Re: [Jmol-users] File name and version number
That is correct. And since most of the daily work is done on 14.3, not 14.2, it should not be too often that 14.2 gets updated. Bob -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Cross Domain Load and Help Request
RCSB definitely does allow all access. Using that on Jsmol.htm right hand column. Direct access via AJAX. No server need except for MSIE Sent from my stupid iPhone On Dec 30, 2013, at 1:09 PM, Otis Rothenberger osrot...@chemagic.com wrote: OK, Thanks. Are the following observations correct? Resolver does this. PubChem does this. RCSB does not do this. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Dec 30, 2013, at 12:45 PM, Robert Hanson hans...@stolaf.edu wrote: as long as the server is allowing full access via its headers. On Mon, Dec 30, 2013 at 11:42 AM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, I could figure this out by trial and error, but you probably know the answer. Will JSmol load sdf text files cross domain? Otis -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Partially unable to load an external html file that contains JSmol scripts
How exactly are you loading HTML into the div? Does each page have its own JSmol.min.js? URL so we can see what it is doing? Iframes will take special consideration if the button calls are across frames. Sent from my stupid iPhone On Dec 26, 2013, at 1:42 PM, Romuald Poteau romuald.pot...@univ-tlse3.fr wrote: Dear Angel, thanks for answering, but your suggestion does not solve this problem. See below Regards, Romuald Le 26/12/2013 12:59, Angel Herráez a écrit : Hello, Romuald There may be several issues there, but there must be a simple solution. and a div container in which external html pages are loaded. Is that an IFRAME? Otherwise, I am not sure how an external page may be loaded into a div, that could be donde by the jQuery library but it is not straightforward. Actually, loading an html file into a div container does work, and it is is still the case when I load external html pages that call jsmol. Every html instruction is well interpreted, with the exception of the pages that contain jsmol controls (buttons or checkboxes). As far as I have read on forums, it seems to be possible to load external html files inside div containers. I have seen other possibilities with iframes, but I did not succeed either. If you do use an iframe, then you can test your pages on their own before loading them as secondary pages. But there should be no difference. I have tested the external pages individually (adding the call to jsmol.min.js, vide infra) and this case everything appears, including the jsmol applet and the control buttons. Important: where do you issue the Jmol commands/links from? From the main page or from the secondary ones? From the secondary one. with links (such as a href=javascript:Jmol.script(JmolPG,'select *;cartoons off;spacefill only')spacefill/a) There is a fundamental difference here. Script just sends instructions to Jmol, while the others create controls in the page. That may be why the first works for you but not the others. , the applet and the rest of the external file appear in the div container, as desired. That's important, meaning your JSmol setup is correct. I would have expected that you need to call Jsmol.min.js in the secondary page. I can see you found the contrary, don't know why. Have you tested if the checkboxes etc work when you add that? - without the call to jsmol.min.js in the external file : everything works fine with links only, but the checkbox is then the only thing that appears when it is additionally used - with a call to jsmol.min.js in the external file : the links appear on the page, but it not the case anymore of the jsmol applet (and of the checkbox, of course) Anyway, the problem may be that the Jmol object is not created --so it seems-- until the page has finished loading, but the code for the controls is being run before, so maybe they fail because the Jmol object does not exist yet. That is the reason why I have tried to define an asynchronous loading, but I am not sure that I really know how to do that Oh, well, you have defined JmolPG in advance, so that should not be the case. Maybe try these changes: give some value to the variable, then use the variable and not the text string: var JmolPG = JmolPG; // within INITIALIZE JMOL $(#JmolappPG).html(Jmol.getAppletHtml(JmolPG, InfoPG)) // within $(document).ready(function() (Not sure about that, but could be the reason) Good try, but unfortunately it is not the reason. This does not change anything. -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol popup menu on an iPad
Doesn't clicking on the logo work? Sent from my stupid iPhone On Dec 25, 2013, at 12:31 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: Whilst the JSmol menu on a “normal” computer pops up nicely, there is no “right click” on a tablet. Is it possible to invoke (set up?) in some other way. Please excuse if its a FAQ. -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Parsing JME string
Fixed just this morning. See http://chemapps.stolaf.edu/jmol/zip Sent from my stupid iPhone On Nov 4, 2013, at 12:27 PM, Otis Rothenberger osrot...@chemagic.com wrote: Right you are on PubChem. When I look at the sdf for glucose, it's loaded with coordinate files! The 13.3.9 thing is real, however. Version 13.3.9 loads no double bond for a C=C SMILES query to Resolver. Version 13.3.3 gets it right. Same for name query. Carvone is OK with 13.3.3 - not so with 13.3.9. Since I'm working with a version link that Bob sent, I guess I should be more specific: 13.3.9_dev_20113.11.02 Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Nov 4, 2013, at 3:03 PM, Angel Herráez angel.herr...@uah.es wrote: 3) PubChem loads are erratically funky. I got several glucose models loaded by one glucose query. This could be PubChem. I'll check it out/ Otis, my experience is that PubChem returns a multimodel sdf when it has several hits for a name. Sometimes they are equivalent, other times they are variants --like different ionization states of an amino acid. Check JSmol popup to see if there are more than 1 frames 4) http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm appears broken on Safari and Chrome. My Chrome Win7 fails to display the JSME object (I think I saw it working yesterday) and reports an alert The global function jsmeOnLoad is not defined or there might be a syntax error in your javascript code -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] XYZ files with unit cell
Check the LOAD command docs. Jmol can add a unit cell to any file input. And add symmetry operation is desired. Very simple with xyz files. Your cored need to be Cartesian. Jmol will transform those into fractional coord prior to applying symmetry. Sent from my stupid iPhone On Nov 4, 2013, at 2:07 PM, Kurt Fredrickson kdf...@physics.utexas.edu wrote: Hi there, I just started using Jmol a week ago, and it is very useful to see vibrations! Right now I am inputting everything with an XYZ file. Is there any way to add a rhombohedral unit cell frame to the vibration animations? Right now, for my crystal I just have my atoms floating in space. captainalright -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] How-to wiki page
Any interest is starting a simple How-To page on the wiki for any number of simple to hard tasks? Could serve as a script or function source. Just search, cut, and paste. Volunteers? Bob Sent from my stupid iPhone -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol bug?
Test2.htm doesn't use controls. See testcb.htm in most recent version. JSmolControls.js Sent from my stupid iPhone On May 17, 2013, at 8:44 AM, Spinney, Richard rspin...@chemistry.ohio-state.edu wrote: I have been trying to get JSmol to work and have had a couple of problems. I have a page (build off of the test2.htm demo) that uses the Java applet (https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info.php) , while this displays the PDB and JVXL files correctly, the controls do not appear. I get an error message of “error Jmol.controls undefined” and links to JSmolApi.js. These lead to lines in the code of: “return Jmol.controls._getMenu(….)”; and “return Jmol.control._getCheckbox(…)”. I copied this page (https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info-b.php) and changed it to use HTML5 (JSmol.min.js). Again the PDB files are read ok but now the JVXL files don’t work while the controls (menu and checkboxs) do work. The error message on this is “g._applet is null” and points to the JSmol.min.js file. I am at a loss on what is wrong here; the calls to the controls are identical between the two pages, as are the load JVXL calls. It does use the serverURL to call jsmol.php and it is version 13.1.16_dev_2013.5.15. Any help would be appreciated. Thanks, Rick -- Dr. Richard Spinney Department of Chemistry and Biochemistry The Ohio State University 120A Celeste Laboratory 120 West 18th Ave Columbus, Ohio 43210 email: rspin...@chemistry.ohio-state.edu Phone: (614) 247 - 6847 Fax: (614) 292 - 1685 -- AlienVault Unified Security Management (USM) platform delivers complete security visibility with the essential security capabilities. Easily and efficiently configure, manage, and operate all of your security controls from a single console and one unified framework. Download a free trial. http://p.sf.net/sfu/alienvault_d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- AlienVault Unified Security Management (USM) platform delivers complete security visibility with the essential security capabilities. Easily and efficiently configure, manage, and operate all of your security controls from a single console and one unified framework. Download a free trial. http://p.sf.net/sfu/alienvault_d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] floating window
Absolutely. It's already in a div so it should be simple enough to do that. Sent from my stupid iPhone On Apr 26, 2013, at 4:20 PM, Pshemak Maslak p...@chem.psu.edu wrote: Can JSmol instance be displayed (and be functional) in a floating window (pop-up window)? I do not know the correct terminology, I do not mean a new browser window, but one than can only float within the browser, like those generated, for example by HighSlide (http://highslide.com/) -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] light and speedy
Wonderful. Please keep me in the loop as you modify JSmolTM. Probably best to
call it something else. JSmolCIF or something like that.
Sent from my stupid iPhone
On Mar 30, 2013, at 4:16 AM, s...@publcif.co.uk wrote:
Yes, a CIF reader is on its way (actually part of something else I'm
working on). That said, I'd prefer to use one app ('jmol') so will
certainly have a look
at JSmolTM...
Cheers
Simon
Quoting Robert Hanson hans...@stolaf.edu:
It would be nice to have a CIF reader; createRadialGradient() is great.
I'll look into that. If you would like to help, Simon, feel free to adapt
JSmolTM.js to incorporate some of this.
Bob
On Fri, Mar 29, 2013 at 10:52 AM, s...@publcif.co.uk wrote:
Just found this while looking for the answer to another unrelated question
(see below). Coincidentally I've been working on much the same sort of
thing -
i.e. a quick 'first view' with the option to load the full Jsmol on demand,
for use on the IUCr's 3d view pages. Its based on GLmol as a model -
basically I've pinched the 'know how' with respect to manipulating a
3d model on the 2d canvas - and I will probably pinch stuff from
elsewhere before I'm done :-)
but I hope that it at least demonstrates that you can still get some
quite nice graphics using the 2d canvas and minimal functionality.
Anyway, there's a version at http://cif.publcryst.co.uk/cifmoldb/smol/
if you're interested.
The original question was related to jsmol - does jsmol add some
properties to the javascript array object?
Cheers
Simon Westrip
Quoting Robert Hanson hans...@stolaf.edu:
How about this?
http://chemapps.stolaf.edu/jmol/jsmol/lite3.htm
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [Jmol-users] light and speedy
Ps. If you could make what you do an extension of JSmolTM that would even be
better. In other words just modify the functions that you need to.
Sent from my stupid iPhone
On Mar 30, 2013, at 7:45 AM, Bob Hanson hans...@stolaf.edu wrote:
Wonderful. Please keep me in the loop as you modify JSmolTM. Probably best to
call it something else. JSmolCIF or something like that.
Sent from my stupid iPhone
On Mar 30, 2013, at 4:16 AM, s...@publcif.co.uk wrote:
Yes, a CIF reader is on its way (actually part of something else I'm
working on). That said, I'd prefer to use one app ('jmol') so will
certainly have a look
at JSmolTM...
Cheers
Simon
Quoting Robert Hanson hans...@stolaf.edu:
It would be nice to have a CIF reader; createRadialGradient() is great.
I'll look into that. If you would like to help, Simon, feel free to adapt
JSmolTM.js to incorporate some of this.
Bob
On Fri, Mar 29, 2013 at 10:52 AM, s...@publcif.co.uk wrote:
Just found this while looking for the answer to another unrelated question
(see below). Coincidentally I've been working on much the same sort of
thing -
i.e. a quick 'first view' with the option to load the full Jsmol on demand,
for use on the IUCr's 3d view pages. Its based on GLmol as a model -
basically I've pinched the 'know how' with respect to manipulating a
3d model on the 2d canvas - and I will probably pinch stuff from
elsewhere before I'm done :-)
but I hope that it at least demonstrates that you can still get some
quite nice graphics using the 2d canvas and minimal functionality.
Anyway, there's a version at http://cif.publcryst.co.uk/cifmoldb/smol/
if you're interested.
The original question was related to jsmol - does jsmol add some
properties to the javascript array object?
Cheers
Simon Westrip
Quoting Robert Hanson hans...@stolaf.edu:
How about this?
http://chemapps.stolaf.edu/jmol/jsmol/lite3.htm
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
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Re: [Jmol-users] JSmol upload
Traveling but will upload later today. Sent from my stupid iPhone On Mar 29, 2013, at 10:34 AM, Charles Harrison Shubert cshub...@mit.edu wrote: I'm having the same experience. --Chuck On Mar 29, 2013, at 10:14 AM, Daniel Barich wrote: I still can't open this link in Windows Explorer either. It says the file is invalid. On Thu, Mar 28, 2013 at 2:59 PM, Oliver Stueker revilo2...@users.sourceforge.net wrote: Hi, The jsmol.zip that I have just downloaded seems to be broken: $ unzip jsmol.zip Archive: jsmol.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive. unzip: cannot find zipfile directory in one of jsmol.zip or jsmol.zip.zip, and cannot find jsmol.zip.ZIP, period. The file's timestamp on the webserver is evening of Mar 25th ( ~6:30 pm Central time if I converted the timezone correctly). Oliver On Mon, Mar 25, 2013 at 3:00 PM, Robert Hanson hans...@stolaf.edu wrote: If you are doing anything with JSmol, I suggest uploading http://chemapps.stolaf.edu/jmol/jsmol.zip once more. It's got some changes in the way the .js files are organized and fixes some problems I introduced yesterday. Most importantly, if you are not loading binary files (PNGJ, ZIP, GZ, Spartan, for instance), and you use jQuery already on your page, this allows you to bypass JSmoljQuery.js and use what you are using already. That file is JSmol.min.nojq.js, and it is only 130K in size. This build also includes JSmol.lite.js (no jQuery) and JSmol.lite.jq.js (with jQuery) that are used in http://chemapps.stolaf.edu/jmol/jsmol/liteNCI.htm and it adds the jquery subdirectory, which includes the latest jQuery 1.9 library, which JSmol seems to be compatible with (but still needs the extensions we add for binary file transfer, MSIE cross-domain AJAX, and mouse binding). Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Own the Future-Intel(R) Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Own the Future-Intel(R) Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Own the Future-Intel(R) Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2___ Jmol-users mailing list
Re: [Jmol-users] Are SMILES communications private?
So in short. They do not have to have any database structure to convert SMILES to 3D. I don't know the algorithm used. -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Adding bonds explicitly for xyz format
David, please switch to the developer list. This is the user list. Not a big deal. Sent from my stupid iPhone On Feb 3, 2013, at 1:00 PM, N David Brown hubd...@gmail.com wrote: Hi Angel, Yes I'm aware xyz doesn't provide connectivity information, that's why I disabled autobond so non were predicted. I'm circumventing the CACTVS system so SMILES structures can have positions generated locally instead using a handcrafted method. Maybe mol format will solve the problem then. I'll try generating that and specify bonds explicitly there. Thank you for suggesting this. David On 3 February 2013 17:57, Angel Herráez angel.herr...@uah.es wrote: Hi David I don't know about doing this at the development level, but with scripting he regular app or applet: xyz format does not provide connectivity (bonds) mol format is also quite simple and does include bond information -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How to be as safe as possible with Java
The only thing I would add is that disabling java in firefox is no longer necessary. The browser will simply wait to start it until you request it to do so. I now that this breaks frameless (hidden) applets. Sent from my stupid iPhone On Feb 2, 2013, at 7:50 PM, Eric Martz ema...@microbio.umass.edu wrote: I have gathered some information on strategies for being safe when using Java. In view of recent developments with Java (see Java is a security threat) http://proteopedia.org/wiki/index.php/Java#Java_is_a_security_threat the new section on safety is a 'must read' for Jmol users. http://proteopedia.org/wiki/index.php/Java#How_to_be_as_safe_as_possible_with_Java Proteopedia is a wiki so please feel free to improve this article -- or send suggestions directly to me. Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://Martz.MolviZ.Org Top Five 3D MolVis Technologies http://Top5.MolviZ.Org FirstGlance, used by Nature - http://firstglance.jmol.org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.molviz.org Interactive Molecules in Public Spaces http://MolecularPlayground.Org Workshops: http://workshops.molviz.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Fwd: Jmol iPad app
Begin forwarded message: From: Robert Hanson hans...@stolaf.edu Date: January 24, 2013 4:14:54 PM GMT+02:00 To: undisclosed-recipients:; Subject: Jmol iPad app Dear Jmol users, The Jmol iPad app. The obvious next step, right? So, I'd like to start a discussion with Jmol users and Jmol page developers. IF we were to work on an iPad app, what would it take to make it the killer app that would equal Jmol as the killer applet.? What is it that makes Jmol/JSmol unique as an applet/JavaScript library? Some ideas: -- scriptability - One of Jmol's key features is its high-level scripting language that lets both web developers and (knowledgeable) web users interact with it in ways that Jmol developers ourselves haven't conceptualized. -- adaptability - Web page developers can put the applet in a context of their own choosing, with all sorts of interesting content around the applet that makes this particular page for a page visitor a particularly interesting and unique interactive experience. Of these two, the first is probably very easy to implement in a Jmol app. What about the second? My thinking goes like this: There are three groups: -- Jmol code developers (meaning those of us writing the Java code) -- Jmol page developers (those using Jmol for their own creative ends using the code and interfaces developed by the Jmol code developers) -- Jmol users (those who visit the pages created by the Jmol page developers) If you think about it, that second category is what makes Jmol unique. There are programs out there like pyMol and Mercury, and others that are created by code developers and used by users. But what other programs involve the middle category? I think of Adobe Flash as something like that. Is that it? Jmol is more like Flash than it is like pyMol? Jmol provides the technology that page developers can use to design a unique experience for their page's visitors. This is what makes Jmol quite different from, say, a JavaScript library that allows one to pop up a 3D model on a page and pretty much leaves it at that. That's what the combination of controls and high-level scripting gets us. Right? It seems to me, that if a Jmol app were to be valuable, it would still involve this triad of involvement. Wouldn't it be a waste of time to develop just another molecule viewer even if it is Jmol? That would be more like morphing the Jmol application into an iPad app, not the Jmol applet. But how would we maintain that middle tier? One idea: The Jmol app by itself does little. But what it does do is interact with a cloud-based server (or perhaps any web site?) to pull context down and surround the viewer window with that context. So what a Jmol context developer (I can't think of the analogy in terms of iPad apps, because I don't think there is this category yet) would do would be to develop an actual web page with an actual computer using a standard browser and then through some sort of registered process upload, perhaps, a link to that page along with a thumbnail image and a set of searchable keywords or abstract. While that page could be viewed on the browser, some version of it could also be viewed within the Jmol app. When the Jmol app is opened, it would be like getting an index to all the Jmol pages in existence -- those adapted to this iPad idea. The user would select the [what? -- applet? (does sound about right...)] of choice and off they go. That applet would pull context from the web, surround the Jmol window with that context, and there you have it. What do you think? Feedback? Suggestions? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] R: Re: JSmol Question
Definitely. Use Firefox though. Make sure the file name indicates it's nature. So eg 1crn.pdb vs 1crn.pdb.gz. On Jan 25, 2013, at 12:17 AM, pino.stricc...@libero.it pino.stricc...@libero.it wrote: Is it still possible to create a Jsmol page locally, make the changes and then upload it? With one of last version i downloaded i receive message error unrecognized file format. Pino -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] disable pop-up menu in JSmol?
