@gmail.com>> wrote: Yes, the url is correct, I rechecked the address, it's pu

[Jmol-users] JSmol write protected Console?

>From my server with Jmol 14.2.0_2014.06.13 and 14.0.17_2014.06.09 , the lower >panel of Console from JSmol applet is write protected, i.e. can’t type >commands to be executed. On Jmol 14.1.16 it was Ok. Can others reproduce this? Jaim * 14.2.0_2014.06.1 ---

Re: [Jmol-users] is there a way to undisplay Jmol_S on the applet?

simply "frank off" should also work. Jaim On Jun 18, 2014, at 1:04 PM, Rolf Huehne wrote: > On 06/18/2014 11:50 AM, Ravi Raja Merugu wrote: >> Hello everyone, >> >> Is there a way i can undisplay Jmol_S logo on the viewer in the right >> bottom, Is there any option like "set frank off/false"

Re: [Jmol-users] WebGL support in OS X Yosemite

is available on WebGL at this time. Jaim -- Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA,

Re: [Jmol-users] Jmol 14.1.14 released

On Apr 26, 2014, at 6:58 AM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.14/ Was the release 14.1.14 removed from sourceforge.net? The latest version I’m able to access is 14.1.13 Jaim ---

Re: [Jmol-users] jmol-14.1.12_2014.03.22.zip WHERE?

chemapps.stolaf.edu/jmol/zip/jmol-14.1.12_2014.03.22.zip On Mar 23, 2014, at 6:55 PM, Eric Martz wrote: > I am getting "file not found" for the URL below. > Someone please tell me where to get the current 14.1.12 -- thanks! Eric > > At 3/23/14, Robert Hanson wrote: >>

Re: [Jmol-users] jmol-14.1.12_2014.03.21.zip -- important update

On Mac 10.9.2, both Safari and Firefox 28.0, JSmol fails with message: TypeError: 'undefined' is not an object (evaluating 'this.stm.jmolStatusListener.isStereoSlave') JSmol loads, able to open popup menu, no frank. Java version, Jmol_S, works Ok. Jaim On Mar 22, 2014, at 2:05 AM, Robert Hans

Re: [Jmol-users] JSmol broken on Mac Safari back button

body onload= 2) JSmol ready function 3) JSmol structure loaded callback Maybe also, server setting related to caching??? Otis -- Otis Rothenberger o...@chemagic.com<mailto:o...@chemagic.com> http://chemagic.com On Jan 30, 2014, at 11:57 AM, Jaime Prilusky mailto:jaime.prilu...@weizma

Re: [Jmol-users] JSmol broken on Mac Safari back button

pt by defining an empty unbeforeunload function. I was never sure if either of these affected supporting files, however. I'm not sure you want to go this route. JSmol in user cache is a big plus. Otis -- Otis Rothenberger o...@chemagic.com<mailto:o...@chemagic.com> http://chemagic.com

[Jmol-users] JSmol broken on Mac Safari back button

Is there a way to force loading JSmol when loading/rendering a page? JQuery should be able to do this. This is why we might need to start with a fresh loaded JSmol: When clicking a ‘back to previous page’ button on On Mac 10.9.1, Safari 7.0.1, JSmol renders non-operational. On Firefox 26.0, sam

Re: [Jmol-users] Where's my ATP?

wrote: select hetero ? On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky mailto: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 mailto:angel.herr...@uah.es>> wrote: > I'm

Re: [Jmol-users] Where's my ATP?

Thank you Angel for the explanation. Still looking for a solution. Jaim On Jan 22, 2014, at 5:00 PM, Angel Herráez 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 rem

[Jmol-users] Where's my ATP?

getProperty ligandInfo returns a nice list of elements in the HET record of the PDB file, with some exceptions, like ATP and ADP. Those are not included in the ligandInfo report. Tested on Jmol 14.0.7 (both Java and HTML5) on several structures, including 1s22 and 1php Is there other getProper

Re: [Jmol-users] display echo while calculating

e column, half-way down: "echo/surface test". I'm guessing the "flash" is the calculation. everything before that is file loading. Bob On Thu, Jan 16, 2014 at 3:10 PM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: Thank you for the new versio

Re: [Jmol-users] display echo while calculating

Dear Bob, On Safari Mac, with jsmol 14.1.6_dev_2014.01.16 , the notice while working performs great with delay 0.1 instead of refresh Thank you for the suggestion. Jaim On Jan 16, 2014, at 10:10 PM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: Thank you for the new vers

