[Chimera-users] Bond change

Eric Pettersen pett at cgl.ucsf.edu
Mon Nov 30 14:28:11 PST 2009

Hi Bruno,
	What version of Chimera are you using?   The problem you're reporting  
was fixed on March 17th of this year so if you use the current  
production release candidate you shouldn't have this problem.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Nov 30, 2009, at 12:38 PM, Bruno Cramer wrote:

> Hi
> After getting the conformations as *.sdf (or *.pdb) files with
> Macromodel (from Shroedinger) and/or Vconf(VeraChem) I use Chimera to
> add missing H's and add charges with amber 99.
> After these steps are completed, I split the sdf conformations-file
> into single *.mol2 files. All works fine except for the last step,
> that changes a single bond into a double bond in each molecule. I am
> correcting this manualy opening the *.mol2 file with Texd editors and
> changing the double bond into single bond the the benzene rings.
> Opening a chosen conformation from the  *.sdf file it looks
> correct.So, the problem happens during conversion/splitting process.
> Question:
> How can this  arbitrary bond change be avoided?
> Attached zip file with *.mol2 examples of one compound after  
> splitting  process.
> Thank you
> Regards
> Bruno
> <ex.zip>_______________________________________________
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> Chimera-users at cgl.ucsf.edu
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