[Chimera-users] Hydrogens in proteins

[Walter Novak]

Hi Elaine,

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!

Thanks,
Wally

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  
> 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
>


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