VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Mon Jul 05 2010 - 10:08:27 CDT

Thanks!
I did a grep " A " to check my chains but that also missed the HETATM records.
Good catch. If onl I had tried H I would have seen all this.

HETATM15306 O HOH A3236 56.008 85.864 28.971 1.00 74.20 O

SO what happens to a water that's at the interface of chain A and some other
chain?

Tom

On Monday 05 July 2010 09:46:18 am Leonardo Trabuco wrote:
> Dear Tom,
>
> On Mon, Jul 5, 2010 at 4:30 PM, Thomas C. Bishop <bishop_at_tulane.edu> wrote:
> > Dear VMD,
> >
> > It seems that if I load a raw ".ent" file obtained directly from the RCSB
> > as a ".pdb" and then use the chain selection command then I do not get
> > the same residues as if I load ONLY the ATOM records from the ".ent"
> > file.
> >
> > What's happening ? see script below to reproduce the problem.
>
> You are missing the HETATM records when grepping. If you do instead
> 'egrep "^(ATOM|HETATM)" pdb1kx5.ent > 1kx5.pdb' you'll see that you
> get the same results as when using the .ent file directly.
>
> Cheers,
> Leo
>
> > Thanks!
> > Tom
> >
> >
> > Cut and paste the following commands in a unix shell to reproduce the
> > problem... just read the list of resnames in each case. (not there's no
> > nastly rm commands or the sort! )
> >
> > wget ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/pdb1kx5.ent
> >
> > cat > test.vmd << EOF
> > set thischain [atomselect top "chain A " ]
> > \$thischain get resname
> > quit
> > EOF
> >
> > vmd -pdb pdb1kx5.ent -e test.vmd
> >
> > grep "^ATOM" pdb1kx5.ent > 1kx5.pdb
> >
> > vmd -pdb 1kx5.pdb -e test.vmd
> >
> >
> >
> >
> > *******************************
> > Thomas C. Bishop
> > Tel: 504-862-3370
> > Fax: 504-862-8392
> > http://dna.ccs.tulane.edu
> > ********************************
>

*******************************
   Thomas C. Bishop
    Tel: 504-862-3370
    Fax: 504-862-8392
http://dna.ccs.tulane.edu
********************************