Re: [Jmol-users] display echo while calculating

t;> wrote: Yes, I think I found it. delay 0.01 should work even though refresh does not: set echo top left echo working... delay 0.01 echo Please try that; I'll also get refresh working. Testing now. On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky mailto:jaime.prilu...@weizm

Re: [Jmol-users] display echo while calculating

Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne wrote: > On 01/16/2014 06:14 PM, Jaime Prilusky wrote: >

Re: [Jmol-users] display echo while calculating

ze that there is no updating it, because the calculation is not interruptable at all, including updating any such message. On Wed, Jan 15, 2014 at 6:18 AM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: I would like to have a message “Working …” while Jmol is calculatin

[Jmol-users] display echo while calculating WORKING Ok

Please disregard previous mail. Your suggestion of using waitmessage works perfect. Thank you again, Jaim On Jan 15, 2014, at 3:06 PM, Jaime Prilusky wrote: > Thank you for a prompt reply, but it’s not working for me on 14.0.5. > The command waitmessage is undocumented. Maybe it’s som

Re: [Jmol-users] display echo while calculating

Thank you for a prompt reply, but it’s not working for me on 14.0.5. The command waitmessage is undocumented. Maybe it’s something you added? On Jan 15, 2014, at 1:48 PM, Rolf Huehne wrote: > On 01/15/2014 12:18 PM, Jaime Prilusky wrote: >> I would like to have a message “Working …” w

[Jmol-users] display echo while calculating

ial way is correct; just add a REFRESH command prior to that if you want the model to be displayed during the alert. On Mon, Jan 13, 2014 at 6:21 AM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: Even if adding refresh to Jmol.script, the alert happens before the m

Re: [Jmol-users] platformSpeed on mouse zoom CORRECTION

ust curious. Jaim On Mon, Jan 13, 2014 at 7:02 AM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: On 14.0.5 , rendering with HTML5, set platformSpeed works perfect when the zooming action is driven by shift-cursor up/down. It does not work when zooming with the m

Re: [Jmol-users] Jmol.script() not returning

the function with no argument. Otis -- Otis Rothenberger o...@chemagic.com<mailto:o...@chemagic.com> http://chemagic.com On Jan 13, 2014, at 7:36 AM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: Have you tried it on 14.0.5 with HTML5? Jaim On Jan 13, 2014, at 2:26 PM

Re: [Jmol-users] Jmol.script() not returning

Have you tried it on 14.0.5 with HTML5? Jaim On Jan 13, 2014, at 2:26 PM, Otis Rothenberger mailto:osrot...@chemagic.com>> wrote: I use the javascript command frequently. From past experience, arguments in functions can cause issues. At a minimum, I would put quotes around the javascript itse

Re: [Jmol-users] Jmol.script() not returning

Even if adding refresh to Jmol.script, the alert happens before the model gets loaded: Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;'); alert(“Back”); Jaim On Jan 13, 2014, at 2:03 PM, Angel Herráez wrote: > I agree that the use of refresh is often needed; that's my

Re: [Jmol-users] Jmol.script() not returning

he same for both Java and HTML5 modes. Bob On Mon, Jan 13, 2014 at 5:12 AM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: We used to have a call to javascript as part of the script text, but that is not longer working: Jmol.script(jmol0,'load data/123.pdb; javascrip

[Jmol-users] platformSpeed on mouse zoom CORRECTION

On 14.0.5 , rendering with HTML5, set platformSpeed works perfect when the zooming action is driven by shift-cursor up/down. It does not work when zooming with the mouse wheel. Jaim -- CenturyLink Cloud: The Leader in Ent

[Jmol-users] platformSpeed on mouse zoom

It would be good for set platformSpeed to apply also when zooming in or out the model. It does work as advertised on rotation. Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses

[Jmol-users] Jmol.script() not returning

We used to have a call to javascript as part of the script text, but that is not longer working: Jmol.script(jmol0,'load data/123.pdb; javascript alert(“Back”);’); On the following example, the alert() happens before the script gets executed. The threading mechanism plays here against us. Jmo

Re: [Jmol-users] JSmol menu doesn't open

Are you in any way disabling or capturing events from mouse right-click ? Jaim On Jan 7, 2014, at 5:56 PM, Eric Martz wrote: > I cannot seem to get the JSmol menu to open in 14.0.3 e.g. > > http://firstglance.jmol.org/fg.htm?mol=1d66&use=html5 > > Any suggestions? > > Eric > > > > >

Re: [Jmol-users] Jmol 14.x.4 released

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.0/Version%2014.0.4 Not much here, but one important fix for ribbons, so if you do anything with proteins be sure to download this modification in 14.0 and 14.1. Bob Thank you. Fixed the misplaced rockets elements. PSE conversion work

