[Chimera-users] Hydrogens in proteins

[Elaine Meng]

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  
deuterium:
- 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:
<http://molprobity.biochem.duke.edu/>
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.

Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html


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