[Chimera-users] Hydrogens in proteins

Walter Novak wnovak at brandeis.edu
Wed Aug 13 06:31:25 PDT 2008

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,

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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