VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 07 2007 - 13:34:35 CST

Hi,
 Yes, this is a PDB containing multiple conformations.
If you use VMD 1.8.5 or one of the new VMD 1.8.6 test versions, you
can use the "Conformation" coloring method to clearly identify the
various conformations stored in the file. Beyond that, we provide
a few built-in atom selection macros to make it easy to view
or to select the various conformations in your scripts:
  conformationall (only the part that's shared between all conformations)
  conformationA
  conformaitonB
...

Using combinations of these selections, you can write out a
single-conformation PDB file, which is what psfgen and autopsf are
really looking for.

Let us know if you need more help with this.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 06, 2007 at 03:24:17PM -0500, hl332_at_drexel.edu wrote:
> 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
> > 

-- 
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