VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Mon Jul 05 2010 - 09:46:18 CDT

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
> ********************************
>
> 

-- 
Leonardo Trabuco, Ph.D.
CellNetworks, BioQuant
University of Heidelberg, Germany