VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 06 2007 - 12:52:25 CST

Hi,
  Was this PDB file you're using from the RCSB PDB web site, or is it
something that you got elsewhere? If it's a standard PDB, tell me what
the accession code is and I'll have a look at the structure file.
My guess is that this PDB simply uses the alternate location identifier
field, and so these are different conformations of the same structural
elements. Starting with VMD 1.8.5, you can load such PDB files and
display just the conformations you're interested in, and it should not
cause VMD any trouble with the analysis of the structure as long as it's
a standard PDB. If you're still using one of the older versions of VMD,
this would be a good time to upgrade, since the new versions handle these
structures in a much better way.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 06, 2007 at 12:38:08PM -0500, hl332_at_drexel.edu wrote:
> Hi all,
> I have worked with vmd for a few months and never encountered this kind of thing in any pdb. One of the pdb I am using now has unusual residue names for several of them. One of them is as below: instead of PHE, it has APHE and BPHE where every atom coordinates have been given two times:
>
> ATOM 191 CA PHE B --furtherdata
> ATOM 192 C PHE B --furtherdate
> ATOM 193 O PHE B "
> ATOM 194 CB PHE B "
> ATOM 195 CG APHE B
> ATOM 196 CG BPHE B
> ATOM 197 CD1APHE B
> ATOM 199 CD2BPHE B
> ATOM 202 CE1BPHE B
> ATOM 203 CE2BPHE B
> ATOM 204 CE2APHE B
> ATOM 205 CZ APHE B "
> ATOM 206 CZ BPHE B
>
> it shows two benzene rings of PHE residue in vmd as each atom in that ring has been provided two coordinates. PSFGEN confuses this and makes some other structure (generates correctly only half of residue).
>
> One of the solution i think is to manually edit which i guess is not wise. Please let me know if there is better solution(I am sure it does)
>
> Regards
> harish
>
>
>
>
>
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823 

-- 
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