VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Apr 19 2004 - 11:24:14 CDT

Hi,

PSF files use a different segment for each protein chain. I don't think
you can use 60 different chain ids since that's a single-character field.

-Jim

On Sun, 18 Apr 2004, John Stone wrote:

>
> Daniel,
> As far as I know there isn't a way to set the chain during psfgen
> generation, but once again Jim Phillips may have more tips here.
> If not, then one way to get unique chains would be to load in the
> newly created pdb file into VMD, then use the atomselect command to
> set the chain of the 60 units the way you want them to be. You could
> use the segment id's that are set in that structure merging script for
> this purpose if you like.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Apr 15, 2004 at 05:00:24PM +0300, Dr. Daniel James White PhD wrote:
> > Hi again John,
> >
> > So the tcl script below didnt work, no redsidue named CA, but then....
> > I realised I was being dumb... CA is obviously the Calcium ions.
> >
> > Anyway, I removed them all from the pdb file and now the script works.
> >
> > however, I still have the same old problem that the chain identifiers
> > of all 60 molecules are the same.
> > I need them to be different so that I can open the file properly in
> > Bodil for modelling.
> >
> > Is there a way to give each chain/molecule a unique PDB chain ID in the
> > PDB output file.
> >
> > (by the way, the His residies has hydrogens added to them incorrectly
> > and were excluded from the main chain.
> > Is this normal?)
> >
> > cheers
> >
> > Dan
> >
> > >
> > ><mergemultiframepdb.tcl>
> >
> >
> > Dr. Daniel James White BSc. (Hons.) PhD
> > Cell Biology
> > Department of biological and environmental science
> > PO Box 35
> > University of Jyväskylä
> > Jyväskylä FIN 40014
> > Finland
> > +358 14 260 4183 (work)
> > +358 468102840 (new mobile)
> > NEW PHONE NUMBER!!!
> >
> > http://www.chalkie.org.uk
> > dan_at_chalkie.org.uk
> > white_at_cc.jyu.fi
> >
>
> --
> 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
>