It's the same scripting language. Sent from my stupid iPhone On Jan 14, 2013, at 3:26 AM, Angel Herráez angel.herr...@uah.es wrote: Quick question: Can the (recently implemented) pop-up menu in JSmol be disabled/enabled? It would be good to have that feature and, if possible, to use something similar to the applet method, i.e. set disablePopupMenu TRUE in script Another choice would be some tag in the Info variable -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol | Context Menu for JSmol
What's the latest? I'd like to test this some tomorrow.
Sent from my stupid iPhone
On Dec 19, 2012, at 5:56 PM, Michael Evans evan...@illinois.edu wrote:
Guess I was feeling lazy when I wrote menuRemoveItem...it's an easy fix. The
array.splice(indexToStart, numberOfElements) function is perfect for it. Now
fixed; see the new method below.
menuRemoveItem: function(menu, index) {
if(index = 0 index menu.items.length)
menu.items.splice(index, 1);
}
I see what you mean about the action listener, Bob. Shouldn't be too tough to
make that happen. Thanks for the debugCode tip; should be easier to get a
handle on that now as well. Finally, feel free to copy over any or all of my
code to the official JSmol code (probably don't have to tell you that...
:D).
Cheers, Mike
---
Michael Evans
Organic Chemistry Graduate Student, Moore Group
University of Illinois, Urbana-Champaign
On Wed, Dec 19, 2012 at 3:05 PM, Robert Hanson hans...@stolaf.edu wrote:
Wow, this is great! Almost there, I think.
On Wed, Dec 19, 2012 at 12:48 PM, Michael Evans evan...@illinois.edu wrote:
Bob et al.,
Progress has been made on a popup menu for JSmol. I've implemented PopupMenu,
MenuItem, CheckboxMenuItem, and RadioButtonMenuItem, among other things.
Check it out:
http://www.metallacycle.com/play/netmol/tests/popupMenu/jmolPopupMenu.js
OK! You are way ahead of me!
The demo is still functional as well:
http://www.metallacycle.com/play/netmol/tests/popupMenu/popupMenu.html
Two things I'm struggling with:
1) What's the difference between a ButtonGroup and a set of
RadioButtonMenuItems?
I think it's the same. I think really in JavaScript it's just a set of radio
buttons with the same name. Be sure to use
applet._id
as a prefix to every name or id so that multiple applets on a page do not
have the same name or id for anything.
2) Event handling in general. For example, a checkbox menu item doesn't
know its parent, so when it's clicked, it can't run commands on its parent
applet without bubbling an event up to its parent jmol object. I will
continue to work on this, but event handling in JS is not one of my
specialties. I'll look into custom events mediated by jQuery, but in the
meantime, if there are any JS event experts out there, help would be
appreciated! :-)
Actually, it does. What you are missing is that when a checkbox is created,
the following command sequence is run:
/**
* @j2sNative
*
* if (isRadio) {
*item = new Jmol.Menu.RadioButtonMenuItem(entry);
*item.setArmed(state);
* } else {
*item = new Jmol.Menu.CheckBoxMenuItem(entry);
*item.setState(state);
* }
* item.setSelected(state);
* item.addItemListener(this);
*
*/
So that addItemListener is giving the checkbox a reference to the instance
of org.jmol.awt2d.JSPopup that created it. Store that as jmolPopup in the
item. Then:
.jmolPopup.checkBoxStateChanged();
Similarly, all normal menu items have:
/**
* @j2sNative
*
* item = new Jmol.Menu.MenuItem(entry);
* item.addActionListener(this);
*
*/
(notice Action here, not Item)
This is going to respond to clicks:
.jmolPopup.checkMenuClick(, .getActionCommand());
where getActionCommand() returns background yellow should take care of it.
Finally, there are a few items that are special and start with Focus. These
also get a mouse listener so that we can track when they are entered and
exited:
/**
* @j2sNative
*if (id != null id.startsWith(Focus)) {
* item.addMouseListener(this);
* id = menu.getName() + . + id;
*}
*item.setName(id == null ? menu.getName() + . : id);
*/
Then that needs to be set up so that we can run:
item.jmolPopup.checkMenuFocus(item.getName(), item.getActionCommand(),
true);
item.jmolPopup.checkMenuFocus(item.getName(), item.getActionCommand(),
false);
And we should be done!
By the way, your comment there that it should be OK to use a null instead of
removing an item is not right. This could happen extensively, and we need to
actually remove that array element.
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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Re: [Jmol-users] Jmol-JSO: specifying signed applet
You must both specify the jar file and whether or not it is signed. JmolJSO
doesn't make the call on that.
Sent from my stupid iPhone
On Oct 14, 2012, at 3:04 PM, Angel Herráez angel.herr...@uah.es wrote:
Dear users,
I'm setting up a page that uses Jmol-JSO syntax (13.1.6)
I see that there are defaults for Info that suit the unsigned applet but not
the
signed applet.
This code works:
var myInfo = {
jarFile: 'JmolAppletSigned0.jar',
jarPath: '.',
isSigned: true
};
var myJmol = Jmol.getApplet(myJmol, myInfo);
but this one does NOT work:
var myInfo = {
isSigned: true
};
var myJmol = Jmol.getApplet(myJmol, myInfo);
giving a Java ClassNotfoundException error for JmolApplet.class
I would expect that setting the 'isSigned' value should be enough for the
correct jarfile to be used. In addition to that being simple and expected,
otherwise, what is the purpose for the isSigned parameter if I must anyway
specify the signed jar file?
Clarification:
Apparently the unsigned version is trying to be used (according to
debug:true). Since I had not included a copy of the unsigned jar files, I am
getting the error. When all the files are present, the applet opens unsigned
even though isSigned is set true.
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Re: [Jmol-users] Rotation of LCAO cartoon orbitals
One option would be to raise the cutoff to a much higher value. I've had success with JVXL loading for molecular surfaces. MOs would be easier. Sent from my stupid iPhone On Aug 20, 2012, at 7:07 PM, Greeves, Nick ngree...@liverpool.ac.uk wrote: Bob et al, I wonder if you could use actual MOs. We are trying to use actual calculated MOs as well but as usual they are overly complex. The MOs are calculated for the combination of the diane and the dienophile so the HOMO is on the diene at the start of the animation and becomes the alkene in the product. Meanwhile the LUMO starts out on the dienophile double bond and ends up on the associated carbonyl. If you are really really patient you can see an example here http://138.253.125.24/~ng/externaltest/MOanim.html I recommend having a Java console running so you can tell it is still alive. For reasons I don't understand different browsers seem to show either the HOMO applet or the LUMO applet - memory problems I expect. But for comparison we would like to have LCAOcartoons as well (not at the same time). All the best Nick -- 3D Organic Animations http://www.chemtube3d.com Tel: +44 (0)151-794-3506 (3500 secretary) -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bug in coloring JVXL surfaces
Sure sounds like a bug to me. And me the file, please. Sent from my stupid iphone On May 21, 2012, at 10:31 AM, Spinney, Richard rspin...@chemistry.ohio-state.edu wrote: 12.2.25 will display a color mapped JVXL surface in a single color only (see http://undergrad-ed.chemistry.ohio-state.edu/bonding/polar-covalent.html). 12.3.26 displays it as red/blue with holes in the surface. It seems the defaults “roygb” color scheme is not working. Bob is this a bug or a change in the default behavior? Thanks, Rick -- Dr. Richard Spinney The Ohio State University Department of Chemistry 0109 Newman Wolfrom Laboratory 100 West 18th Ave Columbus, Ohio 43210 email: rspin...@chemistry.ohio-state.edu Phone: (614) 247 - 6847 Fax: (614) 292 - 1685 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] SMILES
Same thing with CH2Cl2. I think there's a special exception for H. I could look into that. Sent from my stupid iphone On May 20, 2012, at 3:52 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, A while back you modified Jmol SMILES and COMPARE so that coordination compounds involving square planar and octahedral would generate SMILES that could me distinguished by Jmol compare. This all works quite well, there is an interesting exception. If you use our square planar template on the virtual model kit to make either XeHHYY, the resulting SMILES does not reflect stereochemisty. If, however, you do the same thing with deuterium, the stereochemisry IS reflected in the SMILES. Bug or inherent behavior of H replace in modelkitmode? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol/ChemDoodle -- test2
Otis is PubChem now available via ajax directly, like for NCI? That is, no server relay and so no problem with being locked out? As soon as I get a chance -- traveling all day today -- I will add direct NCI access in JmolCD.js. I've sent a request for that to RCSB. If we had all three it would be terrific. Sent from my stupid iphone On Apr 19, 2012, at 7:31 AM, Otis Rothenberger osrot...@chemagic.com wrote: Very nice. I'm a believer. I need to look at the code to see how to fit this into our Web application. I should remind users that now that PubChem files can be loaded, MEP surfaces can also be displayed. It's true that the PubChem SDF's use an abbreviated approach to partial charges, still the MEP's still have some classroom utility in my opinion. I assume PubChem's abbreviated partial charges are rooted in making charge profile searches practical. Bob added the Jmol reading of these PubChem partial charges in 2010, I think. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote: More goodies at http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm -- pubChem search -- keyword lookup at RCSB -- general way to swap the applet for a block of HTML information if desired Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol/ChemDoodle -- test2
So markus says. Haven't tried that yet. Sent from my stupid iphone On Apr 19, 2012, at 12:58 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, I'm not sure because I didn't know you could do that! Do you mean I don't have to use a server readURL script on my server to query Resolver. I can simply query Resolver directly via an AJAX script? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 19, 2012, at 3:14 PM, Bob Hanson wrote: Otis is PubChem now available via ajax directly, like for NCI? That is, no server relay and so no problem with being locked out? As soon as I get a chance -- traveling all day today -- I will add direct NCI access in JmolCD.js. I've sent a request for that to RCSB. If we had all three it would be terrific. Sent from my stupid iphone On Apr 19, 2012, at 7:31 AM, Otis Rothenberger osrot...@chemagic.com wrote: Very nice. I'm a believer. I need to look at the code to see how to fit this into our Web application. I should remind users that now that PubChem files can be loaded, MEP surfaces can also be displayed. It's true that the PubChem SDF's use an abbreviated approach to partial charges, still the MEP's still have some classroom utility in my opinion. I assume PubChem's abbreviated partial charges are rooted in making charge profile searches practical. Bob added the Jmol reading of these PubChem partial charges in 2010, I think. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote: More goodies at http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm -- pubChem search -- keyword lookup at RCSB -- general way to swap the applet for a block of HTML information if desired Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Selection Tool
Fixed. Sent from my stupid iphone On Apr 12, 2012, at 5:09 PM, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de wrote: Hi all, I just discovered something weird: Once I have antialiasdisplay enabled, rectangular selection (via left mouse button with shift pressed) does not work as expected: the rectangle is not drawn beginning at the mouse click, but somewhat shifted to the top left. Anyone else seen this? Best Kilian -- __ MSc. Chem. Kilian Bärwinkel Lehrstuhl für Anorganische Chemie III Fakultät NW 1 Universität Bayreuth Universitätsstr. 30 95447 Bayreuth Tel:+49 921 55 - 4387 Fax:+49 921 55 - 2788 e-mail: kilian.baerwin...@uni-bayreuth.de http://www.senker.uni-bayreuth.de -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Regarding Mol2
Send a sample file to me. I probably have not implemented unit cells in mol2.
Do you have a reference to that specification ? In the mean time you certainly
can load files with UNITCELL option.
Sent from my stupid iphone
On Jan 25, 2012, at 8:59 AM, Kilian Baerwinkel
kilian.baerwin...@uni-bayreuth.de wrote:
Hi all,
I am using mol2 as the intermediate format to display the frames of a
molecular dynamics run on a periodic system.
While it is possible to activate the display of the unit cell when a
structure is loaded, it does not work to use load some_file.mol2 {2 2 2} to
display multiple cell images.
Am I doing something wrong here, or is this feature not implemented in Jmol?
If what I am trying is not possible, is anyone aware of a file format
allowing me to import atomic positions and unit cell parameters both into
Jmol (and and still use cell images) - the file containing the whole
trajectory?
Best
Kilian
--
__
MSc. Chem. Kilian Bärwinkel
Lehrstuhl für Anorganische Chemie III
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Universitätsstr. 30
95447 Bayreuth
Tel:+49 921 55 - 4387
Fax:+49 921 55 - 2788
e-mail: kilian.baerwin...@uni-bayreuth.de
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Re: [Jmol-users] Need some advice on server side static image processing with Jmol...
JmolData is simply Jmol with no graphics at all. Great for batch processing but no graphics. -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bind command and picked atoms
Ok I see the problem. Select and picking are intimately associated. You are trying to separate those. The zoomto patch is not the best solution because it only solves this one problem of yours Alex. I'll check in tonight or tomorrow a way of getting atom bond and point pick information into a user defined binding. The following tokens in a user defined binding will all be available: _X _Y _TIME _MODE _ATOM _BOND _POINT _ACTION _DELTAX _DELTAY ACTION is an integer that encodes the mouse/key combination and the click count. MODE indicates the state including 1 dragged 2 clicked 3 wheeled 4 pressed 5 released. I noticed a few bugs with this and will have them fixed today. Internet access is spuratic still. -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bind command and picked atoms
_picked is a variable. I thought it was defined prior to the callback. Sent from my stupid iphone On Jan 20, 2012, at 10:35 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi all, when using Jmol I find myself using either 'set picking CENTER' or 'set picking SELECT GROUP', so I would like to switch as fast and easy as possible between the two modes via the mouse. My first idea was to use the 'bind' command to bind centering to ALT-LEFT and selecting a group to LEFT. However there is no _center jmol-action for the bind command and the _select jmol-action seems not to work when 'set picking CENTER' is active. The bind command also allows to pass a jmol script instead of a jmol-action, but inside that passed script the information which atom was picked is not available so you can't center on it or select its group. There is also the pick callback, but this does not give you the modifier key that was pressed when the atom was picked. In my opinion the addition of a _centerOnPickedAtom jmol-action for the bind command would be useful. A more flexible solution would be to add a _PICKED variable (containing a selection of the picked atom; maybe also other pickable elements?!) to the things that gets replaced in a script passed to 'bind' command. Based on that variable it is straightforward to implement centering or selecting a group. What do you think? Would anyone else find this useful, too? Best Alexander -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] getProperty Image
That's fixed. See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
and upcoming releases of 12.3.12 and 12.2.12.
Sent from my stupid iphone
On Jan 12, 2012, at 11:40 PM, Michael Evans evan...@illinois.edu wrote:
Lords lasses of Jmol—just wanted to note an issue in 12.2.11 that I think
Dr. Gutow mentioned for 12.2.10 back in December...getProperty image and
the Javascript equivalent jmolGetPropertyAsString('image', 'all') cause the
applet to hang. Is there a workaround? Any idea where the solution might lie?
