[Jmol-developers] RE: bug report from february

Hi miguel, In 5cpa, it was between the hetero atoms (hoh) surrounding the structure, jmol was drawing bonds between the hoh atoms that were close enough to assume a bond. The latest build of jmol doesn't draw these bonds anymore. 1e8a.pdb still forms those strange spider webs - the atoms at the c

[Jmol-developers] [ jmol-Bugs-954209 ] set picking *

Bugs item #954209, was opened at 2004-05-14 23:17 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=954209&group_id=23629 Category: User interface Group: None Status: Open Resoluti

[Jmol-developers] [ jmol-Bugs-909861 ] Jmol v9 DisplayControl.setChemModel throws a NPE

Bugs item #909861, was opened at 2004-03-04 16:38 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=909861&group_id=23629 Category: File Input/Output Group: v9 Status: Open Resolution: None

[Jmol-developers] [ jmol-Bugs-908377 ] rss plugin does not display crystal axes

Bugs item #908377, was opened at 2004-03-02 16:41 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=908377&group_id=23629 Category: None Group: None Status: Open Resolution: None Priorit

[Jmol-developers] [ jmol-Bugs-919164 ] Event Model on Win32/NS4

Bugs item #919164, was opened at 2004-03-19 00:44 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=919164&group_id=23629 Category: None Group: None Status: Open Resolution: None Priorit

[Jmol-developers] [ jmol-Bugs-847643 ] Gaussian 98 + NoSymm problem

Bugs item #847643, was opened at 2003-11-23 15:26 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=847643&group_id=23629 Category: File Input/Output Group: None Status: Open Resolution: No

[Jmol-developers] [ jmol-Bugs-847643 ] Gaussian 98 + NoSymm problem

Bugs item #847643, was opened at 2003-11-23 15:26 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=847643&group_id=23629 Category: File Input/Output Group: None Status: Open Resolution:

[Jmol-developers] [ jmol-Bugs-908377 ] rss plugin does not display crystal axes

Bugs item #908377, was opened at 2004-03-02 16:41 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=908377&group_id=23629 Category: None Group: None Status: Open Resolution: None Priority:

[Jmol-developers] [ jmol-Bugs-942440 ] reading jaguar files with vibration data

Bugs item #942440, was opened at 2004-04-26 17:58 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=942440&group_id=23629 Category: File Input/Output Group: v9 Status: Open Resolution: N

[Jmol-developers] [ jmol-Bugs-905330 ] dragging jmol window rotates structure

Bugs item #905330, was opened at 2004-02-26 21:05 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=905330&group_id=23629 Category: User interface Group: None >Status: Closed >Resolution: R

[Jmol-developers] [ jmol-Bugs-831811 ] CML input of crystals misses some atom images

Bugs item #831811, was opened at 2003-10-28 18:00 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=831811&group_id=23629 Category: File Input/Output Group: v8 >Status: Closed >Resolutio

[Jmol-developers] [ jmol-Bugs-738800 ] Fix minor problem with Eband diagram window width

Bugs item #738800, was opened at 2003-05-16 16:29 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=738800&group_id=23629 Category: User interface Group: v6 >Status: Closed >Resolution:

[Jmol-developers] [ jmol-Bugs-912650 ] JmolAppletControl function

Bugs item #912650, was opened at 2004-03-09 12:23 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=912650&group_id=23629 Category: Applet Group: None Status: Open Resolution: None Priority

[Jmol-developers] [ jmol-Bugs-768932 ] no image export on AIX for v6 and v7

Bugs item #768932, was opened at 2003-07-10 09:37 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=768932&group_id=23629 Category: Graphics Group: None >Status: Closed >Resolution: Out

Re: [Jmol-developers] Translation work...

On Friday 14 May 2004 16:27, Miguel wrote: > It would be great if you wanted to do this. I'll see what I can do... Egon --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest

[Jmol-developers] [ jmol-Bugs-918316 ] Wishlist: option to start atom index at 1

Bugs item #918316, was opened at 2004-03-17 22:17 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=918316&group_id=23629 Category: User interface Group: CVS >Status: Closed >Resolution: Fi

[Jmol-developers] [ jmol-Bugs-888841 ] Incorrectly displays connections between atoms

Bugs item #41, was opened at 2004-02-02 04:36 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=41&group_id=23629 >Category: Algorithms Group: None Status: Open Resolution: None

[Jmol-developers] [ jmol-Bugs-910489 ] no mouse control over structure in mac N7

Bugs item #910489, was opened at 2004-03-05 16:00 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=910489&group_id=23629 Category: Applet Group: None Status: Open Resolution: None Priority

[Jmol-developers] [ jmol-Bugs-942440 ] reading jaguar files with vibration data

Bugs item #942440, was opened at 2004-04-26 17:58 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=942440&group_id=23629 Category: File Input/Output Group: v9 Status: Open Resolution: None

