Re: [Jmol-developers] Incorrectly Drawn Bonds in Zipped 2d .mol files

2009-04-14 Thread Angel Herráez
I think it happens for 2D mol files that have funny bond distances. If the file is 3D (and so has proper bond lengths) or it is 2D with reasonable bond lengths, no problem. But when the file is 2D and has too short bond lengths (some programs do this, considering that a 2D structural formula

[Jmol-developers] [ jmol-Patches-2760297 ] fix for autoBonds and $HOME/.jmol/properties

2009-04-14 Thread SourceForge.net
Patches item #2760297, was opened at 2009-04-14 01:56 Message generated for change (Comment added) made by aherraez You can respond by visiting: https://sourceforge.net/tracker/?func=detailatid=379135aid=2760297group_id=23629 Please note that this message will contain a full copy of the comment

Re: [Jmol-developers] JMOL for Simple Gene Modelling

2009-04-14 Thread Angel Herráez
(Apologies if you receive duplicated posts; my email server has gone nuts last week) Jairav, I've had a couple ideas: 1. You can generate the necessary xyz coordinates by script 2. Using Jmol connect and then minimize commands can produce the wanted approach of certain residues Have a look

Re: [Jmol-developers] JMOL for Simple Gene Modelling

2009-04-14 Thread Angel Herráez
Jairav, I've had a couple ideas: 1. You can generate the necessary xyz coordinates by script 2. Using Jmol connect and then minimize commands can produce the wanted approach of certain residues Have a look at this: http://www31.websamba.com/jpeg62/Jmol/gene_simulation.htm I have used alpha

[Jmol-developers] [ jmol-Patches-2760297 ] fix for autoBonds and $HOME/.jmol/properties

2009-04-14 Thread SourceForge.net
Patches item #2760297, was opened at 2009-04-14 01:56 Message generated for change (Comment added) made by pimpimpim You can respond by visiting: https://sourceforge.net/tracker/?func=detailatid=379135aid=2760297group_id=23629 Please note that this message will contain a full copy of the comment

[Jmol-developers] autoBond and the .jmol/properties file

2009-04-14 Thread pim schravendijk
Hi, I remembered I had svn login and committed my bug fix to svn. I hope it is ok this way! -- Greetings, Pim http://www.molmod.com -- This SF.net email is sponsored by: High Quality Requirements in a Collaborative

Re: [Jmol-developers] autoBond and the .jmol/properties file

2009-04-14 Thread Bob Hanson
Great. Did you remember to fix both 11.6 11.7? Sent from my iPhone On Apr 14, 2009, at 4:01 PM, pim schravendijk pimli...@googlemail.com wrote: Hi, I remembered I had svn login and committed my bug fix to svn. I hope it is ok this way! -- Greetings, Pim http://www.molmod.com --- ---