Here's the original bug report (still broken, if you follow Gutow's
instructions):
http://sourceforge.net/tracker/index.php?func=detailaid=3466163group_id=23629atid=379133
And an example from my stuff (just try building a molecule, then Javascript
in the web console or Jmol commands in the script console):
http://metallacycle.com/uiji/
Cheers, Mike
---
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University of Illinois, Urbana-Champaign
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Re: [Jmol-users] write image NullPointerException
Found it. I'll get it uploaded this weekend. It's a problem specific to jpg not png. Sent from my stupid iphone On Jan 9, 2012, at 2:26 PM, Eric Martz ema...@microbio.umass.edu wrote: Yes, Bob, I can write image ... from the signed applet URL you gave (Jmol 12.3.10). And I confirm that I can write an image just fine from Jmol application 12.3.10. As I reported initially, the NullPointerException occurs on all my attempts to write an image in Jmol application 12.2.11 and 12.2.4. I just tested 12.2.7 and it also failed to write an image. So it may be that whatever is wrong is consistent through the entire 12.2 series of releases. As I reported initially, 12.0.31 writes images with no problems. I have been using it extensively for this purpose. In conclusion, I think there is something preventing many or all of the 12.2 series of application OFFICIAL releases from writing images. As long as 12.2.11 remains the official release, it may be worthwhile fixing its ability to write images. Thanks, -Eric At 1/8/12, you wrote: Almost certainly a bad build. Please try that at http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm Sent from my stupid iphone On Jan 8, 2012, at 2:01 PM, Eric Martz ema...@microbio.umass.edu wrote: The following session is with Jmol 12.2.11, Jmol graphics window set to 500 x 400 pixels. I will send the state script to you directly, Bob, off list. -Eric $ load =1d66 TRANSCRIPTION/DNA 06-MAR-92 1D66 DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX $ write image jpg test.jpg script ERROR: ERROR creating image: java.lang.NullPointerException write image jpg test.jpg $ write state image-bug.spt OK SPT 7842 /Users/emartz/Downloads/SAVED/jmol-12.2.11/image-bug.spt $ At 1/7/12, Bob Hanson wrote: Not seeing the error. if you could save the state and send me that maybe I could spot the problem. Sent from my stupid iphone On Jan 4, 2012, at 1:28 PM, Eric Martz ema...@microbio.umass.edu wrote: Dear Bob, With Jmol 12.2.11 and 12.2.4 I am unable to write an image. Most of the time I get a NullPointerException. --- $ write image jpg m1.jpg script ERROR: Error during rendering: java.lang.OutOfMemoryError: Java heap space write image jpg m1.jpg $ zap 2,990 atoms selected 3,053 atoms selected $ write image jpg 1.jpg script ERROR: ERROR creating image: java.lang.NullPointerException write image jpg 1.jpg $ With Jmol 12.0.31, I can write images with no problem. I am using set imagestate false but that doesn't seems to matter regarding this bug. Thanks, -Eric -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
Re: [Jmol-users] Jmol Android released
There are lots of possibilities. Maybe a summer of code project? It would be great fun. Sent from my stupid iphone On Jan 9, 2012, at 11:30 AM, Egon Willighagen egon.willigha...@gmail.com wrote: On Mon, Dec 5, 2011 at 2:49 PM, Robert Hanson hans...@stolaf.edu wrote: https://market.android.com/search?q=jmolso=1 Cool! And now that I actually have an android, even cooler! Q: is it possible to create a URL or so, that would auto load the app with a particular protein? Or better: with a particular Jmol script? What I am getting at, is that I want to have QR codes on slides on lectures, allowing students to open the structures I am displaying on the slide, directly on their phones... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem when coloring cartoons
So actually what is happening is that the last protein residue of a chain if not helix or sheet is being skipped. Fixed but not yet uploaded for release. Later this week for that. Sent from my stupid iphone -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] write image NullPointerException
Almost certainly a bad build. Please try that at http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm Sent from my stupid iphone On Jan 8, 2012, at 2:01 PM, Eric Martz ema...@microbio.umass.edu wrote: The following session is with Jmol 12.2.11, Jmol graphics window set to 500 x 400 pixels. I will send the state script to you directly, Bob, off list. -Eric $ load =1d66 TRANSCRIPTION/DNA 06-MAR-92 1D66 DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX $ write image jpg test.jpg script ERROR: ERROR creating image: java.lang.NullPointerException write image jpg test.jpg $ write state image-bug.spt OK SPT 7842 /Users/emartz/Downloads/SAVED/jmol-12.2.11/image-bug.spt $ At 1/7/12, Bob Hanson wrote: Not seeing the error. if you could save the state and send me that maybe I could spot the problem. Sent from my stupid iphone On Jan 4, 2012, at 1:28 PM, Eric Martz ema...@microbio.umass.edu wrote: Dear Bob, With Jmol 12.2.11 and 12.2.4 I am unable to write an image. Most of the time I get a NullPointerException. --- $ write image jpg m1.jpg script ERROR: Error during rendering: java.lang.OutOfMemoryError: Java heap space write image jpg m1.jpg $ zap 2,990 atoms selected 3,053 atoms selected $ write image jpg 1.jpg script ERROR: ERROR creating image: java.lang.NullPointerException write image jpg 1.jpg $ With Jmol 12.0.31, I can write images with no problem. I am using set imagestate false but that doesn't seems to matter regarding this bug. Thanks, -Eric -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] write image NullPointerException
Not seeing the error. if you could save the state and send me that maybe I could spot the problem. Sent from my stupid iphone On Jan 4, 2012, at 1:28 PM, Eric Martz ema...@microbio.umass.edu wrote: Dear Bob, With Jmol 12.2.11 and 12.2.4 I am unable to write an image. Most of the time I get a NullPointerException. --- $ write image jpg m1.jpg script ERROR: Error during rendering: java.lang.OutOfMemoryError: Java heap space write image jpg m1.jpg $ zap 2,990 atoms selected 3,053 atoms selected $ write image jpg 1.jpg script ERROR: ERROR creating image: java.lang.NullPointerException write image jpg 1.jpg $ With Jmol 12.0.31, I can write images with no problem. I am using set imagestate false but that doesn't seems to matter regarding this bug. Thanks, -Eric -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] True movies from Jmol image files?
write frames Or if you need to you can write a little looping script to do that. Or write a command yourself. Jmol's function calls can now look like commands Sent from my stupid iphone On Jan 3, 2012, at 3:34 PM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: you can make a movie from separate png files using the package ffmpeg (http://ffmpeg.org/) I created a simple animation from a pov file, rendered in PNG image format from different angles to simulate a rotation. It would be exactly the same principle with png files created by Jmol. Also, it might be useful to know that Bob wrote somewhere (but I can't find where !) in the Jmol documentation a function to write sequential png files in a trajectory (by splitting a quaternion in the specified number of frames from what I understood) (I realized that ffmpeg is the package used by the molecular software chimera to create mov files from png in their animation tool.) Paul Le 3 janv. 2012 à 03:26, Eric Martz a écrit : If someone has experience generating true movies from Jmol (movies that will play in a web browser, or at least will play on both Windows and Macs without special software) I would appreciate advice. I think the idea is to save a series of jpg files from a Jmol script. The jpg files are the frames of a movie. One then assembles the jpg files into some sort of movie (mpg?) file. How? What software is easiest for the assembly, to control the speed of the movie, etc.? I have experience using RasMol scripts to save a series of gif files, and assembling those into a multi-gif movie that plays in all web browsers. As far as I can see, Jmol cannot write gif files. I see that Jmol's write image command can save several variations on png image format and ppm format. I don't know if any of those are advantageous for assembling a movie. Thanks, -Eric -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] syntax for writing multisurface Jmol voxel JVXL format
We didn't fully implement multiple surface files. So maybe this is the time to do that. Will check on that. Sent from my stupid iphone On Nov 11, 2011, at 10:50 AM, Wayne Decatur wdeca...@yahoo.com wrote: Hi, I have two named isosurfaces generated that I am trying write to a Jmol voxel JVXL format so that I can reload them. When I issue the command below only as described inthe JVXL format pdf the last created isosurface is made part of the JVXL file. write ISOSURFACE “myfile.jvxl” The wiki has the format for two isosurfaces as part of a single JVXL file at http://wiki.jmol.org/index.php/File_formats/Surfaces and links to a full example with two (http://wiki.jmol.org/index.php/File_formats/Sample_xjvxl). However, my attempt at a work around by generating them one at a time, saving, and then combining each into a single file with editing and changing the count to 2, i.e., ' jvxlSurfaceSet count=2 ', failed. Thanks, Wayne -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] PO4 Missing Double Bond
The p=o is not always shown. There is little evidence that third-row elements such as P and S can form double bonds with O. So it is a matter of opinion really. You can certainly add them if you like. Sent from my stupid iphone On Nov 4, 2011, at 3:08 PM, Sara Bonner bonn...@mit.edu wrote: I wasn't certain how to explain. phosphate ion has 3 oxogen with single bonds and 1 oxogen with a double bond. Looking at http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=PO4 I thought that the double bond is on the positive O. Thanks Sara From: Robert Hanson [hans...@stolaf.edu] Sent: Friday, November 04, 2011 3:22 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] PO4 Missing Double Bond positive O? On Fri, Nov 4, 2011 at 2:18 PM, Sara Bonner bonn...@mit.edumailto:bonn...@mit.edu wrote: Hi All the pdb files containing phosphate ions seem to be missing the double bond on positive oxogen. What is the process for identifying and placing double bonds. Thanks Sara -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Useful Compare Code and Great Toy
Otis, I'm integrating this into Jmol today. Should be able to distinguish
constitutional, configurational, and conformational isomers.
Command will be:
X=compare({1.1},{2.1},ISOMER)
Bob
On Aug 8, 2010, at 2:00 AM, Otis Rothenberger osrot...@chemagic.com wrote:
Bob,
I tacked your compare suggestions on to the end of our two model (same
frame) identity check. After a 1 second delay, your isomer type
comparison is displayed. In case users interested in this type of thing
missed your code in my previous verbose email chain re SMILES problems,
I'll post it in this separate note. All I can say is great and useful
toy. I've been playing with variations (2R,3R)-2-bromo-3-chlorobutane
and others way past bed time.
Otis
Bob Hanson Wrote:
The way I was thinking to categorize two models is this:
var m1 = {molecule=1} # or whatever
var m2 = {molecule=2} # or whatever
# check molecular formulas
var sameMF = (m1.find(MF) == m2.find(MF))
# get SMILES string for molecule 1
var smiles = m1.find(SMILES)
var smiles_enantiomer =
sm.replace(@@,!@).replace(@,@@).replace(!@@,@)
var smiles_nostereo = smiles.replace(@,)
# note: we can't just compare SMILES strings like we can molecular formulas
# because SMILES strings here are not cannonical - but that is no
problem at all
# instead, we find the SMILES string for one model in the other. Using
SMILES
# here instead of SMARTS guarantees an exact search and not a
substructure search
var identical = sameMF (m2.find(SMILES,smiles) 0)
var configurationalIsomers = sameMF !identical
(m2.find(SMILES,sm_nostereo) 0)
var enantiomers = configurationalIsomers
(m2.find(SMILES,smiles_enantiomer) 0)
var diastereomers = configurationalIsomers !enantiomers
var constitutionalIsomers = sameMF !identical !configurationalIsomers
--
Otis Rothenberger
chemagic.com
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Re: [Jmol-users] write POVRAY without a dialog box
Essentially not. The signed applet should always ask the user prior to writing any file of any sort. Sent from my iPhone On Jul 10, 2010, at 3:50 PM, Shore, Jay jay.sh...@sdstate.edu wrote: Hello All, I apologize if this is in the documentation, but I could not find it. Is it possible to export a POVRAY file using the signed applet without the dialog box coming up? Thank you. Jay --- --- --- - This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Html5
At the html5 wikipedia site I note: Deprecated elements will be dropped altogether: acronym, applet, basefont, big,center, dir, font, frame, frameset, isindex,noframes, s, strike, tt, u Another reason to use Jmol.js -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Virtual Model Kit
Otis. Super. I don't think my latest jme reader will have that problem with planar rings. I have the z coordinate given a bit of noise. Keep playing with it. Some boats are probably inevitable. Sent from my iPhone On Apr 10, 2010, at 8:59 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, I have it set up on my home server. I'm only working with small molecules, but I haven't had a clunker yet. Wow, I am impressed! I actually took the stereo bonds off of the JME on the chemagic site. I need to put them back. I'm still going to bypass some other misses. For example, most users would simply draw cyclohexane as JME planar - no stereo bonds. UFF keeps that planar, so I'll just use the unique SMILES to reroute to a direct load from a cyclohexane chair file. Otis On 4/10/2010 6:41 PM, Robert Hanson wrote: Hey, check this out: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 124. JME reader reads stereochemistry and automatically turns 2D to 3D with addition of H atoms The JME format is a two-dimensional file format that is easy to generate but not easily adapted to 3D. Jmol 12.0.RC5 adds the automatic addition of H atoms and transformation of simple JME structures (including stereochemistry) to 3D. The transfer is not perfect, and it may take some testing to get this right. Bob On Sat, Apr 10, 2010 at 4:22 PM, Robert Hanson hans...@stolaf.edu wrote: Otis, if you think it would be valuable, we could look into reading the stereochemistry of bonds and at least shifting a whole branch up or down an angstrom in the Z coordinate based on that. wouldn't be perfect, but it might not be that hard, either. As I started to do this, I realize that the JME reader is totally nonfunctional. I'm adding stereochemical reading, and it seems to work OK, but there is still a problem with the addhydrogens business. WIll fix On Fri, Apr 9, 2010 at 1:28 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bill, I'm passing molfiles from JME. Actually, the SMILES is also passed in the molfile (Name Position), but its the molfile that's rendered. The JME string might be worth a try. While the information is still 2D only, we have found that you can give UFF minimization good starts and bad starts based on the original 2D drawing. It's important to note that Jmol ignores stereo bonds from JME - only 2D info passed. Interestingly, it will pass formal charge information in the molfile, but the atom is not registered in Jmol as having the formal charge - i.e. the charges are only printed on the model. Otis On 4/9/2010 1:07 PM, william reusch wrote: Otis, Are you transferring the JME structure as a Smiles string or as a JME string. The latter has more information in it. Bill Otis Rothenberger wrote: Bill, Thanks for the comments. The 2D to 3D translation is an ongoing problem for us. The JME editor is light weight and it can be embedded directly in the application, but it passes only 2D information to Jmol. Jmol tries to sort this out with the UFF minimization. With really simple molecules this works, but there are serious limitations. We actually have two alternative options, and we need to discuss this in the users manual, a current high priority! --- --- --- - Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com --- --- --- - Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture
Re: [Jmol-users] jmol POVRAY output
It's a bug. Workaround is to create the whole command as a variable and then execute it with Script inline @x Sent from my iPhone On Oct 2, 2009, at 2:05 PM, Kirill Speranskiy ksper...@asu.edu wrote: Hi All, I have a problem writing Pov-ray for single snapshot when I use a variable in the script. Write IMAGE works fine with variables write image @width @height @fileName; but when I use it for write POVRAY @fileNamePovray I have no output at all, although it works in setup like: write POVRAY somename.pov Any help is greatly appreciated. Thanks a lot!!! The following is my script: load_array=Array(); load_array[1]= snapshot_0001.pdb ; load_array[2]= snapshot_0002.pdb ; name = ./frame.gif; namePovray = ./povray.pov; nFrames = 2 ; thisFrame = 0; width = 800; height = 800; message loop; thisFrame = thisFrame + 1; load_file=load_array[thisFrame]; load @load_file; fileName = name.replace(, + ( + thisFrame)[-4][0]); fileNamePovray = namePovray.replace(, + ( + thisFrame) [-4][0]); write image @width @height @fileName; write povray @fileNamePovray; if (thisFrame nFrames);goto loop;endif; --- --- --- - Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] echo'ing a read-only variable
Echo @{xxx}
Sent from my iPhone
On Jun 19, 2009, at 12:06 PM, Angel Herráez angel.herr...@uah.es
wrote:
David, try to put it between braces
echo {_modelName}
I don't yet understand the braces, but there's much JmolMagic in them
:-)
Other choice:
var x = _modelName
echo @x
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Re: [Jmol-users] Extract Orientation
Actually. The best is jmolEvaluate('script(show orientation)')
Sent from my iPhone
On Jun 18, 2009, at 6:49 AM, Lars Skjærven lar...@gmail.com wrote:
hi! thanks for your quick reply.
this is just what I need yes. I tried to implement this into my site,
so I made a javascript function that outputs the orientation to an
alert-box:
ori = jmolScript(show orientation);
alert(ori);
However, jmolScript returns undefined here. I also tried to set
targetsuffix to be sure that it is communicating with the same applet.
Any suggestions?
thanks again. :)
Lars
2009/6/18 Angel Herráez angel.herr...@uah.es:
Hello Lars
The command you need is show orientation.
You will need to parse it or, better, use show orientaton moveto
(only in recent versions of Jmol)
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Re: [Jmol-users] Extract Orientation
Right jmolScript works independently. You need jmolScriptWait On Jun 18, 2009, at 6:49 AM, Lars Skjærven lar...@gmail.com wrote: hi! thanks for your quick reply. this is just what I need yes. I tried to implement this into my site, so I made a javascript function that outputs the orientation to an alert-box: ori = jmolScript(show orientation); alert(ori); However, jmolScript returns undefined here. I also tried to set targetsuffix to be sure that it is communicating with the same applet. Any suggestions? thanks again. :) Lars 2009/6/18 Angel Herráez angel.herr...@uah.es: Hello Lars The command you need is show orientation. You will need to parse it or, better, use show orientaton moveto (only in recent versions of Jmol) --- --- --- - Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --- --- --- - Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and xhtml
I'm amazed that works. Doesn't that just write all the tags as text?
Also,
You can't treat a string like an array in msie-- 667766[4] should
not work anymore in msie.
My network went down or I would test that. I realize the reason Msie
doesn't like my page is that I am missing the ?XML line. But I will
have to fix that tomorrow.
Sent from my iPhone
On May 6, 2009, at 11:17 PM, Jeff Hansen jhan...@depauw.edu wrote:
Bob,
You beat me to it and of course your solution is more sophisticated
than mine. For the record here is what I did.
function _jmolDocumentWrite(text) {
if (_jmol.currentDocument)
var newcontent = document.createElement('div');
newcontent.appendChild(document.createTextNode(text));
var str = '';
for (var i = 0; i text.length; i++)
str += String(text[i]);
document.body.innerHTML=str;
//_jmol.currentDocument.write(text);
return text;
}
You can see it in action here:
http://webme.com/jhansen4/iWeb/Jmol/JmolPlusSVG.xhtml
I'll grab a copy of your revised Jmol.js and begin using that.
Thanks!
Jeff
***
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jhan...@depauw.edu
***
On May 7, 2009, at 12:01 AM, Robert Hanson wrote:
Well, you are quicker than I am. Try this:
http://chemapps.stolaf.edu/jmol/docs/examples-11/t2.xhtml
and
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol.js
On Wed, May 6, 2009 at 8:35 PM, Jeff Hansen jhan...@depauw.edu
wrote:
Bob,
The idea is to use a multiple model file in Jmol, pull out the
energies of each model, and use that data to generate an svg
graph. The svg should highlight the point corresponding to the
model currently being displayed and likewise if the user clicks a
point on the svg it will highlight the point and update the jmol to
display the corresponding model. In other words, the svg will be a
graph of the energies of the models and the svg and applet will
talk to each other.
Currently I am using jmolInitialize, jmolApplet, jmolEval, and
jmolGetPropertyAsArray. Of course I would prefer to use jmol.js
but if necessary can do without it.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On May 6, 2009, at 7:52 PM, Robert Hanson wrote:
Ah, that sounds familiar. Correct. There is no document.write in
XHTML. Sorry. That pretty much rules it out.
As I recall Egon at one point wrote a DOM-specific XHTML version
of a page that worked with Jmol, though not Jmol.js.
