[Chimera-users] Hydrogens in proteins
wnovak at brandeis.edu
Wed Aug 13 17:33:38 PDT 2008
I have tried Molprobity and it doesn't work. I think because Coot
isn't even writing the 2.3 hydrogen names correctly, so it doesn't
assume they are 2.3 names and won't upconvert them either. I may have
to abandon Coot for my real space refinement!
On Aug 13, 2008, at 1:59 PM, Elaine Meng wrote:
> 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
>> 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
>> 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
Walter R.P. Novak, Ph.D.
Rosenstiel Basic Medical Research Center
415 South St. MS 029
Waltham, MA 02454-9110
Phone: (781) 736-4944
Fax: (781) 736-2405
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