VMD-L Mailing List

From: nordgren_at_sas.upenn.edu
Date: Wed May 11 2005 - 05:01:37 CDT

This post reminded me of something I wanted to ask about a while ago...

I figured out for myself, but only after LOTS of trial and error, that when
one uses psfgen commands from within vmd, the two programs don't really
"talk to" each other. I found that, if I wanted a script to (say) modify my
PSF structure using psfgen, then modify the coordinates using vmd, and then
modify the PSF once again, it was necessary to keep writing and reading
intermediate PDB and PSF files to disk, using separate commands for the file
I/O appropriate to each program (psfgen v. vmd).

Anyway, John's comment here is the first I've seen, in authoritative written
form, of any mention of the distinct data structure usage of psfgen/vmd.
So, I was just wondering, is there something written about this in the user
guide and/or some of the tutorials, and I just missed it?

- Erik

C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

Quoting John Stone <johns_at_ks.uiuc.edu>:

>
> Nicolas,
> It appears that you're attempting to combine the "delatom" command
> that applies only to 'psfgen' structures, with the VMD commands for
> writing out structures. This won't work. In order to write out a PDB
> file that contains everything except your selected group of atoms, from
> VMD (not psfgen) you'd use a selection like this instead:
> set sel [atomselect top "not (resname POPC and within 2 of protein)"]
> $sel writepdb myfile.pdb
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Tue, May 10, 2005 at 02:30:50PM +0200, Nicolas Sapay wrote:
> > Hello everybody,
> > I want to delete some residues from a structure. (I mean that I want to
> > remove their coordinates, not only their representations). I have
> > selected a set of atoms :
> > set bad [atomselect top "resname POPC and within 2 of protein"]
> >
> > I have tried to delete them
> > foreach segid [bad get segid] resid [bad get resid] {
> > delatom $segid $resid
> > }
> >
> > And then, I have write my new PDB file
> > animate write pdb myfile.pdb
> >
> > However, deleted residues are still present in myfile.pdb! Then, I have
> > tried this :
> > delres $bad
> >
> > But I get an error message:
> > can't read "segid": no such variable
> >
> > Can someone help me to delete these residues?
> >
> > Thanks
> >
> > Nicolas
> >
> > --
> > _ Nicolas Sapay ________________________ PhD student _
> >
> > IBCP - Institut de Biologie et Chimie des Protéines
> > >> 7, Passage du Vercors
> > 69367 Lyon cedex 07, France
> >
> > >> Tel : (33) (0)4 72 72 26 46
> > >> Fax : (33) (0)4 72 72 26 04
> >
> > ____________________________________ n.sapay_at_ibcp.fr _
> >
>
> --
> 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
>