[Jmol-developers] [ jmol-Bugs-944437 ] popup menus should support chains & models

Bugs item #944437, was opened at 2004-04-29 14:43 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=944437&group_id=23629 Category: None Group: None Status: Open Resolution: None Priorit

[Jmol-developers] [ jmol-Bugs-869549 ] Lanthanide complexes as PDB - problems

Bugs item #869549, was opened at 2004-01-02 21:28 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=869549&group_id=23629 Category: File Input/Output Group: v8 >Status: Closed >Resolution:

[Jmol-developers] bug report from february

Dave, I just saw your bug report ... from Feb ... saying that there are problems with the bond connection algorithm. We are not using the same algorthim as RasMol. We are using something from OpenBabel. I downloaded 5CPA ... but it is huge Can you tell me which bonds are wrong? Miguel -

[Jmol-developers] [ jmol-Bugs-889035 ] SimpleModelAdapter mol/sd file format identification

Bugs item #889035, was opened at 2004-02-02 13:08 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=889035&group_id=23629 Category: File Input/Output Group: None >Status: Closed >Resolution

[Jmol-developers] [ jmol-Bugs-951130 ] Translation with the mouse

Bugs item #951130, was opened at 2004-05-10 11:34 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=951130&group_id=23629 Category: User interface Group: None >Status: Closed >Resolution

[Jmol-developers] [ jmol-Bugs-954141 ] atomno != notifyAtomPicked

Bugs item #954141, was opened at 2004-05-14 21:03 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=954141&group_id=23629 Category: None Group: None Status: Open Resolution: None Priorit

[Jmol-developers] [ jmol-Bugs-954141 ] atomno != notifyAtomPicked

Bugs item #954141, was opened at 2004-05-14 21:03 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=954141&group_id=23629 Category: None Group: None Status: Open Resolution: None P

[Jmol-developers] [ jmol-Bugs-933235 ] cif connectivity

Bugs item #933235, was opened at 2004-04-11 17:04 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=933235&group_id=23629 Category: File Input/Output Group: None >Status: Closed >Resolution

[Jmol-developers] [ jmol-Bugs-869549 ] Lanthanide complexes as PDB - problems

Bugs item #869549, was opened at 2004-01-02 21:28 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=869549&group_id=23629 Category: File Input/Output Group: v8 Status: Open Resolution: None

[Jmol-developers] [ jmol-Bugs-888389 ] JmolModelAdapter + radii

Bugs item #888389, was opened at 2004-02-01 02:09 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=888389&group_id=23629 Category: None Group: None >Status: Closed >Resolution: Fixed Prior

[Jmol-developers] [ jmol-Bugs-891819 ] set 'boundingbox' causes security violation

Bugs item #891819, was opened at 2004-02-06 15:36 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=891819&group_id=23629 Category: Scripting Group: None >Status: Closed >Resolution: Fix

[Jmol-developers] [ jmol-Bugs-846848 ] nucleotide chains and backbone rep

Bugs item #846848, was opened at 2003-11-21 21:27 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=846848&group_id=23629 Category: Graphics Group: None >Status: Closed >Resolution: Fixe

[Jmol-developers] [ jmol-Bugs-946848 ] alpha carbon only structures

Bugs item #946848, was opened at 2004-05-03 11:44 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=946848&group_id=23629 Category: Graphics Group: None >Status: Closed >Resolution: Fixed P

Re: [Jmol-developers] Tech note: extended XYZ file support in Jmol

Peter wrote: >>John's question prompted me to write a short tech note regarding support >>for XYZ files in Jmol v10. [snip] > > Is this documented anywhere. I suspect it to be rather fragile. > > P. Well, this was supposed to be (an admittedly feeble attempt at) the documentation :-) It has bee

Re: [Jmol-developers] Tech note: extended XYZ file support in Jmol

At 10:22 14/05/2004 +0200, Miguel wrote: > In other words, is there a standard specification for > vibrations similar to the standardised formats PDB, > MOL, XYZ, etc for atoms, coords, bonds, ... I don't think so. CML addresses this by capturing the eigenvalues and eigenvectors of a compChem cal

[Jmol-developers] ribbon width & RasMol compatibility

In working on the Ribbons code I found an issue related to ribbon width and RasMol/Chime compatibility. RasMol allows you to say ribbons 2.0 My reading of the documentation was that this would make the ribbon be 2 angstroms wide. However, I have found that this is not correct. In fact, this m

[Jmol-developers] [ jmol-Bugs-866644 ] center {set} bug

Bugs item #866644, was opened at 2003-12-28 14:40 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=866644&group_id=23629 Category: None Group: None >Status: Closed >Resolution: Fixed Prior

Re: [Jmol-developers] Translation work...

> -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 >> * I would like to combine the popup menus and the app menus so that the >> translations only have to be done one time. > > I'm fine with having three resource files to look after... OK >> * Properties files can inherit, so at one level, it

Re: [Jmol-developers] Translation work...