[Jmol-users] 14.0.3 misplaced elements rockets

Jmol 14.0.3 shows misplaced elements when requesting rockets representation on 3STU Try the following, on either Jmol.jar or JmolApplet: file -> get PDB -> 3STU Select -> All Style -> Structures -> Rockets Jmol version 13.2.8 renders Ok. Jmol 14.0.3 shows misplaced elements. Jaim -

[Jmol-users] jvxlInvalidatedVertexData on show isosurface for 14.1.3

3rec; isosurface solvent; show isosurface; Jaim __ Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113

Re: [Jmol-users] isosurfaceData as JVXL string

vaScript, you could use: var xmlData = Jmol.evaluate(jmolApplet0, "script('show isosurface')") On Sat, Dec 28, 2013 at 1:31 PM, Jaime Prilusky mailto:jaime.prilu...@weizmann.ac.il>> wrote: What's the correct syntax to get from JSmol applet the isosurface data

[Jmol-users] isosurfaceData as JVXL string

What's the correct syntax to get from JSmol applet the isosurface data as JVXL string in javascript? I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0, "isosurfaceData") could do. Thank you in advance, Happy Holidays, Jaim -

[Jmol-users] isosurfaceData as JVXL string

What's the correct syntax to get from JSmol applet the isosurface data as JVXL string in javascript? I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0, "isosurfaceData") could do. Thank you in advance, Happy Holidays, Jaim --

Re: [Jmol-users] Platform-specific switch Java/HTML5

On Dec 12, 2013, at 6:19 PM, Robert Hanson wrote: > It's still there. Should work. RCSB uses this. Proteopedia, I think. On Proteopedia we use MobileDetect.php ( http://mobiledetect.net ) to send back to the user a proper configuration based on the platform. It seems that checking for Java can'

Re: [Jmol-users] PHP server

/Teaching_Strategies_Using_Proteopedia Please feel free to write if you have questions or need any help. Regards, Jaim __ Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.a

Re: [Jmol-users] local testing ready iteration 1,203,304,440

Rolf, Maybe the way I work on Proteopedia might help you. I have a CGI script that sends the content of the structure files to Jmol/JSmol: getlateststructure The script gets as a parameter the name of the file to return or the PDB id for that file, and looks for the ending “.gz” on that param

Re: [Jmol-users] Please test (2)

On Nov 27, 2013, at 12:30 AM, Robert Hanson wrote: > Yes, it's related to the fact that BondSet is an "inner class" of Bond. > Something is as happening out of order. Utlimately, Bond.BondSet is created > just fine. Very curious! Found in your code a few other calls to Clazz.superConstructor( t

Re: [Jmol-users] (no subject)

Chrome 31.0.1650.57 and Safari Version 7.0 (9537.71) on Mac 10.9 also gave format error, most probably the same you got. Simply Javascript on Firefox (Gecko engine) runs under different rules than on Chrome/Safari (WebKit engine). Jaim On Nov 26, 2013, at 7:14 PM, pino.stricc...@libero.it wro

Re: [Jmol-users] Please test (2)

The “Bond/BondSet.js” error appears also on Mac Firefox 25.0.1, but the applet continues working. You may see error reports with Firebug. This might come from lines like this one in Bond.js and other files: J/modelset/Bond.js:Clazz.superConstructor (this, J.modelset.Bond.BondSet, []); The call

Re: [Jmol-users] Please test (2)

Thank you for this release. Runs Ok on Mac 10.9 FFox 25.0.1 Unable to convince Safari 7.0 to run a local applet. Also tried with a Proteopedia exported page and (again FFox on Mac) it works great!! Jaim On Nov 24, 2013, at 8:47 AM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: Here's the

Re: [Jmol-users] Important Java changes - January 2014

Excellent. Will this also be true for the applet version? In one year from now we’ll see if Java's still required, and, if the renewal requires a payment, find sources for that. Jaim __ Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of B

Re: [Jmol-users] Using jsmol in MediaWikis

I'm currently improving and simplifying the JSmolExtension for MediaWiki I developed and currently using in Proteopedia.org. Hope to release the new version next week. Please be patient. Regards, Jaim __ Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Depa

Re: [Jmol-users] Recommendations for Jmol web hosting

Art, Have you considered http://proteopedia.org ? Jaim On Sep 18, 2013, at 12:42 AM, Cox, Arthur G. wrote: > I'd like to publish a few web pages with Jmol applets, but don't necessarily > want to use my own computer. > > Does anyone have a recommendation for a hosting company that supports ja

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