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

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

[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

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

Congratulations!! On 23 Mar 2017, at 16:22, Robert Hanson > 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

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 > 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?

[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

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 > wrote: I have

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

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

[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 > wrote: I don't think capture should work from JmolData. Try Jmol.jar Thank you, Jaim -- What NetFlow Analyzer can do for you?

[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

[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:

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 > wrote: Download Jmol-14.4.1_2016.01.04-binary.zip (18.2

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

Can you please implement defaults again? Jaim On 3 Jan 2016, at 3:33 PM, Robert Hanson <hans...@stolaf.edu<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 <jaime.prilu...

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

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

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 > wrote:

Re: [Jmol-users] test please

__ Dr Jaime Prilusky R 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 2015, at 1:37

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 thr...@gmail.com 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;

Re: [Jmol-users] Chemical elements and counts

On Jul 15, 2015, at 11:46 PM, Robert Hanson hans...@stolaf.edu 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 with

[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

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 brentonho...@ymail.com wrote: Hi, I have been using the JSmol extension for

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 RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science

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

Re: [Jmol-users] visible vs. restrict

On Sep 18, 2014, at 8:18 AM, Robert Hanson hans...@stolaf.edumailto: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.

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 gp...@ub.edumailto: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.

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

the zip 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 jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote

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 hans...@stolaf.edumailto:hans...@stolaf.edu wrote: [Sorry for the blog-like nature of this message.

[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

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 m.n.w...@kent.ac.ukmailto: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

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 m.n.w...@kent.ac.ukmailto: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

Re: [Jmol-users] inactive mouse with WebGL

On Sep 3, 2014, at 3:37 PM, Robert Hanson hans...@stolaf.edumailto: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

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 hans...@stolaf.edumailto: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

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,

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

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

Re: [Jmol-users] applet with multiple isosurfaces

:25 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: On Aug 16, 2014, at 9:24 PM, Angel Herráez angel.herr...@uah.esmailto:angel.herr...@uah.es wrote: There is isosurface list, which returns the IDs and some data, but not the jvxl data You are giving

[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

Re: [Jmol-users] applet with multiple isosurfaces

On Aug 16, 2014, at 9:24 PM, Angel Herráez angel.herr...@uah.es 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

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

u v w x y z 0 1 2 Bob On Thu, Aug 14, 2014 at 3:11 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto: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 working on 4v8m, one of the ‘large structures

Re: [Jmol-users] bug fixes

On Aug 12, 2014, at 9:05 PM, Robert Hanson hans...@stolaf.edumailto: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

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 hans...@stolaf.edumailto:hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.5_2014.08.09.zip . bug fix: CIF

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 hans...@stolaf.edumailto:hans...@stolaf.edu wrote: I have just released

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 hans...@stolaf.edu wrote: Please send me a link to

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 hans...@stolaf.edumailto:hans...@stolaf.edu

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 hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

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 rhue...@fli-leibniz.de 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

[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?

Nameserver is unable to translate www.rsquarelabs.comhttp://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 raviraja.mer...@gmail.commailto:raviraja.mer...@gmail.com wrote: Yes, the url is correct, I

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

is available on WebGL at this time. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD 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, http

Re: [Jmol-users] Jmol 14.1.14 released

On Apr 26, 2014, at 6:58 AM, Robert Hanson hans...@stolaf.edumailto: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.nethttp://sourceforge.net? The latest version I’m able to access is

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 ema...@microbio.umass.edu 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

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

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

[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,

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

, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: 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

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

? 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

[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

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 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

Re: [Jmol-users] display echo while calculating

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 jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: I would like to have a message “Working …” while Jmol

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 rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime

Re: [Jmol-users] display echo while calculating

...@stolaf.edumailto:hans...@stolaf.edu 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 jaime.prilu

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 jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Thank

Re: [Jmol-users] display echo while calculating

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 jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Thank you for the new version. I would say that now

[Jmol-users] display echo while calculating

initial 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 jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Even if adding refresh to Jmol.script, the alert

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 rhue...@fli-leibniz.de wrote: On 01/15/2014 12:18 PM, Jaime Prilusky wrote: I would like to have a message

[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 jaime.prilu...@weizmann.ac.il wrote: Thank you for a prompt reply, but it’s not working for me on 14.0.5. The command waitmessage

[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.

