VMD-L Mailing List
From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Mon Jul 05 2010 - 09:30:09 CDT
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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
********************************
- Next message: leila karami: "contact map"
- Previous message: Marek Maly: "Re: Conversion of DCD trajectories to AMBER ones ?"
- In reply to: John Stone: "Re: Sasa implentation/ algorithm VMD"
- Next in thread: Leonardo Trabuco: "Re: possible chain select bug on RCSB ".ent" files"
- Reply: Leonardo Trabuco: "Re: possible chain select bug on RCSB ".ent" files"
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