But you don't necessarily have to have Jmol.js to use Jmol. You
just have to work harder to do it without.
So what is the deal with inline SVG?
Bob
2009/5/6 Angel Herráez angel.herr...@uah.es
It seems that the first hit is caused by document.write not being
supported
by XHTML (documented in several websites)
My test:
XHTML 1.0 Transitional
_jmol.currentDocument.write(text);
at line line 834 within
function _jmolDocumentWrite(text) {
throws an error in Firefox 3
No error in Opera, but no applet
Clue:
Does document.write work in XHTML?
No. Because of the way XML is defined, it is not possible to do
tricks like
this, where markup is generated by scripting while the parser is
still parsing
the markup.
You can still achieve the same effects, but you have to do it by
using the
DOM to add and delete elements.
(source: http://www.w3.org/MarkUp/2004/xhtml-faq#docwrite)
And quoting
http://jmol.sourceforge.net/docs/JmolAppletGuide.html#XHTMLSupport
the standard Jmol.js Javascript library will not work under properly
compliant XML browsers. An alternative, largely similar, but
entirely
unsupported library is available ... insert address here ...
(that JmolAppletGuide doc is old --Miguel's times? . but true
indeed)
I've tested the alternative to document.write given at
http://weston.ruter.net/projects/xhtml-document-write/
http://shepherd-interactive.googlecode.com/svn/trunk/xhtml-document-
write/xhtml-document-write.js
and, althogh it does not solve the problem, is on its way:
Opera displays a functional applet, but below it is the yellow
box that says
you don't have Java (generated by Jmol.js)
Firefox displays a Java box with an error, applet class not found,
and the
yellow box below it
IE8 displays nothing --seems not to like xhtml at all --even with
no Jmol
code in the page, it just displays a blank page and does a
download --of the
page?.
More to come...
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Re: [Jmol-users] SLC Crystal inn
Flight arrive 5:05. Sent from my iPhone On Mar 22, 2009, at 12:18 PM, hrzepa h.rz...@imperial.ac.uk wrote: Bob, Checked in to room 412, with extra key for you. When do you arrive? --- --- --- - Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] user defined covalent radius
I think you may need to use a frame change callback. You can have it running a jmol script function that uses the connect command. It will slow down the animation, but should work. Sent from my iPhone On Mar 22, 2009, at 2:56 AM, k.jaroli...@science.ru.nl wrote: Hi, I am trying to view a molecular dynamics simulation, where bonds are being formed and destroyed. The data is in the XYZ format containing multiple structures. However I would like to use my own cut-off distances for bonds. Is there a way to do this in Jmol ? Are the bonds being evaluated at each MD step or just at the first one ? I was searching the documentation, but there I found that you can change only Van der Vaals radius but not the covalent. Regards, Karol --- --- --- - Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Who is in salt lake city now?
Are we getting together? I'm here through Wednesday night. Sent from my iPhone On Mar 22, 2009, at 11:17 AM, Angel Herráez angel.herr...@uah.es wrote: In addition to Rolf's reply, you can also load two or more files at the same time using load files 1dwd.pdb 1crn.pdb Note that you need double quotes there for each filename, so your javascript could use single quotes: jmolApplet(500, 'load files 1dwd.pdb 1crn.pdb;') --- --- --- - Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Who is in salt lake city now?
Oops. Make that through TUESDAY night. Sent from my iPhone On Mar 22, 2009, at 3:46 PM, Bob Hanson hans...@stolaf.edu wrote: Are we getting together? I'm here through Wednesday night. Sent from my iPhone On Mar 22, 2009, at 11:17 AM, Angel Herráez angel.herr...@uah.es wrote: In addition to Rolf's reply, you can also load two or more files at the same time using load files 1dwd.pdb 1crn.pdb Note that you need double quotes there for each filename, so your javascript could use single quotes: jmolApplet(500, 'load files 1dwd.pdb 1crn.pdb;') --- --- --- - Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Who is in salt lake city now?
Call me 507.301.8653 Sent from my iPhone On Mar 22, 2009, at 5:33 PM, Christopher Masi cm...@wsc.ma.edu wrote: Hey, I'm here through Tuesday night. I'm not as active on this list as I once was, but I'd love to meet with some Jmol users/developers. Chris On Mar 22, 2009, at 5:02 PM, Bob Hanson wrote: Oops. Make that through TUESDAY night. Sent from my iPhone On Mar 22, 2009, at 3:46 PM, Bob Hanson hans...@stolaf.edu wrote: Are we getting together? I'm here through Wednesday night. Sent from my iPhone On Mar 22, 2009, at 11:17 AM, Angel Herráez angel.herr...@uah .es wrote: In addition to Rolf's reply, you can also load two or more files at the same time using load files 1dwd.pdb 1crn.pdb Note that you need double quotes there for each filename, so your javascript could use single quotes: jmolApplet(500, 'load files 1dwd.pdb 1crn.pdb;') --- --- --- --- - - Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --- --- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Learn about Brittle Bone Disease... http://www.oif.org -- Christopher Masi, Ph.D. Assistant Professor of Chemistry, Department of Physical Science Executive Council, Westfield Chapter MSCA Board of Directors, Northeast Region of the American Chemical Society, Inc. Westfield State College 577 Western Ave Westfield, MA 01086 (413)572-5371 --- --- --- - Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Support of 'alchemy' format for rectangular schematic base-pair geometry
I'll set it up tonight
On Dec 9, 2008, at 7:21 PM, Xiang-Jun Lu [EMAIL PROTECTED] wrote:
Dear Bob,
Thank you so much for your detailed explanations.
Date: Tue, 9 Dec 2008 18:19:09 -0600
From: Robert Hanson [EMAIL PROTECTED]
Subject: Re: [Jmol-users] Support of 'alchemy' format for rectangular
schematic base-pair geometry
To: jmol-users@lists.sourceforge.net
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain; charset=ISO-8859-1
Before I write this reader, can I ask if it's possible you could use
another format?
I could, but I really do not have a solid reason to (see below).
Do you have all these files already made, so you are eager to use them
exactly, or do you have a program that produces them?
Yes, I have several (utility) programs within 3DNA that produce and
read such alchemy files for various (internal) purposes. It is nice
that RasMol can render them properly, but essentially, 3DNA is a
suite of command-line driven programs which do not rely on RasMol
for using the alchemy files.
Because if it's a program that produces them, I suggest doing a little
modification to that program to produce Jmol scripts instead. That
would be far more efficient, and it should be pretty easy to make them
- probably just one small subroutine. Then you could do all sorts of
interesting things in relation to dynamically changing them,
displaying them, measuring them, etc., within Jmol. For example, that
one you show as a demo could be something like this:
pt1={-2.2500 5. 0.2500}
pt2={-2.2500 -5. 0.2500}
pt3={-2.2500 -5. -0.2500}
pt4={-2.2500 5. -0.2500}
pt5={2.2500 5. 0.2500}
pt6={2.2500 -5. 0.2500}
pt7={2.2500 -5. -0.2500}
pt8={2.2500 5. -0.2500}
draw box line @pt1 @pt2 @pt3 @pt4 @pt1 @pt5 @pt6 @pt7 @pt8 @pt5
draw side1 plane @pt1 @pt2 @pt3 @pt4
(not complete, but you get the idea)
But even better, you could define a Jmol function that draws the boxes
for you give the eight points:
function drawbox(name, pt1, pt2, pt3, pt4, pt5, pt6, pt7, pt8)
draw ID @{name + _box} line @pt1 @pt2 @pt3 @pt4 @pt1 @pt5 @pt6
@pt7 @pt8 @pt5
draw ID @{name + _side1} plane @pt1 @pt2 @pt3 @pt4
etc.
end function
then just
drawbox({-2.2500 5. 0.2500},{-2.2500 -5. 0.2500}
,{-2.2500 -5. -0.2500} ,\
{-2.2500 5. -0.2500},{2.2500 5. 0.2500},{2.2500
-5. 0.2500},\
{2.2500 -5. -0.2500},{2.2500 5. -0.2500})
for each box. It seems to me, for that matter, you only need three
points to define the box. So that would be even easier.
Now, if you are really fancy, what you do is embed those commands in
the pdb files themselves, so when the pdb file is loaded, the boxes
are all drawn automatically. Rolf can show you how he does that at
Jena.
And, better, if you are doing this based on some simple criterion in
PDB files, then you should be able to define a function that allows
drawing of such boxes for the entire model all within Jmol. That would
be REALLY COOL, because then anyone could do it with any PDB file. I
have such a function (somewhere), for example, for drawing all the
peptide planes.
Bob
Given the amazing support of Jmol from you and others, I have been
considering to use Jmol (and eventually switch to it), and then came
cross the alchemy format issue. All the cool stuffs you mentioned
are very impressive, and I will surely dig more deeply into Jmol in
the future. However, I still think a simple render of the alchemy
format in Jmol would be ideal. Then people like me could simply load
the alchemy file into Jmol to visualize it without writing any Jmol-
specific scripts.
I have checked RasMol v2.6.4 source code, and found the alchemy
reader is via function LoadAlchemyMolecule() in infile.c, and it is
pretty short. The data directory even has an example file
'asprin.alc'.
Since there is no official alchemy document, and given the problem
that 'openbabel' has with my non-chemistry oriented alchemy file
(see my previous post), maybe one could forget the complexity of
atom/bond types, just take them as nodes and linkages, and Jmol
would render the file at face value.
Thanks,
Xiang-Jun
--
Xiang-Jun Lu (Ph. D.)
Creator Maintainer of 3DNA
Email: [EMAIL PROTECTED]
http://3dna.rutgers.edu:8080/forum
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Re: [Jmol-users] scripting an atom's color?
Try changing that first parameter to
Atominfo[0].color
Away from my computer
On Oct 17, 2008, at 1:30 PM, Eric Martz [EMAIL PROTECTED]
wrote:
At 10/16/08, Eran Hodis wrote:
In the commandline or in a Jmol script you can do
numModels = getProperty(modelInfo,modelCount);
if (numModels 1) ...
Thank you Eran, that is exactly what I wanted.
Now I'd like to know the simplest way to get an atom's color into a
Jmol script variable. I got as far as
myAtomColor = getProperty(atomInfo, {3:a.n})
but that gives me a long list of atomInfo including the color. How to
I get just the color RGB value?
Thanks, -Eric
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Re: [Jmol-users] Open dialog appearance on Mac OS...
That makes sense. Still I need to add a box anyway because the information you type there is apparently not available for the previewer. It's very cool to be able to preview remote files. Bob. On Sep 16, 2008, at 9:55 PM, Jonathan Gutow [EMAIL PROTECTED] wrote: Bob, Ok, I can see a mac-like dialog without the text entry box for the applet inside firefox using the web page http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm This appears to be because the dialog is handled by the firefox interface to the JVM, which is requesting a MacOS look and feel. I agree. I see no way of allowing the text entry for URL access without using a separate dialog box. Based on this I think we should maintain the application using its own look and feel rather than the OS look and feel. Jonathan Begin forwarded message: From: Jonathan Gutow [EMAIL PROTECTED] Date: September 16, 2008 8:36:41 PM CDT To: jmol-users@lists.sourceforge.net Cc: Bob Hanson [EMAIL PROTECTED] Subject: Re: Open dialog appearance on Mac OS... I have attached a .png image of the open dialog I see on MacOS 10.4.11 with the latest Apple JVM using Jmol 11.6.RC14_dev (built on my machine). The Jmol application does not use the local look and feel (my recollection is that is the expected behavior, as we are not using the swing and its local look and feel option). Thus I'm surprised if you see Jmol having more mac-like windows when you test it. I typed in the file name in the file name box and the application opens it fine. Jonathan Open file dialog in 11.6.RC14_dev.png On Sep 16, 2008, at 5:45 PM, jmol-users- [EMAIL PROTECTED] wrote: Hmm. Could be a Java version issue. I definitely see what is shown at http://developer.apple.com/releasenotes/Java/Java142RN/WhatsNew/chapter_2_section_5.html You don't? I don't think I did anything to modify that, and the Java documentation supports the idea that there is no such box in Mac Java. In any case, I think I have to get rid of that idea and allow URL entry elsewhere in that dialog. On Tue, Sep 16, 2008 at 7:56 AM, Jonathan Gutow [EMAIL PROTECTED] wrote: Is this an applet only issue? I can definitely type the filename into the open dialog in the application version. Jmol 11.4.6, MacOS 10.4.11 Dr. Jonathan H. Gutow Chemistry Department [EMAIL PROTECTED] UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/faculty_staff/gutow/ Dr. Jonathan H. Gutow Chemistry Department [EMAIL PROTECTED] UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/faculty_staff/gutow/ --- -- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem in firefox
Must use 11.6.rc11
Sent from my iPhone
On Aug 29, 2008, at 10:14 AM, Jeff Hansen [EMAIL PROTECTED] wrote:
I spoke too soon.
var x = jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint)')
isn't working for me. It returns an error message about the
getProperty command.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 29, 2008, at 10:40 AM, Robert Hanson wrote:
mosty I think you will find that the jmolGetStatus() business won't
be helpful. I'm probably the only who ever used that. It was an
early attempt to get around callbacks, and I can't think of any
good reason to use it now.
Try something else, like the following:
alert(jmolGetPropertyAsString(auxiliaryinfo, , divInc))
For getting that property, these days I just use:
var x = jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint)')
rather than doing all the translation of the auxiliaryInfo array
into JavaScript just to get that one element.
But you are using Jmol 11.6.RC6 -- be sure to upgrade that to
11.6.RC11.
Bob
On Thu, Aug 28, 2008 at 11:00 PM, Jeff Hansen [EMAIL PROTECTED]
wrote:
Thanks Bob. If gas prices weren't so high and my family wouldn't
miss me too much I would take you up on the offer.
Of course jmolScriptWait didn't break anything, just my failed
attempts to use it broke something.
I tried your second alternative (callbacks are still a mystery to
me although that code doesn't look too bad). So after loading the
file I called a function.
this.loadString = load ../Jmol/jmol/Models/ + molecule +
;javascript myFunc();;
divWrite(divID,jmolApplet(400, this.loadString,divInc));
In the function I tried to use jmolGetStatus.
function myFunc(){
var result = jmolGetStatus(scriptStatus,divInc);
alert(result);
}
As with all of my attempts thus far this displayed undefined. I
guess I still don't get how this works.
I think ultimately I will put the load command along with some
other commands in a script file rather than continuing to make
these long (and going to get longer) strings.
I'm making progress and having fun. Does that make me a geek?
Thanks for the help and encouragement.
You can see how far I've come at http://web.mac.com/jhansen4/Jmol/NewJmolDivSTD.html
.
Jeff
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 28, 2008, at 10:47 PM, Robert Hanson wrote:
Jeff, why don't you come over to St. Olaf and I'll show you how
this works! :)
Seriously, hang in there. You are trying to do a lot all at once,
and you will catch on. This is precisely what this list is for.
Just keep at it.
jmolScriptWait would not break anything.
jmolScriptWait should only be used if you absolutely have to pause
the JavaScript until that operation is complete. There are times
this is necessary, but it's not a great idea.
Most Jmol commands are given asynchronously using jmolScript()
rather than jmolScriptWait(). Jmol has a built-in queuing system,
so you can fire as many commands at it as you wish, and they will
be processed in order as processing becomes available. You can
also clear the queue using
!exit
and you can abort a specifically running script (but continue
processing later scripts) using
!quit
An alternative to waiting is to have the issued script notify the
web page when it is complete. Eric Martz and Tim Driscoll
masterminded this idea using scriptcallback methods that see a
comment go by and then know it is time to do something. Something
like this:
set scriptcallback myfunc;set debugscript true;load
whatever;#--file is loaded
then myfunc() gets a message every time a script command is
executed, and the #--file is loaded message comes through as well:
function myfunc(app, msg) {
var s = + msg // converts Java string msg into a JavaScript
string
if (s.indexOf(#--file is loaded) == 0) {
[do something]
}
}
Alternatively, I've used the following quite effectively:
jmolScript(load whatever;javascript modelLoaded())
That would run the JavaScript function
function modelLoaded() {
}
as soon as the model is loaded.
Basically, good event driven code is asynchronous. Nothing waits
for anything. Things happen because they get a message that they
need to happen. The more you can do that, the better.
Still, I do use jmolScriptWait() myself at times. Also
jmolEvaluate() is synchronous, and I use that a lot as well.
Bob
On Thu, Aug 28, 2008 at 6:30 PM, Jeff Hansen [EMAIL PROTECTED]
wrote:
I tried jmolScriptWait but couldn't get it to not break the load
command.
Re: [Jmol-users] Jmol -- cool use of quaternions
Not a problem, Frieda. Whether you have one applet or four, it's all the
same, provided they are mouse-synchronized.
First, load an initial file:
load 1.xyz
moveto 0.0 ...
q = script(show rotation)
Then any later load of ANY file looks like this:
qrel = quaternion(script(show rotation)) / q
save orientation o1;
load xxx.xyz
moveto 0.0 ...
q = script(show rotation)
restore orientation o1;
rotate @{qrel * q / quaternion(script(show rotation))}
Just make sure that q= line is in your script when you INITIALLY load
a model into any applet.
When you go to reload the applet, use the other set.
OR, I think you could do a test and see whether there's already a model
there or not:
var haveModel = (_currentModelNumberInFile != 0)
if (haveModel)
qrel = quaternion(script(show rotation)) / q
save orientation o1;
endif
load xxx.xyz
moveto 0.0 ...
q = script(show rotation)
if (haveModel)
restore orientation o1;
rotate @{qrel * q / quaternion(script(show rotation))}
endif
This works because you are synchronizing.
