[Chimera-users] adding H

Eric Pettersen pett at cgl.ucsf.edu
Thu Sep 25 11:02:17 PDT 2008

Hi Barb,
	We don't retain each daily build of Chimera, so I can't compare the  
two builds you mention.  Nonetheless, the current daily build  
correctly protonates the imidazole rings I tested. and it shouldn't  
differ from the 9/21 build in this regard AFAIK.  Is the imidazole- 
containing compound in a standard PDB file and if so can you tell me  
the ID code for it?  If not, would it be possible for you to send me  
your structure file (just the compound part would be fine)?
	Also, what is it about the charge assignments that don't make sense?


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Sep 25, 2008, at 5:10 AM, Barbara Truitt wrote:

> I have a compound which has an imidazole ring. When I Add Hydrogens,  
> no hydrogens are added to the nitrogen atoms when I use the build  
> from 9/21/08. The build from 9/4/08 adds the hydrogens, but some of  
> the charge assignments in the resulting mol2 file don't make sense.
> Barb Truitt
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> Chimera-users at cgl.ucsf.edu
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