VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Mon Jul 05 2010 - 09:30:09 CDT

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.

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
********************************