If you are not synchronizing and you want to TRANSFER the orientation
from one applet to another, and, as you are doing have your own
customized initial orienation, then what you have to do is first query
that applet for qrel and its orientation:
[javascript here, presuming that was created as A -- there is an
applet with ID jmolAppletA]
var qrel = jmolEvaluate('quaternion(script(show rotation)) / q', A)
var o = jmolEvaluate('script(show orientation moveto)',
A).replace(/1.0/,0.0)
Then build a script command that does the SECOND part of the above sequence:
var script = 'load ' + someFileName + ';moveto 0.0 ...;q =
script(show rotation);' + \
o + ';rotate @{quaternion('+qrel+') * q /
quaternion(script(show rotation))};sync . on'
Then send that script to the other applet. We don't need the
save/restore, because the o variable will hold the orientation in it
as a moveTo command. We are defining qrel in the JavaScript, so we just
insert it where needed. Since it is in the form {xx xx xx xx}, we wrap
it with the quaternion() function so that Jmol reads it properly as a
quaternion.
Bob
Reichsman Frieda wrote:
Hi Bob,
I'd like to use this with two side-by-side applets where I am syncing
the mouse movements using
sync * on; sync * set syncMouse true
http://moleculesinmotion.com/aminoacids/
(Surface coloring not correct yet, please ignore.)
Each applet loads an amino acid from a drop-down menu. I have used a
moveto command to orient their initial positions. It looks to me like
I want permutation #6 from your list, but I am not sure how to do this
between two different applets. Can you help?
Frieda
//
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405
//
On Aug 15, 2008, at 10:23 AM, Bob Hanson wrote:
[blogging here]
You ask -- What the heck are these quaternions? Here's an example of
where quaternions come in handy in Jmol.
Say you have two files that you want to display sequentially, 1.xyz
and
2.xyz. They are connected in some way, perhaps because they are two
files along the same mechanistic pathway. When the user clicks a
link to
switch from Model 1 to Model 2 you want the user to experience no jump
of orientation -- just a subtly different file. How can that be done?
1) Well, if the two files have the same basic coordinates, there's no
real problem. You just use
load 1.xyz
...user changes orientation...
save orientation;
load 2.xyz
restore orientation;
The save/restore orientation does the trick.
2) But what if the INITIAL orientations of the two models are
different?
That is, what if generally you might have to use
load 2.xyz
moveto
to make 2.xyz line up with 1.xyz? What then? The problem is that if
the
user has manipulated the model, you can do that restore to get back to
THEIR orientation, but that's for the wrong model, and you can't just
put the restore before the moveto command, because the moveto will
override that. What to do?
3) The solution is to use quaternions. Jmol can report its rotational
state in terms of a quaternion. All you do is:
q1 = script(show rotation)
That's it. You now have saved the rotational state. AND, Jmol can now
rotate any model by that quaternion:
rotate @q1
So, to apply a user's changes to a DIFFERENT model:
load 1.xyz
...user changes orientation...
q1 = script(show rotation)
load 2.xyz
moveto 0.0 ...
rotate @q1
This is different. It saves the user's changes as a quaternion and
then
applies that quaternion after the moveto. Provided you have used 0
seconds for the time on that moveto, you won't even see a flicker with
Jmol 11.6.RC7 (this was recently fixed).
4) Ah, but there's a catch! The catch is that the user also may have
changed the zoom or the translation
Re: [Jmol-users] possible display bug in 11.6RC5
Thomas, I'm not able to reproduce that problem. See, for example: http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?3bzi or http://chemapps.stolaf.edu/pe/protexpl?id=3bzi Either it was something about 11.6.RC5 or there's still something odd there that I don't see. Bob Thomas Stout wrote: Hi Folks -- I'm working with the applet (version 11.6RC5 -- I can't keep up with the versions!) and have just noticed the following: the display of proteins in backbone or cartoon mode seems to be non-functional for me. This is true for all PDB files that I've loaded so far, but one example would be 3BZI. If I issue the following: load 3BZI.pdb # structure comes up in wireframe mode, all visible select protein backbone 0.33 # everything disappears except the waters and a formate spacefill off; wireframe off; backbone 0.33; # again, nothing visible wireframe 0.1; # now the protein is visible again wireframe off; cartoon on; # now I see only the hetatms again Using the pop-up menu gives the same results: Select protein All # 1,865 atoms selected Style Scheme Ball-and-Stick# All visible Style Scheme Trace # Only waters and a formate visible Style Scheme Cartoon # Only waters and a formate visible Style Scheme Spacefill# All visible Style Scheme Sticks# All visible Style Scheme Wireframe # All visible Finally, I tried in the console: calculate structure and re-displaying cartoons, backbone trace, etc and still had the same above behavior. Has anyone seen -- or specifically NOT seen -- this as well? I don't know if it just here or a general issue Thanks, Tom - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol -- cool use of quaternions
[blogging here]
You ask -- What the heck are these quaternions? Here's an example of
where quaternions come in handy in Jmol.
Say you have two files that you want to display sequentially, 1.xyz and
2.xyz. They are connected in some way, perhaps because they are two
files along the same mechanistic pathway. When the user clicks a link to
switch from Model 1 to Model 2 you want the user to experience no jump
of orientation -- just a subtly different file. How can that be done?
1) Well, if the two files have the same basic coordinates, there's no
real problem. You just use
load 1.xyz
...user changes orientation...
save orientation;
load 2.xyz
restore orientation;
The save/restore orientation does the trick.
2) But what if the INITIAL orientations of the two models are different?
That is, what if generally you might have to use
load 2.xyz
moveto
to make 2.xyz line up with 1.xyz? What then? The problem is that if the
user has manipulated the model, you can do that restore to get back to
THEIR orientation, but that's for the wrong model, and you can't just
put the restore before the moveto command, because the moveto will
override that. What to do?
3) The solution is to use quaternions. Jmol can report its rotational
state in terms of a quaternion. All you do is:
q1 = script(show rotation)
That's it. You now have saved the rotational state. AND, Jmol can now
rotate any model by that quaternion:
rotate @q1
So, to apply a user's changes to a DIFFERENT model:
load 1.xyz
...user changes orientation...
q1 = script(show rotation)
load 2.xyz
moveto 0.0 ...
rotate @q1
This is different. It saves the user's changes as a quaternion and then
applies that quaternion after the moveto. Provided you have used 0
seconds for the time on that moveto, you won't even see a flicker with
Jmol 11.6.RC7 (this was recently fixed).
4) Ah, but there's a catch! The catch is that the user also may have
changed the zoom or the translation. The solution again uses
quaternions, but this time in combination with save/restore. Quaternions
encode the rotation of a model in a RELATIVE SENSE. Thus, if
q1 = [first rotational state]
q2 = [later rotational state]
then the division
q3 = q2 / q1
gives you the CHANGE in going from the first state to the second
(sometimes referred to as the quaternion difference or quaternion
derivative).
So, check this out:
load 1.xyz
...user changes orientation...
q1 = script(show rotation)
save orientation o1;
load 2.xyz
moveto 0.0 ...
q2 = script(show rotation)
restore orientation o1;
rotate @{q2 / q1}
rotate @q1
See what that does? We are saving:
q1 the user's current rotation of model 1
o1 the user's full orientation change, including rotation q1, zoom,
and translation
q2 our default rotation for model 2
The restore takes us to rotation q1 and applies any user zoom or
translation changes.
The first rotation takes us back to our default rotation for Model 2, q2.
The second rotation applies the change the user made.
By the way, sequential rotations are applied using LEFT multiplication.
Those two rotations can be combined as:
rotate @{q1 * q2 / q1}
That's called a similarity transform.
5) Now, what if you have to rotate BOTH files to get the default
orientation you want? Then it's a bit more tricky, but not too bad:
load 1.xyz
moveto 0.0 ...
q1a = script(show rotation)
...user changes orientation...
q1b = script(show rotation)
save orientation o1;
load 2.xyz
moveto 0.0 ...
q2 = script(show rotation)
restore orientation o1;
rotate @{q2 / q1b}
rotate @{q1b / q1a}
See what that does? We are saving:
q1a our default rotation for model 1
q1b the user's current rotation of model 1
o1 the user's full orientation change, including rotation q1b, zoom,
and translation
q2 our default rotation for model 2
The restore takes us to rotation q1b, along with the user's changes to
translation and zoom.
The first rotation takes us back to our default rotation for Model 2,
q2, but leaves the user's zoom and translation unchanged.
The second rotation applies the change the user made relative to our
default for Model 1.
6) Finally, what if we want to allow the user to switch back and forth
between models with NO orientation jump? This is really cool. Here you go:
First, load an initial file:
load 1.xyz
moveto 0.0 ...
q = script(show rotation)
Then any later load of ANY file looks like this:
qrel = quaternion(script(show rotation)) / q
save orientation o1;
load xxx.xyz
moveto 0.0 ...
q = script(show rotation)
restore orientation o1;
rotate @{qrel * q / quaternion(script(show rotation))}
and now the code is fully symmetric. Put in any file name for xxx.xyz,
and this code will preserve orientation based on a custom default rotation.
7) Summary
Quaternions encode rotations. Their multiplication represents a series
of rotations, and their
Re: [Jmol-users] getProperty usage
In Jmol math you can drill down into properties by adding parameters
rather than using the dot notation.
nModels = getProperty(modelInfo,modelCount)
does what you want. If you know there is only one file loaded, but it
might have multiple models, AND you know they are numbered sequentially
starting with 1, so that the highest model number is the model count,
then this will work:
nModels = {*}.model.max
similarly, if there is a sequential array, as there is here:
print getproperty(modelInfo,models,3,file)
gives you the file for the third model. (Zero there instead of 3 would
give you information about the LAST model, -1 would be for the NEXT TO
LAST model, etc.)
It's not exactly obvious, but by looking at the full output for
modelInfo you might be able to guess what parameters you will need.
models is listed as a Vector[3], each of which includes a number of
items.
Ah, I have a great idea. We should be able to do this using the
following notation:
print getProperty(modelInfo.models[3].file)
Let me see if I can implement that.
modelinfo
modelSetHasVibrationVectorsfalse
modelCount3
modelSetName1CDR
modelSetProperties
PATH_SEPARATOR;
PATH_KEY.PATH
modelsVector[3]
atomCount1269
_ipt0
name1
bondCount1289
file_model1.1
polymerCount2
fileC:\jmol-dev\workspace\Jmol\bobtest\1.pdb
chainCount1
num1
vibrationVectorsfalse
title1CDR
groupCount80
,
atomCount1269
_ipt1
name2
bondCount1289
file_model1.2
polymerCount2
fileC:\jmol-dev\workspace\Jmol\bobtest\1.pdb
chainCount1
num2
vibrationVectorsfalse
title1CDR
groupCount80
,
atomCount725
_ipt2
name5
bondCount737
file_model1.3
polymerCount1
fileC:\jmol-dev\workspace\Jmol\bobtest\1.pdb
chainCount1
num5
vibrationVectorsfalse
title1CDR
groupCount49
Bob
Rolf Huehne wrote:
Hi,
I would like to use the Jmol math 'getProperty(modelInfo)' function to
get information on the currently loaded models within the application.
But I couldn't figure out how to access specific information like the
'modelCount' after the following command within Jmol 11.5.35:
modelInfo = getProperty(modelInfo);
When I print the whole content with 'print modelInfo', I get a long list
of information. I tried for example 'count = modelInfo.modelCount' but
got an error message.
When I tried to access 'modelInfo' like an array, I only got single
letters back.
Regards,
Rolf
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] getProperty usage
version=11.6.RC8_dev
# new feature: print getProperty(modelinfo.models[3].file) syntax
Rolf Huehne wrote:
Bob Hanson wrote:
Ah, I have a great idea. We should be able to do this using the
following notation:
print getProperty(modelInfo.models[3].file)
Let me see if I can implement that.
That would be very nice because it is already familiar. Actually it was
one of the other things I tried
('modelCount=getProperty(modelInfo.modelCount)').
Regards,
Rolf
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-
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Build the coolest Linux based applications with Moblin SDK win great prizes
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Re: [Jmol-users] pdb files
Well, it's supposed to be a comment. But I've adjusted Jmol to deal with these header-less HEADER lines. Bob rspinney wrote: Hi Bob, They were generated by Spartan or babel both of which have the HEADER as the first line. What should be after HEADER? Rick OK, I can fix that -- but it's due to a faulty PDB format. Where are these files from? They seem to have just the word HEADER at the top without anything after it. Bob rspinney wrote: I have just downloaded jmol-11.6.RC4 and have a problem opening pdb files. I get an error message of: Error reading file at line 1: HEADER String out of index range: -1 I seem to get this error message for any pdb file I try to open (all of which worked fine until now). Any ideas? - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] mol2 files
Where do these files come from? The mol2 format does not allow for anything between the number and the element symbol on that atom line. http://www.tripos.com/tripos_resources/fileroot/mol2_format_Dec07.pdf Bob Reichsman Frieda wrote: Hi Bob, I have some mol2 files wherein Jmol cannot read the embedded EPS (or are they more correctly called partial charge) values, and also Jmol fails to render one atom in the file. An example file is attached, along with one that Jmol reads fine: ala-problem.mol2 (Jmol won't read EPS) and ala.mol2 (Jmol does read EPS), Comparing the two mol2 files, the format is slightly different. I am not sure if the file is formatted incorrectly (generated by the program AtomSmith), or if Jmol is too strict. The differences are as follows. In the ala-problem.mol2 file, 1. The eps values from are offset by one additional space from the coordinates, and 2. the three-letter abbreviation for the amino acid is missing in each row from inbetween the number 1 and the EPS values. When I change both these aspects to mimic the file ala.mol2, Jmol can read the eps values. 3. In the ala-problem.mol2 file I also had to remove the ALA that appears as characters 4, 5 and 6 in the line for atom #1, in order for Jmol to be able to render that particular atom. Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] mol2 files
Just send them that documentation. Pretty clear that they have that wrong and will want to correct it. Reichsman Frieda wrote: They come from AtomSmith, which is from Bitwixt software. The file that works in Jmol is included with the program; the file that does not work in Jmol is AtomSmith's output when it starts with a pdb file, puts an EP surface around it, and exports it as mol2. If it's their formatting needs changing, then I can urge them to deal with it - I have already emailed them about it twice. Frieda On Aug 14, 2008, at 2:19 PM, Bob Hanson wrote: Where do these files come from? The mol2 format does not allow for anything between the number and the element symbol on that atom line. http://www.tripos.com/tripos_resources/fileroot/mol2_format_Dec07.pdf Bob Reichsman Frieda wrote: Hi Bob, I have some mol2 files wherein Jmol cannot read the embedded EPS (or are they more correctly called partial charge) values, and also Jmol fails to render one atom in the file. An example file is attached, along with one that Jmol reads fine: ala-problem.mol2 (Jmol won't read EPS) and ala.mol2 (Jmol does read EPS), Comparing the two mol2 files, the format is slightly different. I am not sure if the file is formatted incorrectly (generated by the program AtomSmith), or if Jmol is too strict. The differences are as follows. In the ala-problem.mol2 file, 1. The eps values from are offset by one additional space from the coordinates, and 2. the three-letter abbreviation for the amino acid is missing in each row from inbetween the number 1 and the EPS values. When I change both these aspects to mimic the file ala.mol2, Jmol can read the eps values. 3. In the ala-problem.mol2 file I also had to remove the ALA that appears as characters 4, 5 and 6 in the line for atom #1, in order for Jmol to be able to render that particular atom. Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url
Re: [Jmol-users] Issues with Polyhedra and cavities in solid structures
Nick Greeves wrote:
Hi All,
We have been trying to use Jmol to display coordination polyhedra for
a range of inorganic structures and have encountered what seems to us
anomalous behaviour. I have set up some of the pages on an external
server using Jmol 11.6RC6 so that anyone interested can take a look.
These pages are unfinished and may disappear without warning. I
suspect some of these may require expert input from Bob but others may
sound familiar to other users.
NiAs http://osxs.ch.liv.ac.uk/~ng/sandbox/
http://osxs.ch.liv.ac.uk/%7Eng/sandbox/_NiAs-test.htm
http://xserve.ch.liv.ac.uk/%7Eskho/_NiAs-test.htm
1st Ni Polyhedron button
why is third octahedron not visible?
perhaps the code restrict cell={2 2 2}; set unitcell {1 1 1}; centre
unitcell; polyhedra 6 ((_ni) and visible); colour polyhedra
translucent; zoom 200 only works properly when the polyhedra are
inside the cells, and not when the polyhedra overlaps into a second cell?
Only two Ni in cell {2 2 2} have 6 As around them. The third is in cell
{1 1 1}
Li3Bi http://osxs.ch.liv.ac.uk/~ng/sandbox/
http://osxs.ch.liv.ac.uk/%7Eng/sandbox/_Li3Bi(2)-test.htm
http://xserve.ch.liv.ac.uk/%7Eskho/_Li3Bi%282%29-test.htm
Various attempts at showing BOTH the tetrahedra and octahedra for both
types of Li.
Perhaps problems displaying 2 types of polyhedra of the same element
(Li) together (changing colours or translucent/opaque)
also, an example where polyhedra do not extend beyond unitcell (notice
missing Oh polyhedra on one side)
Polyhedra won't go to atoms that are not there. The thing to do is start
with
select _li and connected(4)
or
select _li and connected(6)
then do the polyhedra -- with different colors. I found it worked to use
select _li and connected(4) and atomno 30;polyhedra 4 red
select _li and connected(6) and atomno 50;polyhedra 6 green
that way you get some spacial separation as well.
YCl3 http://osxs.ch.liv.ac.uk/~ng/sandbox/
http://osxs.ch.liv.ac.uk/%7Eng/sandbox/_YCl3(2).htm
http://xserve.ch.liv.ac.uk/%7Eskho/_YCl3%282%29.htm
BiI3 http://osxs.ch.liv.ac.uk/~ng/sandbox/_BiI3(2).htm
http://xserve.ch.liv.ac.uk/%7Eskho/_BiI3%282%29.htm
These use code hideNotselected, to hide unwnated ions but how can we
select polyhedra as well so they show up?
