[Chimera-users] Hydrogens in proteins

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 13 10:59:24 PDT 2008

Hi Wally,
I believe Chimera keeps the input atom names, and there is no option  
to translate hydrogen names from one version of PDB format to  
another.  For this, I recommend using another program such as the  
MolProbity server (more on this below).  Can anyone suggest other  
utilities/servers for translating hydrogen names between different  
programs and/or versions of PDB format?

A separate issue is that you have encountered bugs in writing out  
- names such as D1,D2,D3 displaced one column to the left
- D in rightmost column changed to H
I will file a bug report on writing out deuterium and add you to the  
notification list for when these problems are fixed.

I should also mention there was a bug in writing the new-format  
hydrogen names, fixed mid-July (4-char hydrogen names were "wrapped"  
like 1HG1 instead of HG11).

For hydrogen name translation, you might try the MolProbity  
(Richardson lab) server:
It can do a ton of things to fix up the structure, but I believe it  
can read in and write out v2.3 or v3.0 as instructed.  It may be  
tedious if you need to process very many structures, however.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 13, 2008, at 6:31 AM, Walter Novak wrote:

> Hi group,
> So I am struggling with hydrogens in proteins. I have neutron data
> which shows H-atom positions. Well, Deuterons, but here are the
> issues. If I open a pdb in Chimera with old school hydrogen names like
> HG1, how can I get it to write out the new ones (like HG11) without
> explicitly adding the hydrogens in Chimera? I don't want the atom
> positions to change. Also, I notice Chimera doesn't seem to handle
> deuterons optimally. Writing out the pdb moved the atom name column to
> the left one space and changed the atom type in the last column back
> to H.
> The problem is caused by Coot, which we use to perform real space
> refinement of atom positions, but to quote George Sheldrick, "I think
> that we will have to 'remediate' Coot (and the whole of CCP4 for good
> measure). I advise all SHELXL users NEVER to deposit hydrogen atoms,
> it saves lots of hassle."
> Unfortunately, the point of my project is to see the hydrogens!!!!
> Thanks for any help you can offer,
> Wally
> Walter R.P. Novak, Ph.D.
> Postdoctoral Fellow
> Rosenstiel Basic Medical Research Center
> Brandeis University
> 415 South St. MS 029
> Waltham, MA 02454-9110
> Phone: (781) 736-4944
> Fax: (781) 736-2405

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