Re: [Jmol-users] Mac -- Latest java try

According to Philip Bays: If I am reading your note correctly, you are confirming my observation. Now I need a way to get back to java 1.4.2 without the update 1. or we all need to find where the problem is and have Jmol.js back on track. Jaim -- Dr Jaime Prilusky

Re: [Jmol-users] color temperature on an absolute scale

-of-scale point. By requesting a non standard temperatureRange we can filter the display based on temperature values. Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot

[Jmol-users] no downgrading Java on Mac OS X

way of doing so is to reinstall the entire system. Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959

Re: [Jmol-users] Multiple models

.pdb file. You can then restrict the display to a single model by using the 'frame' command. Thanks for the tip. I would certainly try this. I have currently the small problem of a too updated Java on Mac OS X now :-( Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD

Re: [Jmol-users] Jmol10pre13 release

According to Miguel: Jmol version 10 prerelease 13 was released on Sun 15 Aug 2004. * support for color by temperature Great!!. Thanks a lot. Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science

Re: [Jmol-users] Multiple models

a little longer, but switching between conditions is very fast. Take a look at http://bip.weizmann.ac.il/oca-docs/jmoltest/jmolModels.html ( For slow sites or large files it could be good to have a progress bar for loading model ... ) Jaim -- Dr Jaime Prilusky | [EMAIL

[Jmol-users] Jmol and Java 1.4.2 on Mac OS X

with the problematic Java 1.4.2 update on Mac OS X as long as you avoid Jmol.js Maybe the whole problem resides in the way Jmol.js finds and manages applets in the page. Take a look to http://bip.weizmann.ac.il/oca-docs/jmoltest/jmol2.html Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD

Re: [Jmol-users] Jmol and Java 1.4.2 on Mac OS X

is to forget about any JavaScript calls that try to invoke applet methods and stick to the JmolAppletControl. Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel

Re: [Jmol-users] MacOSX Java problems

button created by jmolRadioGroup([ [frame 1;, positive,checked], [frame 2;, negative], ]); jmolApplet0 will try to run: -frame 2; - src/plugin/src/macosx/native/apple/applet/JavaWebKitView.m:655: failed assertion `pthread_main_np() == 0' Jaim -- Dr Jaime Prilusky

[Jmol-users] another Jmol based site

Jmol to rotate itself the molecule and place the 'hotspot' facing the user. Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8

Re: [Jmol-users] PDB and SCOP

on the fly a 'rasmol' script from PDB abd SCOP information that is then given to Jmol for display. The script source is also available on each OCA Atlas page, under the section 'Structure-derived information' Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics

Re: [Jmol-users] My protein dipole moment server now uses jmol

browser (Firefox 1.0.7, SuSE Linux 9.3). -- Dr Jaime Prilusky | [EMAIL PROTECTED] Head of Bioinformatics ISPC| RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8

[Jmol-users] Jmol's single letter amino acid code

Hi, I have problems in using %m for displaying a label with a single letter amino acid code. On Jmol 10.00.48, %m expands into X while %n correctly displays the three-character name. Is this not the correct placeholder for expansion? Thanks in advance, Jaim -- Dr Jaime Prilusky

Re: [Jmol-users] Jmol's single letter amino acid code

According to Bob Hanson: fixed %m now expands to the single character representation of the 20 amino acids and ? otherwise. Great!!. Thanks for a prompt reply. Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] Head of Bioinformatics ISPC| RD Bioinformatics

Re: [Jmol-users] request for comment -- draw

According to Bob Hanson: http://www.stolaf.edu/people/hansonr/jmol/test/json/pmesh.htm draw anyIdentifier optional scale atom expression or xyz-coordinate Great! It looks good. Nice demo page. Have you considered allowing to add the 'arrow' tip to the line? Jaim -- Dr Jaime Prilusky

Re: [Jmol-users] Jmol and mmCIF

-- Dr Jaime Prilusky | [EMAIL PROTECTED] Head of Bioinformatics ISPC| RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 info URL http

[Jmol-users] altLocation special entry

While developing Jmol support to altLocations, you may want to try 1zir (X-RAY, resolution 1.36). this might be one of the PDB entries with largest number of alternative atom locations. http://bip.weizmann.ac.il/oca-bin/altloc?al=1id=1zir Jaim -- Dr Jaime Prilusky

[Jmol-users] altLocations over whole PDB

At the bottom of the page http://bip.weizmann.ac.il/oca-bin/altloc you will find a link to a plain text report of altLocations on PDB entries. The collecting script's still running, but the scan already covers over 31,700 PDB files, which is about 84% of the PDB. Jaim -- Dr Jaime Prilusky

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] 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] 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_2014.07.29.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] 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] 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] 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] 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

[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] 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

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] 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

[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] 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.

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] 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] 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] 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] 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] 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

[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] 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

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] 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-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:

[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] 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] 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

[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] 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

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

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] 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?

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));

[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] 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

[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] 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] 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

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