OK, so I see:
select *; hide none; centre; boundbox off; unitcell off; axes off;
wireframe off; spacefill off; polyhedra off; polyhedra 6 (_Bi) to (_I)
collapsed edges; select atomno=261 or atomno=213 or atomno=111 or
atomno=264 or atomno=161 or atomno=113 or atomno=3 or atomno=164 or
atomno=57 or atomno=272 or atomno=221 or atomno=119 or atomno=169 or
atomno=172 or atomno=171 or atomno=121 or atomno=13 or atomno=67 or
atomno=70 or atomno=69 or atomno=227 or atomno=230 or atomno=229 or
atomno=280 or atomno=127 or atomno=130 or atomno=129 or atomno=180 or
atomno=21 or atomno=285 or atomno=239 or atomno=137 or atomno=288 or
atomno=185 or atomno=139 or atomno=31 or atomno=188 or atomno=83 or
atomno=296 or atomno=247 or atomno=145 or atomno=193 or atomno=196 or
atomno=195 or atomno=41 or atomno=147 or atomno=93 or atomno=96 or
atomno=95 or atomno=253 or atomno=256 or atomno=255 or atomno=304 or
atomno=153 or atomno=156 or atomno=155 or atomno=204 or atomno=49 or
atomno=143 or atomno=240 or atomno=291 or atomno=140 or atomno=192 or
atomno=39 or atomno=191 or atomno=35 or atomno=92 or atomno=257 or
atomno=259 or atomno=260 or atomno=157 or atomno=159 or atomno=160 or
atomno=305 or atomno=207 or atomno=56 or atomno=205 or atomno=107 or
atomno=152 or atomno=297 or atomno=199 or atomno=197 or atomno=200 or
atomno=48 or atomno=99 or atomno=97 or atomno=100 or atomno=117 or
atomno=214 or atomno=267 or atomno=114 or atomno=168 or atomno=11 or
atomno=167 or atomno=7 or atomno=66 or atomno=231 or atomno=233 or
atomno=234 or atomno=133 or atomno=131 or atomno=134 or atomno=183 or
atomno=281 or atomno=28 or atomno=181 or atomno=81 or atomno=74 or
atomno=71 or atomno=73 or atomno=20 or atomno=173 or atomno=176 or
atomno=175 or atomno=126 or atomno=273; set hideNotSelected TRUE; hide
hidden and not polyhedron; spacefill 12%; centre [_Bi] 5; show centre;
centre; zoom 120
but hide hidden and not polyhedron does nothing, because polyhedron
is not defined (I think). I wouldn't use hideNotSelected here. Why not
just say, for example,
select _Bi;polyhedra 6;hide not connected(6)
Then using Jmol.jar to view close-packed structures and hoping to
display the holes in ccp, hcp, and bcc (attached) leads to many problems.
The command within {atomno= } seems to only display exterior
holes rather than internal ones.
within what?
And using command isosurface interior cavity ___ , hcp are holes
displayed, but cannot find code to display any holes in ccp.
that is definitely a challenge.
For bcc,
isosurface interior cavity 0.001 within 5.0 (atomno=11) sasurface 0.04
isosurface interior cavity 0.05
Re: [Jmol-users] Secondary structure determination in Jmol
Eran,
Eric has it essentially correct. Jmol does not use DSSP, and I'm not at
all surprised that its algorithm is, in his words, flawed. It's a very
simplistic algorithm, just using PSI and PHI and not meant to be taken
too seriously. Jmol is a viewer, with no claim to be full-blown DSSP
calculator by any means. Mostly that algorithm is just a fall-back
method for cases that have no structure indicated, which is probably no
actual PDB files in the PDB database. (I'm guessing.)
That said, you can customize secondary structure just about any way you
want in Jmol. You are not at all restricted to what the author has
indicated. To do this, simply issue the (hmm, undocumented) STRUCTURE
command:
structure HELIX {atomExpression}
structure TURN {atomExpression}
structure SHEET {atomExpression}
structure NONE {atomExpression}
This command was undocumented, originally intended only for defining the
state. But in 11.5.32 I mistakenly thought it was unnecessary for the
state and removed it. However, it IS needed in the state, so it's back
in and will be documented. (It works in 11.5, but doesn't save properly
in the state until 11.6.RC7.)
Bob Hanson
Eric Martz wrote:
At 8/13/08, [EMAIL PROTECTED] wrote:
Here are the issues Shaun Lott [Univ. Auckland NZ, a Proteopedia
user] raised with me:
Hi Eran
1) Secondary structure definitions - How does Jmol generate them? Are
they user definable? Jmol is clearly using a different algorithm to
sPDBv, so students are seeing inconsistency when they use both
routes. (For the record, I agree with sPDBv's pick!)
Dear Shaun and Eran,
Here is my preliminary take. I am copying this to jmol-users and
deepview-users for correction and discussion.
When the PDB file header includes HELIX, SHEET, and TURN records, that
is, the secondary structure was specified by the authors of the PDB
file, then Jmol obeys those (as do RasMol and Chime). (I have no
experience on SwissPDBViewer's secondary structure handling, so will
not comment on it.)
Authors' secondary structure specifications can, on occasion, be
somewhat subjective. For example, consider a long helix with a slight
bend in the middle. Objective criteria might deem that bend to be
slightly outside helix criteria, therefore breaking the helix into two
helices. The authors might just call the whole thing one helix,
bearing in mind that with vibrations in solution at physiological
temperature, what is or is not a strictly-defined helix might change
from one moment to the next.
Also, most authors don't specify TURN records. Nearly 90% of PDB
entries have HELIX and/or SHEET records, but only 4% have TURN
records. Yet Chime finds turns in nearly all proteins.
You can indeed specify secondary structure by hand-editing of the
HELIX, SHEET, and TURN records in the PDB file header. If there is
another easier way to do this in Jmol, I don't know about it.
There is an alternative to using the Author's secondary structure. You
can enter (in Jmol's console) these commands to get an objective
determination:
select all
connect
wireframe off
calculate structure
select protein
cartoon
color cartoon structure
This determines secondary structure using Jmol's implementation of the
DSSP scheme of Kabsch and Sander, 1983. See
http://en.wikipedia.org/wiki/Secondary_structure for more on DSSP.
Jmol does not seem to designate any turns. In contrast, RasMol and
Chime do.
RasMol and Chime also obey the PDB file header HELIX, SHEET, and TURN
records if present. If not, or manually, you can enter the commands
select protein
structure
cartoon
color structure
and get the calculated result, including turns colored blue.
---
Specifically, for chain A of 1PRX:
Helix 4 (a 5-residue helix) is specified in the PDB file header as
109-113.
HELIX4 4 GLU A 109 LEU
A 113
1
5
Jmol's calculate structure extends this helix one residue towards
the N terminus, to include range 108-113. Chime's structure makes no
change in this helix.
Strand 4 in sheet B (a 5-stranded sheet) is deemed to consist of
residues 66-72.
SHEET4 B 5 VAL A 66 SER
A 72 1 N LYS A 67 O TRP
A 33
Jmol's calculate structure extends this strand's C terminus to
residue 75, causing the strand to include an obvious turn. Chime
makes no change in the length of the strand, and deems residues 73-74
to constitute a turn (blue).
-
TENTATIVE CONCLUSIONS
These disagreements between Rasmol/Chime and Jmol, plus Jmol's
extension of a strand around a turn, suggest that Jmol's objective
algorithm is flawed.
Since you find that Jmol and SPDBV disagree, and since I think Jmol is
using what is in the PDB Header, this suggests that by default, SPDBV
is doing its own objective calculation, and discarding the authors'
secondary structure. I've copied this to the SPDBV list
Re: [Jmol-users] testing needed
that's fine. Plenty to do here. Reichsman Frieda wrote: Bob, will testing still be timely if it waits until the weekend? Frieda On Aug 13, 2008, at 7:48 AM, Bob Hanson wrote: A chance to contribute! Nico has just released Jmol 11.6.RC6. This release needs serious testings in the next few days. Please check this in any way you can and get back to us. Refreshing -- Some core functionality was tweaked. Specifically, I reduced the number of times Jmol does refreshes. My first attempt at this (Jmol 11.5.RC5) was not successful, but I'm hoping 11.5.RC6 is better. These changes should significantly reduce the number of times Jmol tries to refresh, leading to smoother scripting. But it's also possible that I have removed a few too many of these. So the thing to look out for is odd refreshing behavior. Synchronization --- Eric Martz, I'm hoping you can check out synchronization issues, since you seem to be working on that. The changes I made should not affect synchronization, but they may. Documentation - Up to date? Working ok? Does the applet console Help menu item work? (I know there's a problem with the top item. Anybody care to fix that? What I'd like there is a Search item.) Point Groups Are we done? Images -- This is really incredible. Put an image anywhere using SET ECHO IMAGE, in 2D or 3D. Scale it anyway you want. Note that set fontScaling works the same as for 3D echo text as for echo images. Scaling can be accomplished right now using a not-so-obvious scaling factor in the FONT ECHO command. I would really appreciate someone doing some testing of this. Suggestions? Do we still need alpha translucency? -- That is, so that the applet can appear in a layer in front of an image? If so, please let me know how to do that. I think it's an easy addition. General --- So just a simple yes, this works on my site would be helpful. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] just for fun ;)
OK, I'm expecting you to do incredible things with this, Frieda. Bob Reichsman Frieda wrote: Excellent Bob! And quite the final touch! Frieda On Aug 11, 2008, at 10:12 PM, Bob Hanson wrote: OK, just for fun... http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm click the long red link. SOMEONE's going to have some fun with this. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jvxl pdf unavailable
http://chemapps.stolaf.edu/jmol/docs/JVXL-format.pdf Reichsman Frieda wrote: Hi Bob, Your JVXL format pdf file is apparently not available right now at this URL: http://www.stolaf.edu/people/hansonr/jmol/docs/JVXL-format.pdf The connection times out in Safari3/Mac, and in FF2/Mac, never gets past starting... Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol 11.6.RC5 -- background IMAGE
I believe this is the final feature to be added prior to 11.6. Complementing the set echo IMAGE command, we now have: background IMAGE somefilename.xxx format can be JPG, PNG, or GIF unlike echo, this command stretches the image to fit. See the example at: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Java exception in 11.5.51 that wasn't present in 11.5.37....
Thomas Stout wrote: Hi again Bob -- I've been able to test Jmol 11.6RC4 and I'm sorry to say that I get the same behavior Is there any other information I can provide you to help track this down?? -Tom FileManager.openFile(../../struct/protein1_aligned.pdb) //../../struct/protein1_aligned.pdb FileManager opening http://comte/struct/protein1_aligned.pdb http://comte/struct/EphB4/02252331/EphB4_02252331_aligned.pdb The Resolver thinks Pdb openFile(../../struct/protein1_aligned.pdb): 156 ms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 models in this collection. Use getProperty modelInfo or getProperty auxiliaryInfo to inspect them. ModelSet: autobonding; use autobond=false to not generate bonds automatically FileManager opening http://comte/structures3/sandbox_11.6RC4/color_models.spt java.lang.ClassCastException: java.util.BitSet cannot be cast to java.lang.String at org.jmol.viewer.Eval.expression(Unknown Source) at org.jmol.viewer.Eval.expression(Unknown Source) at org.jmol.viewer.Eval.select(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.script(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.runEval(Unknown Source) at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) at org.jmol.viewer.Viewer.scriptWait(Unknown Source) at org.jmol.applet.Jmol.scriptProcessor(Unknown Source) at org.jmol.applet.Jmol.scriptWait(Unknown Source) at JmolApplet.scriptWait(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.plugin.javascript.JSInvoke.invoke(Unknown Source) at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.plugin.javascript.JSClassLoader.invoke(Unknown Source) at sun.plugin.com.MethodDispatcher.invoke(Unknown Source) at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source) at sun.plugin.com.DispatchImpl$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at sun.plugin.com.DispatchImpl.invoke(Unknown Source) java.lang.Exception: java.lang.ClassCastException: java.util.BitSet cannot be cast to java.lang.String at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source) at sun.plugin.com.DispatchImpl$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at sun.plugin.com.DispatchImpl.invoke(Unknown Source) On 8/10/08, *Thomas Stout* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Terrific - looking forward to it! Thanks Bob, Tom On Sun, Aug 10, 2008 at 12:14 AM, Bob Hanson [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: I found it. That's fixed for 11.6RC4 Thomas Stout wrote: Hi Bob -- It looks like 11.6RC2 behaves the same way. I had bigger problems with 11.6RC3, so I can't evaluate that version with respect to this. Here's the bottom of the java console dump: FileManager.openFile(../../struct/protein1_aligned.pdb) //../../struct/protein1_aligned.pdb FileManager opening http://comte.exelixis.com/struct/protein1_aligned.pdb The Resolver thinks Pdb openFile(../../struct/protein1_aligned.pdb): 94 ms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 models in this collection. Use getProperty modelInfo or getProperty auxiliaryInfo to inspect them. ModelSet: autobonding; use autobond=false to not generate bonds automatically FileManager opening http://comte.exelixis.com/structures3/sandbox_11.6RC2/color_models.spt java.lang.ClassCastException: java.util.BitSet cannot be cast to java.lang.String at org.jmol.viewer.Eval.expression(Unknown Source) at org.jmol.viewer.Eval.expression(Unknown Source) at org.jmol.viewer.Eval.select(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.script(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.runEval(Unknown Source) at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) at org.jmol.viewer.Viewer.scriptWait(Unknown Source) at org.jmol.applet.Jmol.scriptProcessor(Unknown Source) at org.jmol.applet.Jmol.scriptWait(Unknown Source) at JmolApplet.scriptWait(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source
Re: [Jmol-users] Sync bug(?) and questions
Eric, I'm glad you are looking at sync. I'll take a look myself and see
what I can come up with.
Eric Martz wrote:
Dear Bob,
1. Bug: At http://moleculesinmotion.com/patterson_aas2/aminoacids/
(Jmol 11.5.50)
If you open one console and enter sync * on, and then rotate any
molecule with the mouse, the entire bottom row flips upside down
(does a 180 degree X rotation). I see this in both Safari/OSX and
Firefox/Win98.
cool effect. ;)
I have seen intermittant problems of this sort many times in my JTAT
sync demos, but never had one so reproducible that I could report it
as a bug. The above page seems to demonstrate the bug nicely.
I'll look at that page.
2. Why is it that when show syncmouse reports synchmouse = false
(the default), a sync * on command nevertheless synchronizes
mouse-initiated movements? What is the effect of set syncmouse true?
The code at http://chemapps.stolaf.edu/jmol/docs/examples-11/sync4.htm
uses the following. drive is a checkbox.
function sync() {
var syncing = document.getElementById(drive).checked
var s = (syncing ? 'sync * on;sync * set syncMouse on;set syncScript
off;sync jmolAppletC SLAVE;sync jmolAppletD SLAVE': 'sync * off')
jmolScript(s, A);
}
Applet A is being designated as the driver. It gets sent
sync * on
which enables all the sync on all four applets.
sync * set syncMouse on;set syncScript off
sends the message to all applets to turn mouse syncing on and script
syncing off. Script syncing is off so that you can selectively render
structures in any one of the four applets.
sync jmolAppletC SLAVE;sync jmolAppletD SLAVE
sets both C and D as slaves, but leaves A and B as drivers.
The difference between
set syncMouse TRUE
and
set syncMouse FALSE
is that in the first case, the mouse syncing is carried out at a lower
level using special non-script commands. Using
set LogLevel 5
you can check that out. Just look at the Java Console:
sync * set syncMouse TRUE
jmolAppletB__3539942059766625__ sending to
jmolAppletC__3539942059766625__: Mouse: rotateXYBy 2 2
jmolAppletC__3539942059766625__ syncing with script: Mouse: rotateXYBy 2 2
jmolAppletB__3539942059766625__ sending to
jmolAppletD__3539942059766625__: Mouse: rotateXYBy 1 1
jmolAppletD__3539942059766625__ syncing with script: Mouse: rotateXYBy 1 1
jmolAppletB__3539942059766625__ sending to
jmolAppletA__3539942059766625__: Mouse: rotateXYBy 1 1
jmolAppletA__3539942059766625__ syncing with script: Mouse: rotateXYBy 1 1
jmolAppletA__3539942059766625__ sync mode=3; synced? true; driving?
true; disabled? true
sync * set syncMouse FALSE
jmolAppletB__3539942059766625__ sending to
jmolAppletD__3539942059766625__: !moveto 0.1 { -344 540 -768 158.35}
100.0 0.0 0.0 {10.5935 10.2105 6.079} 17.392593 {0.0 0.0 0.0} 11.275982
-43.427624 50.0;
jmolAppletD__3539942059766625__ syncing with script: !moveto 0.1 { -344
540 -768 158.35} 100.0 0.0 0.0 {10.5935 10.2105 6.079} 17.392593 {0.0
0.0 0.0} 11.275982 -43.427624 50.0;
jmolAppletB__3539942059766625__ sending to
jmolAppletA__3539942059766625__: !moveto 0.1 { -344 540 -768 158.35}
100.0 0.0 0.0 {10.5935 10.2105 6.079} 17.392593 {0.0 0.0 0.0} 11.275982
-43.427624 50.0;
jmolAppletA__3539942059766625__ syncing with script: !moveto 0.1 { -344
540 -768 158.35} 100.0 0.0 0.0 {10.5935 10.2105 6.079} 17.392593 {0.0
0.0 0.0} 11.275982 -43.427624 50.0;
jmolAppletA__3539942059766625__ sync mode=3; synced? true; driving?
true; disabled? true
So the difference there is mostly efficiency. The first should be cleaner.
3. After sync * on, show sync reports synchronize = not set. ???
There is no variable synchronize. sync * on is a command, not a
variable definition. Right now there is no way for the applet to find
out what its sync state is.
4. I do not see syncMouse or syncScript in the state report. Should
they be there if they remain at defaults?
I thought not. The state is the state of the isolated applet, not its
state relative to other applets. Right now, at least, you can't save the
state, reset the sync, and then restore the state to the earlier sync
state. Sounds like a real can of worms to me. Or, to put it another way,
applet synchonization is above the state. Note that you can zap and
load models and initialize and all the synchronization is still intact.
