[Jmol-users] progress ... ?
http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.12.02b.zip http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm -- Robert M. Hanson Larson-Anderson 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 -- 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=84349351&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] 13.3.9_dev_2013.12.01 pdb alert pop up.
Bob, Jmol 13.3.9_dev_2013.12.01 gives the following JavaScript alert on standard pdb load: JmolCore.js: synchronous binary file transfer is requested but not available This alert does not interfere with the pdb load. Is this alert intended in the case of a load involving a text file? Otis -- Otis Rothenberger o...@chemagic.com www.chemagic.com -- 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=84349351&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Local testing
I agree. On Dec 2, 2013, at 4:17 PM, Miller, Benjamin wrote: > For safari (jsmol.htm), can you check the browser console for error? I > was seeing a null pointer exception. Once the console ws open, doing a > refresh allowed jsmol to load. > > > > On 12/2/13, 4:10 PM, "Philip Bays" wrote: > >> Following are the results of launching pages locally: >> >> Safari >> jsmol.htm ‹ HTML5 applet does not load >> test2.htm ‹ HTML5 applet loads, but neither java applet loads. giving >> the following error alert >> java.lang.reflect.InvocationTargetException >> >> Firefox >> jsmol.htm ‹ HTML5 applet does not load >> test2.htm ‹ HTML5 applet loads rapidly; I sometimes get an alert that >> jquery is busy, >> but the continue button continues >> the load >> Signed applet loads fine >> Unsigned applet throws AccessControl Exception >> >> Chrome >> jsmol.htm ‹ HTML5 applet does not load >> test2.htm ‹ HTML5 applet does not load; stalls at: loading... >> j2s/J/awtjs2d/Platform.js >> >> I note that for server loading of the WebGL version, Safari seems to >> require that you turn WebGL on in the developer menu. >> >> Philip Bays >> Emeritus Professor of Chemistry >> Saint Mary's College >> Notre Dame, IN 46556 >> pb...@saintmarys.edu >> >> >> >> -- >> >> 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=84349351&iu=/4140/ostg.clktr >> k >> ___ >> 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=84349351&iu=/4140/ostg.clktrk > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- 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=84349351&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Local testing
For safari (jsmol.htm), can you check the browser console for error? I was seeing a null pointer exception. Once the console ws open, doing a refresh allowed jsmol to load. On 12/2/13, 4:10 PM, "Philip Bays" wrote: >Following are the results of launching pages locally: > >Safari > jsmol.htm ‹ HTML5 applet does not load > test2.htm ‹ HTML5 applet loads, but neither java applet loads. giving >the following error alert > java.lang.reflect.InvocationTargetException > >Firefox > jsmol.htm ‹ HTML5 applet does not load > test2.htm ‹ HTML5 applet loads rapidly; I sometimes get an alert that >jquery is busy, > but the continue button continues >the load >Signed applet loads fine >Unsigned applet throws AccessControl Exception > >Chrome > jsmol.htm ‹ HTML5 applet does not load > test2.htm ‹ HTML5 applet does not load; stalls at: loading... >j2s/J/awtjs2d/Platform.js > >I note that for server loading of the WebGL version, Safari seems to >require that you turn WebGL on in the developer menu. > >Philip Bays >Emeritus Professor of Chemistry >Saint Mary's College >Notre Dame, IN 46556 >pb...@saintmarys.edu > > > >-- > >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=84349351&iu=/4140/ostg.clktr >k >___ >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=84349351&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Local testing
Following are the results of launching pages locally: Safari jsmol.htm — HTML5 applet does not load test2.htm — HTML5 applet loads, but neither java applet loads. giving the following error alert java.lang.reflect.InvocationTargetException Firefox jsmol.htm — HTML5 applet does not load test2.htm — HTML5 applet loads rapidly; I sometimes get an alert that jquery is busy, but the continue button continues the load Signed applet loads fine Unsigned applet throws AccessControl Exception Chrome jsmol.htm — HTML5 applet does not load test2.htm — HTML5 applet does not load; stalls at: loading... j2s/J/awtjs2d/Platform.js I note that for server loading of the WebGL version, Safari seems to require that you turn WebGL on in the developer menu. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- 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=84349351&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 12/02/2013 02:29 PM, Rolf Huehne wrote: > Jaim, thanks for the hint. This sounds similar to what my CGI script > does since the beginning of the 'Jena3D Viewer'. The downside is sending > the data uncompressed. That's why I am working on using the > 'Content-encoding' response header parameter to get compressed CGI data > to a browser which has sent 'gzip' in the 'Accept-encoding' request > header parameter. This would mimic what Paul and Bob have suggested by > changing the Apache web server configuration. > It works now. The only drawback compared to the 'jsmol.php' solution will be, that for browsers that don't accept compressed content it will be several times slower, based on my experience with uncommpressed PDB files. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- 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=84349351&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] FINAL CALL: Jalview course + workshop at Oxford, Dec 12-13th
Apologies for cross-posting. This may be of interest to anyone who uses Jmol to analyse RNA and protein biomolecular function: There are only two days left to register for the two day training course and workshop on Jalview that takes place in Oxford next week. This workshop is an ideal opportunity for students, educators and researchers of all abilities who want to get to know Jalview better, and for bioinformaticians to get started with the JalviewLite applet and Jalview's source. The event is heavily subsidised and registration for both days including a workshop dinner is just £35, with a very limited number of rooms available for £10 per night. Register by 4th December via http://bit.ly/jalviewOx2014 Link for more information: http://www.jalview.org/training/training-courses/4th-Jalview-and-JABA-Residential-Workshop PDF Poster at : http://www.jalview.org/file/152 Thanks - and please forward this to people in your institute who might be interested! Jim Procter. -- 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=84349351&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol for testing....
