VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 18 2004 - 19:34:43 CDT

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
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