Thanks, -Eric
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
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___
Jmol-users mailing list
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https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
Re: [Jmol-users] Sync bug(?) and questions
Eric Martz wrote: Dear Bob, 1. Bug: At http://moleculesinmotion.com/patterson_aas2/aminoacids/ (Jmol 11.5.50) If you open one console and enter sync * on, and then rotate any molecule with the mouse, the entire bottom row flips upside down (does a 180 degree X rotation). I see this in both Safari/OSX and Firefox/Win98. That's not a bug. It's your files. Those two files (asp.mol2 and val.mol2) are not stored in the same way -- try RESET on both consoles and you will see that the flip is related to that. If you want to synchronize those, using the Jmol application open them both into separate frames, and then frame * select 1.1 and use rotateselected to align one just the way you want it. Then use write coord MOL filename.mol2 to create a new MOL file with the coordinates. Oh, that may not save the charges - you may have to go in and do that by hand. In any case, you need to create a new mol file with the proper, aligned rotations. Oh -- ok, wait, THAT's the real difference with syncMouse. If you just use sync * on; sync * set syncMouse true I think it will track the way you intend. When TRUE, rotations with the mouse are delivered, so the slave can be manipulated separately. When FALSE, then you can manipulate the slave, but the instance you drag the driver you deliver the exact MOVETO to the slave, not the mouse action. That's what that is. Note that you cannot just use: set syncMouse true You have to use sync * set syncMouse true so that ALL the applets get that message. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] just for fun ;)
OK, just for fun... http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm click the long red link. SOMEONE's going to have some fun with this. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Java exception in 11.5.51 that wasn't present in 11.5.37....
Oh, I think it's fixed. The following works at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm load 1crn.pdb m = 2,3,4 print m select @m It was the @m in the select command that was the problem in earlier versions. 1) Make sure ALL your browsers windows have been closed. This generally flushes the Java cache and allows a new Jmol version to load. 2) Use the jar files in http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip 3) If it still does not work, send me the full console report, including the line that shows what Jmol version was loaded. Also, if you can, please send me the model and the script so I can try it here myself. Bob Thomas Stout wrote: Hi again Bob -- I've been able to test Jmol 11.6RC4 and I'm sorry to say that I get the same behavior Is there any other information I can provide you to help track this down?? -Tom FileManager.openFile(../../struct/protein1_aligned.pdb) //../../struct/protein1_aligned.pdb FileManager opening http://comte/struct/protein1_aligned.pdb http://comte/struct/EphB4/02252331/EphB4_02252331_aligned.pdb The Resolver thinks Pdb openFile(../../struct/protein1_aligned.pdb): 156 ms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 models in this collection. Use getProperty modelInfo or getProperty auxiliaryInfo to inspect them. ModelSet: autobonding; use autobond=false to not generate bonds automatically FileManager opening http://comte/structures3/sandbox_11.6RC4/color_models.spt java.lang.ClassCastException: java.util.BitSet cannot be cast to java.lang.String at org.jmol.viewer.Eval.expression(Unknown Source) at org.jmol.viewer.Eval.expression(Unknown Source) at org.jmol.viewer.Eval.select(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.script(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.runEval(Unknown Source) at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) at org.jmol.viewer.Viewer.scriptWait(Unknown Source) at org.jmol.applet.Jmol.scriptProcessor(Unknown Source) at org.jmol.applet.Jmol.scriptWait(Unknown Source) at JmolApplet.scriptWait(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.plugin.javascript.JSInvoke.invoke(Unknown Source) at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.plugin.javascript.JSClassLoader.invoke(Unknown Source) at sun.plugin.com.MethodDispatcher.invoke(Unknown Source) at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source) at sun.plugin.com.DispatchImpl$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at sun.plugin.com.DispatchImpl.invoke(Unknown Source) java.lang.Exception: java.lang.ClassCastException: java.util.BitSet cannot be cast to java.lang.String at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source) at sun.plugin.com.DispatchImpl$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at sun.plugin.com.DispatchImpl.invoke(Unknown Source) On 8/10/08, *Thomas Stout* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Terrific - looking forward to it! Thanks Bob, Tom On Sun, Aug 10, 2008 at 12:14 AM, Bob Hanson [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: I found it. That's fixed for 11.6RC4 Thomas Stout wrote: Hi Bob -- It looks like 11.6RC2 behaves the same way. I had bigger problems with 11.6RC3, so I can't evaluate that version with respect to this. Here's the bottom of the java console dump: FileManager.openFile(../../struct/protein1_aligned.pdb) //../../struct/protein1_aligned.pdb FileManager opening http://comte.exelixis.com/struct/protein1_aligned.pdb The Resolver thinks Pdb openFile(../../struct/protein1_aligned.pdb): 94 ms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 models in this collection. Use getProperty modelInfo or getProperty auxiliaryInfo to inspect them. ModelSet: autobonding; use autobond=false to not generate bonds automatically FileManager opening http://comte.exelixis.com/structures3/sandbox_11.6RC2/color_models.spt java.lang.ClassCastException: java.util.BitSet cannot be cast to java.lang.String at org.jmol.viewer.Eval.expression(Unknown Source) at org.jmol.viewer.Eval.expression(Unknown Source) at org.jmol.viewer.Eval.select(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.script(Unknown
Re: [Jmol-users] Java exception in 11.5.51 that wasn't present in 11.5.37....
I found it. That's fixed for 11.6RC4 Thomas Stout wrote: Hi Bob -- It looks like 11.6RC2 behaves the same way. I had bigger problems with 11.6RC3, so I can't evaluate that version with respect to this. Here's the bottom of the java console dump: FileManager.openFile(../../struct/protein1_aligned.pdb) //../../struct/protein1_aligned.pdb FileManager opening http://comte.exelixis.com/struct/protein1_aligned.pdb The Resolver thinks Pdb openFile(../../struct/protein1_aligned.pdb): 94 ms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 models in this collection. Use getProperty modelInfo or getProperty auxiliaryInfo to inspect them. ModelSet: autobonding; use autobond=false to not generate bonds automatically FileManager opening http://comte.exelixis.com/structures3/sandbox_11.6RC2/color_models.spt java.lang.ClassCastException: java.util.BitSet cannot be cast to java.lang.String at org.jmol.viewer.Eval.expression(Unknown Source) at org.jmol.viewer.Eval.expression(Unknown Source) at org.jmol.viewer.Eval.select(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.script(Unknown Source) at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.Eval.runEval(Unknown Source) at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) at org.jmol.viewer.Viewer.scriptWait(Unknown Source) at org.jmol.applet.Jmol.scriptProcessor(Unknown Source) at org.jmol.applet.Jmol.scriptWait(Unknown Source) at JmolApplet.scriptWait(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.plugin.javascript.JSInvoke.invoke(Unknown Source) at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.plugin.javascript.JSClassLoader.invoke(Unknown Source) at sun.plugin.com.MethodDispatcher.invoke(Unknown Source) at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source) at sun.plugin.com.DispatchImpl$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at sun.plugin.com.DispatchImpl.invoke(Unknown Source) java.lang.Exception: java.lang.ClassCastException: java.util.BitSet cannot be cast to java.lang.String at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source) at sun.plugin.com.DispatchImpl$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at sun.plugin.com.DispatchImpl.invoke(Unknown Source) On 8/8/08, *Bob Hanson* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: I'm pretty sure I found that and fixed it last week. Please try 11.6.RC2 Thomas Stout wrote: When running Jmol 11.5.37, the following script (color_models.spt) works fine: n_models = getProperty(modelInfo,modelCount); clist=array(green,palevioletred,lightblue,coral,yellow,cyan,\ dodgerblue,aqua,salmon,greenyellow,lavender,\ lightgoldenrodyellow,lightseagreen,lightskyblue,\ lime,limegreen,mistyrose,olive,orange,peachpuff,\ sandybrown,seagreen,tan,teal,wheat,yellowgreen); ini = 2; fin = n_models; for (var i = ini; i = fin; i = i + 1) m = */+i+.1; select @m and :Z and *.C??; print clist[i]; s = clist[i]; color @s; end for This results in different colors for the carbons of multiple chains Z from superimposed PDB files. Unfortunately in Jmol 11.5.51, I'm finding that this same script causes a java exception and locks up the Jmol applet graphics. Here is the output to the Java console when it works (Jmol 11.5.37): *FileManager.openFile(../../struct/protein1_aligned.pdb) //../../struct/protein1_aligned.pdb FileManager opening **http://comte.exelixis.com/struct/protein1_aligned.pdb* *The Resolver thinks Pdb openFile(../../struct/protein1_aligned.pdb): 32 ms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 models in this collection. Use getProperty modelInfo or getProperty auxiliaryInfo to inspect them. ModelSet: autobonding; use autobond=false to not generate bonds automatically FileManager opening **http://comte.exelixis.com/structures3/bin-release/color_models.spt* *flowContextfor 10 end flowContextfor palevioletred * And here is the same output from Jmol 11.5.51: FileManager.openFile(../../struct/protein1_aligned.pdb) //../../struct
[Jmol-users] Jmol 11.6.RC3, point groups, dot density
version=11.6.RC3 # new feature: set dotDensity [-3 to 3] [Eric Martz, please check that out] # bug fix: minor error in pointgroup # new feature: draw pointGroup [type] [index] SCALE [x] # where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or the character n [Dean Johnston, please check that out] http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm files in http://chemapps.stolaf.edu/jmol/docs/examples-11 Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 11.6.RC3, point groups, dot density
Dean Johnston wrote: On Fri, Aug 8, 2008 at 8:46 AM, Bob Hanson [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: version=11.6.RC3 # bug fix: minor error in pointgroup # new feature: draw pointGroup [type] [index] SCALE [x] # where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or the character n [Dean Johnston, please check that out] http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm Very nice - I like that you can select what to draw and the different color for the horizontal plane. How is the default scale determined? (It seems with some molecules [C2h], the planes extend well beyond the outermost atoms, while with others [Ih], they end in the middle of some atoms.) right now it's just 3 Angstroms in diameter. I can't think of any general way to improve on that. Molecules come in all shapes and sizes, after all. I suppose it could be scaled based on the bounding box. Do you want me to try that? Dean - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Java exception in 11.5.51 that wasn't present in 11.5.37....
I'm pretty sure I found that and fixed it last week. Please try 11.6.RC2 Thomas Stout wrote: When running Jmol 11.5.37, the following script (color_models.spt) works fine: n_models = getProperty(modelInfo,modelCount); clist=array(green,palevioletred,lightblue,coral,yellow,cyan,\ dodgerblue,aqua,salmon,greenyellow,lavender,\ lightgoldenrodyellow,lightseagreen,lightskyblue,\ lime,limegreen,mistyrose,olive,orange,peachpuff,\ sandybrown,seagreen,tan,teal,wheat,yellowgreen); ini = 2; fin = n_models; for (var i = ini; i = fin; i = i + 1) m = */+i+.1; select @m and :Z and *.C??; print clist[i]; s = clist[i]; color @s; end for This results in different colors for the carbons of multiple chains Z from superimposed PDB files. Unfortunately in Jmol 11.5.51, I'm finding that this same script causes a java exception and locks up the Jmol applet graphics. Here is the output to the Java console when it works (Jmol 11.5.37): *FileManager.openFile(../../struct/protein1_aligned.pdb) //../../struct/protein1_aligned.pdb FileManager opening **http://comte.exelixis.com/struct/protein1_aligned.pdb* *The Resolver thinks Pdb openFile(../../struct/protein1_aligned.pdb): 32 ms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 models in this collection. Use getProperty modelInfo or getProperty auxiliaryInfo to inspect them. ModelSet: autobonding; use autobond=false to not generate bonds automatically FileManager opening **http://comte.exelixis.com/structures3/bin-release/color_models.spt* *flowContextfor 10 end flowContextfor palevioletred * And here is the same output from Jmol 11.5.51: FileManager.openFile(../../struct/protein1_aligned.pdb) //../../struct/protein1_aligned.pdb FileManager opening http://comte.exelixis.com/struct/protein1_aligned.pdb The Resolver thinks Pdb openFile(../../struct/protein1_aligned.pdb): 31 ms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 models in this collection. Use getProperty modelInfo or getProperty auxiliaryInfo to inspect them. ModelSet: autobonding; use autobond=false to not generate bonds automatically FileManager opening http://comte.exelixis.com/structures3/sandbox_11.5.51/color_models.spt java.lang.ClassCastException: java.util.BitSet cannot be cast to java.lang.String at org.jmol.viewer.Eval.expression(Eval.java:1467) at org.jmol.viewer.Eval.expression(Eval.java:1391) at org.jmol.viewer.Eval.select(Eval.java:5338) at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:991) at org.jmol.viewer.Eval.script(Eval.java:5073) at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:973) at org.jmol.viewer.Eval.runEval(Eval.java:280) at org.jmol.viewer.Viewer.evalStringWaitStatus(Viewer.java:3495) at org.jmol.viewer.Viewer.scriptWait(Viewer.java:3441) at org.jmol.applet.Jmol.scriptProcessor(Jmol.java:689) at org.jmol.applet.Jmol.scriptWait(Jmol.java:717) at JmolApplet.scriptWait(JmolApplet.java:185) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.plugin.javascript.JSInvoke.invoke(Unknown Source) at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.plugin.javascript.JSClassLoader.invoke(Unknown Source) at sun.plugin.com.MethodDispatcher.invoke(Unknown Source) at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source) at sun.plugin.com.DispatchImpl$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at sun.plugin.com.DispatchImpl.invoke(Unknown Source) java.lang.Exception: java.lang.ClassCastException: java.util.BitSet cannot be cast to java.lang.String at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source) at sun.plugin.com.DispatchImpl$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at sun.plugin.com.DispatchImpl.invoke(Unknown Source) Might anything have changed between these versions that would cause this? Can I infer from the java error stream that there is something about string handling that has gone awry? Thanks, Tom - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/
Re: [Jmol-users] Jmol 11.6.RC3, point groups, dot density
OK, that's changed. With a scale of 1.0, the planes go exactly through the outermost atoms, which creates a supremely nice effect for the Ih group, and axes are a bit longer. Dean Johnston wrote: Very nice - I like that you can select what to draw and the different color for the horizontal plane. How is the default scale determined? (It seems with some molecules [C2h], the planes extend well beyond the outermost atoms, while with others [Ih], they end in the middle of some atoms.) right now it's just 3 Angstroms in diameter. I can't think of any general way to improve on that. Molecules come in all shapes and sizes, after all. I suppose it could be scaled based on the bounding box. Do you want me to try that? Yes - I think planes should default to somewhat larger than the bounding box - so that the atoms are completely within the circle. Do the axes have the same default? I think they should be longer. Dean - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Parallel multiple-model animation
Great. Enjoy!
Matthew Zwier wrote:
Dear Bob,
This works like a charm! Kudos to you and the rest of the devs for
putting together such a flexible system. The only change necessary
(recorded here for the next person with this question) was a change to
the following:
var nFrames = {1.0}.model.max
This presumably because {*}.model.max always gave nothing, since the
selection would contain more than one model.
Thanks for your help!
Matt Z.
On Thu, Aug 7, 2008 at 7:57 PM, Bob Hanson [EMAIL PROTECTED] wrote:
Matt, no problem. You have the right idea, now just animate it yourself.
For sure, do
load files
frame 0.0;display 1.1,2.1
Now create the animation loop yourself. You could have a problem
incrementing floating point numbers, so I would recommend instead:
set echo echoBegin [50 50]
echo [GO]
set echo echoBegin script !quit;doAnimate
background echo yellow
set echo echoQuit [120 50]
echo [QUIT]
set echo echoQuit script !quit
background echo yellow
set debugscript
function doAnimate()
var nFrames = {*}.model.max
for (var i = 1; i nFrames; i = i + 1)
script inline display 1. + i + , 2. + i
delay 0.10
refresh
end for
end function
When that quit button is pressed, the animation will stop. You can
have any sort of buttons -- (now images if you want!) -- just make sure
that you have the ! there at the beginning. That tells Jmol to interrupt
the currently running script and process the command.
I bet you can build a nice animator using scripts and such right within
the applet window now, with no JavaScript. Give it a try.
Bob
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
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___
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
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[Jmol-users] Jmol 11.6.RC2 --- images and pointgroups
Something to check out: incorporation of images as 2D or 3D objects (very fun!) full support for point groups http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm I could imagine there are some issues with the image business that still need resolving. (Like rendering speed.) Please let me know if you have trouble accessing this page -- St. Olaf is in the midst of some server changes. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 11.6.RC2 --- images and pointgroups
Oh -- if you want to check out the Jar files yourself, for now use the ones in http://chemapps.stolaf.edu/jmol/docs/examples-11/ Bob Bob Hanson wrote: Something to check out: incorporation of images as 2D or 3D objects (very fun!) full support for point groups http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm I could imagine there are some issues with the image business that still need resolving. (Like rendering speed.) Please let me know if you have trouble accessing this page -- St. Olaf is in the midst of some server changes. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Better dot density management
Eric, I know you've been interested in this for some time. My pleasure to finally implement a simple solution that I hope will suffice. Dot density is based on a clever algorithm involving geodesics. There are 5 levels. But to save memory, we use only 4 of those for dots. OK, Try this. 11.6.RC3 has: set dotDensity [0 to 6] The number you choose (3 being default) determines the density at the various automatic cutoffs. This means that, for example, if you choose 6, then the highest level will always be used -- there will be no shifting; if you choose 5, then the maximum density will still be the same, but that maximum density will appear at a lower zoom. I checked this out with a small peptide, and I think it works pretty well. See what you think. You can see this in action at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm Jmol 11.5.RC3 is at http://chemapps.stolaf.edu/jmol/docs/examples-11 Eric Martz wrote: I have situations in which (at the desired zoom) the dot density is too low or too high. I would like to suggest two ways this could be improved. FIRST SUGGESTION There could be an option to control the base density of dots. If, for example, we define the default dot density to be 100, then I'd like to be able to say e.g. dots 200 or dots 50 to make the base density twice, or half of the default (at all zooms). In Chime, such a dot density control (with exactly the above syntax) is implemented. However, it is effective at only one zoom, since the density does not change automatically with zooming in Chime. Miguel Howard's innovation in Jmol of having automatic dot density changes during zooming is a huge improvement. SECOND SUGGESTION It appears to me that there are three zoom levels at which dot density is automatically stepped up or down. I think this is too course. I think there should be twice as many steps for the zoom range currently involved, plus more steps at higher zooms. I think the second suggestion should be implemented first. It is possible that with finer step points, command-level density control would be unnecessary. Bob, I would welcome some improvements along these lines and the opportunity to test them. Thanks, -Eric - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Parallel multiple-model animation
Matt, no problem. You have the right idea, now just animate it yourself.