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On Friday 14 May 2004 15:32, Miguel wrote: > > earlier today I've updated the properties files for Jmol so that > > translation > > into other languages is easier maintainable... see the HOWTO in > > Jmol.properties... > > > > I noticed that the popup

[Jmol-developers] terminal atoms

Jan wrote: > with regards to the discontinuous chains like in 1esf > http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1esf > select backbone, *.O?T > wireframe > I would argue to include the terminal atoms > protein C-terminus > *.OXT > nucleic acid termini > *.O5T > *.O3T > to the set of backbone

Re: [Jmol-developers] [ jmol-Bugs-923774 ] links on website

>>Actually, I used www.openrasmol.org/doc/rasmol.htm > > you mean ? Yes. Actually, I just dropped the rasmol.html and made a reference to the /doc/ directory. > soory to be dense, but I can't find the reference on the Web site itself > to check it. No

Re: [Jmol-developers] popup menus vs. default behavior

Miguel sent (2004.05.14 at 3.22p [+0200gmt]) : > >>>The default Jmol size is spacefill 20%; wireframe 0.15 >>> >>changed popup menu command to match default Jmol spec. > >I actually wanted to have a little discusion about this :-) > oops. sorry! >Do you think that the default size (which was ar

Re: [Jmol-developers] [ jmol-Bugs-923774 ] links on website

Miguel sent (2004.05.14 at 3.20p [+0200gmt]) : > >Tim wrote: > > >>>I would strongly suggest to link the documentation of the living >>>RasMol clone: >>>http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1.1/doc/ >>>rasmol.html Regards, Jan >>> >> >>...except this url must change with every

Re: [Jmol-developers] Translation work...

> -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > > Hi all, > > earlier today I've updated the properties files for Jmol so that > translation > into other languages is easier maintainable... see the HOWTO in > Jmol.properties... > > I noticed that the popup resources are not in that file, but

Re: [Jmol-developers] popup menus vs. default behavior

>>The default Jmol size is spacefill 20%; wireframe 0.15 >> > changed popup menu command to match default Jmol spec. I actually wanted to have a little discusion about this :-) Do you think that the default size (which was arbitrarily chosen) is OK? Miguel ---

[Jmol-developers] Translation work...

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi all, earlier today I've updated the properties files for Jmol so that translation into other languages is easier maintainable... see the HOWTO in Jmol.properties... I noticed that the popup resources are not in that file, but in jmol/ui... Q: s

Re: [Jmol-developers] [ jmol-Bugs-923774 ] links on website

Tim wrote: >>I would strongly suggest to link the documentation of the living >>RasMol clone: >>http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1.1/doc/ >>rasmol.html Regards, Jan >> > > ...except this url must change with every incremental release of RasMol, > or become out-of-date. h

Re: [Jmol-developers] popup menus vs. default behavior

Miguel sent (2004.05.14 at 2.50p [+0200gmt]) : >Tim, > >A few comments about the popup menus. > > >Render -> Scheme -> Wireframe > >The popup menu has a rendering scheme called 'Wireframe'. But this >is not the same thing as 'wireframe on'. Instead, it is something >like 'wireframe 0.1' > >I think

Re: [Jmol-developers] [ jmol-Bugs-923774 ] links on website

SourceForge.net sent (2004.05.14 at 5.20a [-0700gmt]) : >Bugs item #923774, was opened at 2004-03-26 10:50 Message generated >for change (Settings changed) made by michaelthoward You can respond >by visiting: >https://sourceforge.net/tracker/?func=detail&atid=379133&aid=923774&; >group_id=23629 >

[Jmol-developers] popup menus vs. default behavior

Tim, A few comments about the popup menus. Render -> Scheme -> Wireframe The popup menu has a rendering scheme called 'Wireframe'. But this is not the same thing as 'wireframe on'. Instead, it is something like 'wireframe 0.1' I think that the popup menu command 'Wireframe' should be implement

[Jmol-developers] [ jmol-Bugs-923774 ] links on website

Bugs item #923774, was opened at 2004-03-26 10:50 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=923774&group_id=23629 Category: Website Group: None >Status: Closed >Resolution: Fixed

[Jmol-developers] Tech note: extended XYZ file support in Jmol

> In other words, is there a standard specification for > vibrations similar to the standardised formats PDB, > MOL, XYZ, etc for atoms, coords, bonds, ... John's question prompted me to write a short tech note regarding support for XYZ files in Jmol v10. Jmol supports extended XYZ files which ma

Re: [Jmol-developers] gaussian files & partial charge + abinit

At 01:41 14/05/2004 +0200, Miguel wrote: Egon (& others), Q: I was looking at a Gaussian output file and I think I saw some things that looked like partial charges. Is it the case that Gaussian calculates partial charges? Yes - and many other programs as well. They may not be obvious in the outpu