Bob: I privately sent you some error messages earlier this morning. Did you get the email? I have a Safari 7.0 update As I reported in that prior message, jsmol.htm does not load the applet from your site. I have put a copy of the jsmol directory on my campus server. The applet in jsmol.htm does not load from there either. HOWEVER, test2.htm works from both your and my servers, in all three modes — HTML5, Signed, and unsigned — and that is without the error console. The HTML5 version stalls a little on loading at the Elements.js point, particularly the first time, but goes ahead and loads. I have not fully tested the other links. However, both Firefox and Chrome will not load the surface for the caffeine MMFF link though they do load the initial structure. Safari not only will not load the surface, but then freezes the page altogether. Hope this helps. Phil On Dec 1, 2013, at 9:42 PM, Robert Hanson wrote: > Thanks, Phil. I left "/jsmol" out of a bunch of those links; the download > link is right. (Isn't it nice to have trusted-signed applets? Perhaps we will > soon forget the days of all those warning messages.) By the way, at least for > me, Chrome and MSIE are working for non-binary file formats on local drives > with file:// protocol. > > http access tests : > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA > > loading caffeine > loading 1hxw > loading Pymol session > loading =blu > > saving PNG image > > -- > http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm > http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm > http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm?_USE=SIGNED > > searching for a compound name, CAS number, SMILES, InChI, etc. > going back and forth 2D/3D > > > -- > http://chemapps.stolaf.edu/jmol/jsmol/jsv.htm > > spectrum loads > > http://chemapps.stolaf.edu/jmol/jsmol/testjsv_mol.htm > > molecule interactive with spectra. > > > -- > Robert M. Hanson > Larson-Anderson 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 > > -- > 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=84349351&iu=/4140/ostg.clktrk___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- 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=84349351&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 12/02/2013 02:13 PM, Jaime Prilusky wrote: > > Rolf, > > Maybe the way I work on Proteopedia might help you. > > I have a CGI script that sends the content of the structure files to > Jmol/JSmol: getlateststructure > > The script gets as a parameter the name of the file to return or the > PDB id for that file, and looks for the ending “.gz” on that > parameter. This “.gz” ending gets removed from the actual name of the > requested data and kept as a flag of the type of data required. No > additional CGI parameter is required. > > If the “.gz” flag is present then the script will do whatever its > necessary to get the data and send it gzipped. Otherwise it will send > it uncompressed. This is, depending on the request, the script will > uncompress compressed files before sending, or will compress plain > data, to keep the receiving applet happy. > Jaim, thanks for the hint. This sounds similar to what my CGI script does since the beginning of the 'Jena3D Viewer'. The downside is sending the data uncompressed. That's why I am working on using the 'Content-encoding' response header parameter to get compressed CGI data to a browser which has sent 'gzip' in the 'Accept-encoding' request header parameter. This would mimic what Paul and Bob have suggested by changing the Apache web server configuration. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- 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=84349351&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Rolf, Maybe the way I work on Proteopedia might help you. I have a CGI script that sends the content of the structure files to Jmol/JSmol: getlateststructure The script gets as a parameter the name of the file to return or the PDB id for that file, and looks for the ending “.gz” on that parameter. This “.gz” ending gets removed from the actual name of the requested data and kept as a flag of the type of data required. No additional CGI parameter is required. If the “.gz” flag is present then the script will do whatever its necessary to get the data and send it gzipped. Otherwise it will send it uncompressed. This is, depending on the request, the script will uncompress compressed files before sending, or will compress plain data, to keep the receiving applet happy. Jaim On Dec 2, 2013, at 2:20 PM, Rolf Huehne wrote: > On 12/01/2013 09:42 PM, Robert Hanson wrote: >> On Thu, Nov 28, 2013 at 12:12 PM, Rolf Huehne wrote: >>> If someone could tell me a way to convince browsers to uncompress >>> gzip-compressed CGI output before feeding it into JSmol I would be happy >>> to implement it. >>> >> I think your server is not set up to deliver gzipped files automatically. >> Perhaps? >> > The problem whith this is here that the file content is served by a CGI > script instead of a static file. As far as I could find out the Apache > web server configuration options don't seem to be usable in this case. > And switching to direct file serving is not really an option for me. > > I am working on a way to mimic it by the CGI script but it doesn't work yet. > > There might be an additional more general way (not only for standard > compressed binary files) to avoid sending the data three times involving > a PHP script. A CGI script could serve the binary data directly encoded > as base64 without the need for an additional PHP script and two > additional data transfers. > > I think there would be needed two configurable options for this: > > 1) A special CGI binary mode indicator in the file URL (like the '.bin' > file extension). In my case this could be for example "cgi-bin/idb_send.pl". > > 2) A special parameter attached to the CGI URL, e.g. "&ENCODING=base64" > by JSmol. > > Option 2) would prevent that base64 encoding would have to be done also > with Java although it wouldn't be necessary there. Since the actual > 'Jena3D Viewer' CGI script (3d_mapping.pl) doesn't know in advance if > Java or HTML5 will be chosen by the client it would be better to add the > 'ENCODING' parameter only if necessary on the client side by JSmol. > > Regards, > Rolf > > -- > > Rolf Huehne > Postdoc > > Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) > Beutenbergstrasse 11 > 07745 Jena, Germany > > Phone: +49 3641 65 6205 > Fax: +49 3641 65 6210 > E-Mail: rhue...