For sure, do
load files
frame 0.0;display 1.1,2.1
Now create the animation loop yourself. You could have a problem
incrementing floating point numbers, so I would recommend instead:
set echo echoBegin [50 50]
echo [GO]
set echo echoBegin script !quit;doAnimate
background echo yellow
set echo echoQuit [120 50]
echo [QUIT]
set echo echoQuit script !quit
background echo yellow
set debugscript
function doAnimate()
var nFrames = {*}.model.max
for (var i = 1; i nFrames; i = i + 1)
script inline display 1. + i + , 2. + i
delay 0.10
refresh
end for
end function
When that quit button is pressed, the animation will stop. You can
have any sort of buttons -- (now images if you want!) -- just make sure
that you have the ! there at the beginning. That tells Jmol to interrupt
the currently running script and process the command.
I bet you can build a nice animator using scripts and such right within
the applet window now, with no JavaScript. Give it a try.
Bob
Matthew Zwier wrote:
Dear Eric,
Thanks for your quick, thoughtful reply. Sorry for the ambiguity. I
meant one copy of Jmol; two datasets displayed side-by-side in a
single Jmol. Or rather, two datasets superimposed in the display.
My data is in multi-frame XYZ files. Each file is of the same
molecule, moving slightly differently through time. Frame number N in
file 1 occurs at the same time in the simulation as frame N in file 2.
I'd like to see the same frame number from more than one file at
once, to compare how the trajectories are evolving in time.
Displaying two models using
load traj1.xyz
load append traj2b.xyz
frame all
display 1.169,2.169
gives the single-point version of what I'm looking for. I'd like to
animate that.
My current impression is that when Jmol animates multiple files, it
goes like this (excluding the effect of frame range ... commands):
for each file:
for each frame in file:
display frame
In contrast, I'd like the following (assume the same number of frames
in each file):
for each frame number (call it nframe):
display file1.nframe, file2.nframe, file3.nframe ...
Attached are three PNG files showing what I'm after. For the curious,
the simulation is of the photodissociation of ethane. Red is from the
first file and blue from the second. The molecular fragments begin in
coincident locations but begin to drift apart, as each file records
motion driven by different forces (specifically, different electronic
states).
If the attachments don't make it through the mailing list, they are
also available at
http://www.scs.uiuc.edu/~mzwier2/frame169.png
http://www.scs.uiuc.edu/~mzwier2/frame269.png
http://www.scs.uiuc.edu/~mzwier2/frame498.png
Hope that helps clear things up!
Matt Z
On Thu, Aug 7, 2008 at 4:42 PM, Eric Martz [EMAIL PROTECTED] wrote:
Dear Matthew,
Please clarify what you mean by in parallel.
Do you mean two Jmol's side by side?
Do you mean two datasets displayed side by side in a single Jmol?
Is it important that the two animations run in frame-by-frame synchrony?
Do you want to be able to rotate each animation independently of the
other? Or in (aligned) synchrony?
If not too much trouble, a snapshot illustrating the layout you
envision might help.
-Eric
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] electrostatic potential surface coloring
Reichsman Frieda wrote:
Thanks Bob. If I understand correctly, this means that Jmol is
calculating the surface MEP based on the values in the file, which do
not represent absolute MEP but rather, are partial charges. And that
means that when Jmol calculates the surface MEP for only part of the
amino acid (the side chain), the absence of the 'backbone' atoms
greatly influences the calculation of the potential over the side
chain, yes? And so the absence of those atoms is creating the effect
I'm seeing of diminishing the potential on the charged side chain, and
magnifying it a bit on the uncharged side chain?
That could be.
This leads to another question, would it be possible to show a partial
surface? That is, 'build' the surface for the entire amino acid, but
only display only the surface over the side chain. I imagine this
would be a feature request, would it be feasible to do this?
I think you want
isosurface select {} molecular map select {*} mep
That is, when you run the mep, you want to indicate that for THAT part
of the calculation, you want all atoms selected. I hadn't realized
myself that two selects work here -- I suppose it could be useful. Or not.
Bob
Frieda
On Aug 5, 2008, at 12:11 PM, Bob Hanson wrote:
if you are mapping MEP data, remember that a MEP calculation is
being done that converts charge on atoms to potential at some distance
(on the surface) from a bunch of atoms, collectively. This value falls
off with distance. So that's probably why your numbers are low. They
aren't just charges, and really they are just approximations of
electron
potential, as well. If you want to map the charges themselves, you
will
need to use map property partialcharge. But that will look somewhat
blotchy, I suspsect.
I'm sure you have the color range/absolute business correct.
Bob
Am I misunderstanding what color range/absolute x.xxx y.yyy should
be doing? Is there a way to get the coloring for color range all
but
only show the surface for the side chains?
Frieda
//
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405
//
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If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Load command and NMR structures
Angel Herraez wrote: Chris Weichenberger escribió: It also seems to be inconsistent since the 'load' command asks for consecutive integers starting with 1 whereas the 'frame'/'model' command requires the PDB model number. I've checked the doc and it's correct, frame and model will use the PDB MODEL number if available. In the case of the loading of a single PDB file containing MODEL records, the integer used here corresponds to the number in that record. I guess that for sequential numbers we now have the n.m syntax, that is, frame 1.0 will display the first model, irrespective of its internally-assigned number --or won't it? No! It's frame 1.1 The key issue is that only pdb files have model numbers, so Jmol is taking a general solution for load. Jmol 11.6.RC1 will have a change in the LOAD command such that for PDB files, the number designated is the model number in the MODEL record. Bob May I ask the Jmol developers to extend the 'load' command such that it can cope with model numbers contained in the PDB file? To assist you, I have included pathologic cases I found when scanning our database for this problem. That should be some kind of switch or new parameter, maybe? How about load filename model n ? for backward-compatibility - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] command echo in console
Could be due to changes I implemented, Karl. If you want to see the commands reflected in the output part (applet, right?) then issue set debugscript Bob Karl Oberholser wrote: Hi All, When I enter a command in the console, it is no longer echoed in the output section of the console. This started occurring about two days ago. Any ideas as to what caused this effect? Karl - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bug in select
this is corrected for 11.4.7 Sérgio Ceroni da Silva wrote: Just noticed that 11.4.6 has the old bug where H1, H2 and H3 from DNA bases are selected as backbone. Did it resurface or the fix was applied only to 11.5.x ? -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 Porto Alegre, RS - Brasil - 91501-970 == Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309 http://www6.ufrgs.br/bioquimica - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] extracting chain ID's into an array?
Thomas Stout wrote:
My sincere thanks to you Rolf! I apologize for taking so long to
respond, but I had some unexpected travel to do over the weekend. I
was not seeing the concept of x=script(show chains); -- it is
not intuitively obvious (to me) that that will create an array rather
than just a string (although it is rather flexible and handy that it
does).
Thanks again!
-Tom
PS -- I've been busily working at implementing your suggestion and it
does appear to be working as expected, but I have currently gotten
hung up with something in this portion of my script causing the Jmol
graphics to freeze and stop responding. It's quite odd: the console
still works.
I think that's a bug in mixing : with @{...}.
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] electrostatic potential surface coloring
Reichsman Frieda wrote: Hi All, In response to the command above, Jmol comes back with this for Asp: color range -0.6478 0.2751; mapped data range -0.26758346 to 0.03863874 Frieda, if you are mapping MEP data, remember that a MEP calculation is being done that converts charge on atoms to potential at some distance (on the surface) from a bunch of atoms, collectively. This value falls off with distance. So that's probably why your numbers are low. They aren't just charges, and really they are just approximations of electron potential, as well. If you want to map the charges themselves, you will need to use map property partialcharge. But that will look somewhat blotchy, I suspsect. I'm sure you have the color range/absolute business correct. Bob Am I misunderstanding what color range/absolute x.xxx y.yyy should be doing? Is there a way to get the coloring for color range all but only show the surface for the side chains? Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bug in select
Sérgio Ceroni da Silva wrote: Just noticed that 11.4.6 has the old bug where H1, H2 and H3 from DNA bases are selected as backbone. Did it resurface or the fix was applied only to 11.5.x ? I think the fix was only applied to 11.5.x. We need to move to 11.6 soon and abandon 11.4. Bob -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 Porto Alegre, RS - Brasil - 91501-970 == Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309 http://www6.ufrgs.br/bioquimica - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] selections with more than one variable?
Thomas Stout wrote:
Has anyone ever made selections using more than one variable
simultaneously? I'm referring to something like:
select {((resno=xres) and :{x[i]} )};// this is meant to make a
selection based on separate algorithmic
//
identifications of desired residue number and chain
The : designation for a chain is very specific. It needs a chain
descriptor. Right now there is no way to test for chain descriptors (one
could imagine, perhaps, and chain='A' for example, but that is not
available.
However, there is a simple way to do ANY complex selection. Simply
create the full select command as a string and then execute it using
script inline. So:
var x = select resno=xres and : + x[i]
script inline @x
Also, I don't think that @{x[i]} notation will work. There are a couple
of ways you could do this, though. I would recommend:
select {((resno=xres) and {x[i]} )};
I've tried several different implementations of this:
//within for loop
ChX = x[i];
select {(resno=xres) and :[EMAIL PROTECTED];
and
//within for loop
selection_expression = *:+x[i];
select {(resno=xres) and [EMAIL PROTECTED];
I've actually lost track of all of the different permutations I've
tried, but everything seems to result in a null selection, with no
error. Most recently now, too, the Jmol graphics have been freezing
as a result of issuing this, so I'm wondering if it is even possible?
Thanks for any suggestions,
Tom
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] draw pointgroup disables isosurface commands
Bill, a few issues there. First, the point group business is still in development (after just a few days!) -- there are known bugs in 11.5.52 that are being fixed for 11.5.53. So please be patient. One issue was that draw pointgroup was messing with the set of selected atoms. So when you went to do the isosurface, it was probably creating an isosurface for select none or something like that. I think I have that fixed now. Also, I've fixed the way the pointgroup calculation selects its atoms. Now it is more like the MO command -- when you switch to a new model using the FRAME command, if no atoms of that model are selected, all atoms in the current model are assumed to be part of the calculation. In the version you have, you have to explicitly say select visible to select the atoms in the frame currently viewed. -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] BCCE challenge completed -- calculate pointgroup
A first attempt at automatic calculation of molecular point group, including drawing and description of all point group operations is now uploaded and can be released as Jmol 11.5.52 Thanks to all at the BCCE for the feature requests. For those who were not present, we had a great series of Jmol-filled presentations, including Dean Johnston showing off his symmetry page (http://symmetry.otterbein.edu) and Jonathan Gutow wowing the crowd with Jmol Web Export capability. I posed a challenge (to myself) at my symposium -- the best feature request suggested by the end of the symposium (Monday) would be incorporated into Jmol by the end of the conference. That winning feature was calculate of molecular point group (C3v, S4, etc.), and I am pleased to say that its programming is complete. Three new commands: calculate pointgroup -- echos the group name draw pointgroup -- draws planes and axes write pointgroup -- delivers DRAW script commands used in draw pointgroup note that with x = script(write pointgroup) you can programmatically manipulate this information -- create selection drop-down lists or checkboxes, for example, or selectively draw the elements. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] 11.5.51 new features... CIF Beta_ij
whoa! Alan -- please VERIFY that it works before you endorse it. I ASSUMED this was ORTEP type 0. Nothing more. This needs checking! Also, it occurs to me that MAYBE the reason CIF format docs do not define these terms is that they are not known for sure -- that the betaij values might imply different definitions. Just something to check out. Bob Alan Hewat wrote: Bob Hanson said: This is fixed for 11.5.51 -- Nico, if you would please release that. CIF BETAij anisotropic support -- preliminary -- totally untested Thanks Bob, very welcome. I have installed it on ICSD http://icsd.ill.fr/ in which there are 6,657 structures (out of 100,000+) reporting Beta_ij, as recently as 2007, even though it is not officially defined in CIF :-) __ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE [EMAIL PROTECTED] +33.476.98.41.68 http://www.NeutronOptics.com/hewat __ - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] If Jmol ever has to artifically scale substructure views, how should/would it do so?
David, you can do this using some sort of user-defined functions within a script. You would, for example, select a group, scale it (I presume you mean move it as a group, not scale the bond distances), and move on. Your service would have to define the vectors, but Jmol could run though all the groups and correlate the vector with the group. This could be directed by JavaScript or run using Jmol script functions. You might also think about ways you could do this visually, without the translations. I suggest quaternions. A quaternion relative difference map (quaternion r differencecommand) will precisely describe the orientations of groups *relative to each other* rather than the translational aspects. The two would not have to be oriented in any way the same in space, because quaternion r difference (and quaternion r difference2 -- the second derivative) are independent of that. Sounds like a perfect fit to me. You should add the following setting set PdbSequential TRUE This will to Jmol that your listed atoms in PDB format should be considered connected between groups even if their bonding does not suggest it. Bob [EMAIL PROTECTED] wrote: Certain empirical cases published at “StrucClues” ( http://strucclue.ornl.gov http://strucclue.ornl.gov/) identify pairs of tertiary substructures A and B, where it is intuitively obvious that A is a more “compact” version of B. Not a “smaller” version of B, in the sense that A lacks a helix or strand that is present in B. But rather, a more “compact” version of B, in the sense that A has less residues per helix, and/or less residues per strand, and/or less residues per turn. Since such pairs of tertiary substructures were identified using a novel methodology (SCILD) that does not depend on any degree of primary structure sequence homology between substructures A and B, it is impossible to do a principled structural alignment of A and B using gap insertions because there is no principled reason for putting the gaps one place rather than another. (See StrucClues site for explication of the SCILD methodology.) So … under the assumption that StrucClues cases of this type actually do reflect some “real” or “valid” aspect of tertiary structure, it would seem that the only way to “align” substructure A with substructure B would be by “scaling up” A or “scaling down” B. By “scaling up”, I mean artificially increasing the distiance between any two residues r(i) and r(i+1) of A, without changing the orientation of r(i) with respect to r(i+1). (And vice-versa, for “scaling down”.) How easy would it be to add such a “scaling” capability to JMol displays? Assuming again, of course, that it is empirically defensible to do such scaling (based on the kinds of cases accumulating at StrucClues)? - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] If Jmol ever has to artifically scale substructure views, how should/would it do so?
David, you can do this using some sort of user-defined functions within a script. You would, for example, select a group, scale it (I presume you mean move it as a group, not scale the bond distances), and move on. Your service would have to define the vectors, but Jmol could run though all the groups and correlate the vector with the group. This could be directed by JavaScript or run using Jmol script functions. You might also think about ways you could do this visually, without the translations. I suggest quaternions. A quaternion relative difference map (quaternion r differencecommand) will precisely describe the orientations of groups *relative to each other* rather than the translational aspects. The two would not have to be oriented in any way the same in space, because quaternion r difference (and quaternion r difference2 -- the second derivative) are independent of that. Sounds like a perfect fit to me. You should add the following setting set PdbSequential TRUE This will to Jmol that your listed atoms in PDB format should be considered connected between groups even if their bonding does not suggest it. Bob [EMAIL PROTECTED] wrote: Certain empirical cases published at “StrucClues” ( http://strucclue.ornl.gov http://strucclue.ornl.gov/) identify pairs of tertiary substructures A and B, where it is intuitively obvious that A is a more “compact” version of B. Not a “smaller” version of B, in the sense that A lacks a helix or strand that is present in B. But rather, a more “compact” version of B, in the sense that A has less residues per helix, and/or less residues per strand, and/or less residues per turn. Since such pairs of tertiary substructures were identified using a novel methodology (SCILD) that does not depend on any degree of primary structure sequence homology between substructures A and B, it is impossible to do a principled structural alignment of A and B using gap insertions because there is no principled reason for putting the gaps one place rather than another. (See StrucClues site for explication of the SCILD methodology.) So … under the assumption that StrucClues cases of this type actually do reflect some “real” or “valid” aspect of tertiary structure, it would seem that the only way to “align” substructure A with substructure B would be by “scaling up” A or “scaling down” B. By “scaling up”, I mean artificially increasing the distiance between any two residues r(i) and r(i+1) of A, without changing the orientation of r(i) with respect to r(i+1). (And vice-versa, for “scaling down”.) How easy would it be to add such a “scaling” capability to JMol displays? Assuming again, of course, that it is empirically defensible to do such scaling (based on the kinds of cases accumulating at StrucClues)? - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] version 11.5.49 ... is max broken?
yes. ARGH! I know exactly what I did Thanks for spotting that. I
will have an update available later this evening.
Bob
Thomas Stout wrote:
Hi everyone --
I have a script that iterates over a range of residues that is defined
by choosing the min and max residue numbers. When testing out
version 11.5.49 in order to take advantage of some of the great new
additions, I find that the line in my script with max is throwing
errors...specifically:
select ligand;
nAtoms= {selected}.size;
rx = {selected}.resno.min;
ry = {selected}.resno.max;
for (var i=rx;i=ry;i=i+1)
ETC
and here is the resulting error:
84 atoms selected
script ERROR: unrecognized atom property: 0x300092
line 4 command 4 of file null:
ry = { selected } . resno . max
This happens both from my script and when entering the commands into
the console. BTW, I am using the applet in a web page
I would expect that I've created my own mistake, but this does work as
written in version 11.5.37. http://11.5.37.
Thoughts?
Thanks,
Tom
-
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
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