[gmx-users] add missing atom(s)

[Justin A. Lemkul]

you zou wrote:
> Hi,
> 
> Which tool(s) is/are useful? I don't have any idea for this problem.
> 

The WHATIF server, Swiss-PDBviewer, maybe even PyMOL.  A quick look around the 
web will probably give you some additional tools that I'm not thinking of.

-Justin

> Thank you
> 
> 
> you zou wrote:
>> Hi again,
>> 
>> Sorry, in "REMARK 470" there is:
>> 
>> REMARK 470 
>> 
>> REMARK 470 MISSING ATOM 
>> 
>> REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; 
>> 
>> REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; 
>> 
>> REMARK 470 I=INSERTION CODE): 
>> 
>> REMARK 470 M RES CSSEQI ATOMS 
>> 
>> REMARK 470 SER A 2 OG 
>> 
>> REMARK 470 GLN A 678 CA C O &a
>  mp;nbs
>> p; CB CG CD OE1 NE2 
>> 
>> REMARK 470 SER B 2 OG 
>> 
>> REMARK 470 GLY B 679 CA C O 
>> 
>> This means there are missing atoms. Is it possible to add these atoms 
>> from other residue what are SER and GLN and GLY?( Copy and Paste OG from 
>> other SER for example?) I think after EM these are fixed, it is true?
>> 
> 
> If you have several missing atoms you will have to use some external tool(s) to 
> re-create these residues. Using cute tricks to build back one atom is easy 
> enough, but re-creating a fragmented structure is much easier using tools 
> designed for the task.
> 
> -Justin
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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