@fli-leibniz.de > Website: http://www.fli-leibniz.de > > Scientific Director: Prof. Dr. K. Lenhard Rudolph >Head of Administration: Dr. Daniele Barthel > Chairman of Board of Trustees: Dennys Klein > > VAT No: DE 153 925 464 > Register of Associations: No. 230296, Amtsgericht Jena > Tax Number: 162/141/08228 > > > -- > 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=84349351&iu=/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=84349351&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 12/01/2013 09:42 PM, Robert Hanson wrote: > On Thu, Nov 28, 2013 at 12:12 PM, Rolf Huehne wrote: >> If someone could tell me a way to convince browsers to uncompress >> gzip-compressed CGI output before feeding it into JSmol I would be happy >> to implement it. >> > I think your server is not set up to deliver gzipped files automatically. > Perhaps? > The problem whith this is here that the file content is served by a CGI script instead of a static file. As far as I could find out the Apache web server configuration options don't seem to be usable in this case. And switching to direct file serving is not really an option for me. I am working on a way to mimic it by the CGI script but it doesn't work yet. There might be an additional more general way (not only for standard compressed binary files) to avoid sending the data three times involving a PHP script. A CGI script could serve the binary data directly encoded as base64 without the need for an additional PHP script and two additional data transfers. I think there would be needed two configurable options for this: 1) A special CGI binary mode indicator in the file URL (like the '.bin' file extension). In my case this could be for example "cgi-bin/idb_send.pl". 2) A special parameter attached to the CGI URL, e.g. "&ENCODING=base64" by JSmol. Option 2) would prevent that base64 encoding would have to be done also with Java although it wouldn't be necessary there. Since the actual 'Jena3D Viewer' CGI script (3d_mapping.pl) doesn't know in advance if Java or HTML5 will be chosen by the client it would be better to add the 'ENCODING' parameter only if necessary on the client side by JSmol. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- 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=84349351&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] compare subset fails in some cases and locks Jmol
Precisely. When there was no rotation, the driving angle was 0, and the
translation failed. Now I have it set up so that if the rotation angle is
0, it is instead set to a ridiculously high number, and while that is
animated, it is skipped since it is so large (1,000,000), allowing the
translation to proceed.
On Mon, Dec 2, 2013 at 3:26 AM, Angel Herráez wrote:
> Thanks, Bob. I will check the update.
>
> This is what I found (with the old versions):
>
> When the atom subset has in both models exactly the same relative
> postitons (this is possible since they come from drawn formulas), the
> RMSD calculated by "compare" is exactly zero. Then, the "rotate
> translate" options produces the problem: the model being moved
> disappears and Jmol gets unresponsive (there is still mouse
> interaction but no commands may be issued, you need to quit the
> application)
>
> I found that by modifying slightly one of the coordinates in one of
> the atoms involved in comparison (e.g. {atomNo=5}.atomX =
> {atomNo=5}.atomX + 0.05), the problem goes away (and I can even
> re-modify back the coordinate later, atomX = atomX - 0.05)
>
> So that's a workaround for older versions (I cannot plug this updated
> Jmol into MP right now).
>
>
>
>
> --
> 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=84349351&iu=/4140/ostg.clktrk
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Larson-Anderson 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
--
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!
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Re: [Jmol-users] compare subset fails in some cases and locks Jmol
Thanks, Bob. I will check the update.
This is what I found (with the old versions):
When the atom subset has in both models exactly the same relative
postitons (this is possible since they come from drawn formulas), the
RMSD calculated by "compare" is exactly zero. Then, the "rotate
translate" options produces the problem: the model being moved
disappears and Jmol gets unresponsive (there is still mouse
interaction but no commands may be issued, you need to quit the
application)
I found that by modifying slightly one of the coordinates in one of
the atoms involved in comparison (e.g. {atomNo=5}.atomX =
{atomNo=5}.atomX + 0.05), the problem goes away (and I can even
re-modify back the coordinate later, atomX = atomX - 0.05)
So that's a workaround for older versions (I cannot plug this updated
Jmol into MP right now).
--
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=84349351&iu=/4140/ostg.clktrk
___
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