[Chimera-users] partial failure in addH BUG?

[Eric Pettersen]

On May 4, 2011, at 10:05 AM, Francesco Pietra wrote:

> Hello:
> i had partial failure in addH to a natural product. H at a quaternary,
> chiral C was not added in spite of repeated attempts.

Hi Francesco,
	My guess is that Chimera does not believe that the problem carbon is  
sp3, which Chimera decides based on the carbon's bond geometry.  You  
can see what atom type Chimera assigned to that carbon by selecting it  
and then doing Actions->Label->IDATM type.  An sp3 carbon would be  
"C3".  An sp2 carbon would be "C2".  A full table of atom types is here:

http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/idatm.html

You can force Chimera to believe the carbon is sp3 by selecting it and  
then using this command:

	setattr a idatmType C3 sel

It would also probably be helpful if you used Help->Report A Bug to  
submit a bug report on this problem, attaching the structure file.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

>
> All Hs were added by my favorite drawer (for organic compounds);
> however, this changes the coordinates, which is not what I want.
>
> I solved the issue by transferring the chimera pdb output to vmd,
> adding the missing H with Molefacture.
>
> On the other hand, Molefacture, if asked to add all Hs, resulted in
> incorrect stereochemistry at -O-CH3 and some -C-CH3 (inverted
> umbrella, which could not be reversed).
>
> francesco pietra
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> Chimera-users at cgl.ucsf.edu
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