VMD-L Mailing List

From: hl332_at_drexel.edu
Date: Tue Mar 06 2007 - 14:24:17 CST

Hi John,
  Thanks for your prompt reply. Yes, it is a standard pdb from rcsb pdb with code: 1ZNJ.PDB. please have look on following specific residues and let me know what should i do while building file using psfgen which i have done a few times before.
 

RESID CHAIN
25 B
17 D
25 B
8 E
4 F
4 G

there are lot others down in further chains. Thanks in advance.

regards
harish
-------------------------------------------------
Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823

----- Original Message -----
From: John Stone <johns_at_ks.uiuc.edu>
Date: Tuesday, March 6, 2007 1:52 pm
Subject: Re: vmd-l: unusual residue type problem..

> 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
> whatthe accession code is and I'll have a look at the structure
> file.
> My guess is that this PDB simply uses the alternate location
> identifierfield, 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'sa 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
> thesestructures 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>