[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] 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

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

is the same for both Java and HTML5 modes. Bob On Mon, Jan 13, 2014 at 5:12 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto: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

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 angel.herr...@uah.es wrote: I agree that the use of refresh is often

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 osrot...@chemagic.commailto: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

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

? Just curious. Jaim On Mon, Jan 13, 2014 at 7:02 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto: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

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 ema...@microbio.umass.edu wrote: I cannot seem to get the JSmol menu to open in 14.0.3 e.g. http://firstglance.jmol.org/fg.htm?mol=1d66use=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

[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

; isosurface solvent; show isosurface; Jaim __ Dr Jaime Prilusky Head Bioinformatics RD 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 OCA, http

Re: [Jmol-users] isosurfaceData as JVXL string

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

[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 hans...@stolaf.edu 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

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 RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.il

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

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

On Nov 27, 2013, at 12:30 AM, Robert Hanson hans...@stolaf.edu 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

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 hans...@stolaf.edumailto:hans...@stolaf.edu

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 RD Bioinformatics and Data Management Department of Biological Services

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 RD Bioinformatics and Data Management Department

Re: [Jmol-users] Jsmol: Problem downloading png/jmol

Add php to the file location. Change the path to /jmol/jsmol/php/jsmol.php Jaim On Sep 17, 2013, at 1:57 PM, björn bjoern-oliver.goh...@charite.de wrote: Hello, i use jsmol on my website. Everthing works fine but i cannot download the view anymore (as png or jsmol). I changed nothing.

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 java

[Jmol-users] Jmol 13.0.1 connect_atoms error

Is this structure not longer valid? We have several scripts using it in the past and things were Ok. Today, running on Jmol 13.0.1 it returns parsing error. Does it works Ok on previous versions of Jmol? On newer versions? Jaim data connect; connect_atoms 91 198040960.4

Re: [Jmol-users] Jmol 13.0.1 connect_atoms error

calculated for this bond (only relevant for hydrogen bonds) 6 is the human-readable meaning of the coded bond type (ignored) Bob On Mon, Sep 16, 2013 at 1:45 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Is this structure not longer valid? We have several

[Jmol-users] arbitrary hover string for each atom

Is there a way to set an arbitrary string for each atom to be displayed when hovering the atom? A real arbitrary string, not composed out of atom number, element, etc? Jaim -- Learn the latest--Visual Studio 2012,

Re: [Jmol-users] arbitrary hover string for each atom

Hola Angel, Thank you for a prompt reply. I was looking for an extension of the following way of setting properties for individual atoms. Besides spacefill and color, I would like to have an individual hover arbitrary string for each atom. select atomno=11; spacefill 4.00; color [xFF66FF]

Re: [Jmol-users] arbitrary hover string for each atom

This looks interesting. Thank you again, Jaim On Sep 1, 2013, at 1:06 PM, Angel Herráez angel.herr...@uah.es wrote: I found that hover can reflect the label text, and label can indeed be assigned per atom. So, as long as you don't need to use labels, this seems to do the trick: hover

Re: [Jmol-users] bugs in version 13

On Jul 24, 2013, at 2:47 PM, Robert Hanson wrote: OK, this is fixed. http://chemapps.stolaf.edu/jmol-13.3.3_2013.07.24.zip No visible side effects at http://ispcsrv.weizmann.ac.il/a2jmolb/browse Jaim -- See everything

Re: [Jmol-users] a new logo-banner-icon for Jmol + JSmol

Very nice!! Jaim __ Dr Jaime Prilusky Head Bioinformatics RD 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 OCA, http://oca.weizmann.ac.il

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