Subject: Re: [modeller_usage] PDB updates for Modeller
From: Eswar Narayanan <>
Date: Mon, 4 Oct 2004 17:41:05 -0700
Cc:
Procter is right. BUILD_PROFILE can be seen as a command that
supersedes SEQUENCE_SEARCH, to identify potential templates and get a
reliable alignment for modeling.
Eswar.
On Oct 4, 2004, at 6:37 AM, J B Procter wrote:
It is possible to build new sequence databases for modeller - and, as
Eswar said, there are two relevant commands. Writing a script to do
this
is unavoidable, though, unless the caretaker has one ready for everyone
to download!
As a very quick fix, you could get the current pdb sequence list from
here :
ftp://ftp.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt
Then, follow the script in
modeller7v7/examples/commands/build_profile.top, which shows how you
can read in a simple FASTA sequence flatfile database, like the one
from
the pdb website, and then use it to align against your sequence in
order
to build a sequence profile (and by that, retrieve all homologous
sequences from the PDB).
To do the job properly, you need to apply the make_chains command
(modeller7v7/examples/commands/make_chains.top) to generate the extra
information that is written into the PIR information fields, and used
by
modeller fetch the correct PDB file for each sequence in the database.
If you have a mirror of the PDB, then this script (for unix) might
work:
#!/bin/bash
# makes chain records and places them pdb_seq.chn in the current
working
# directory.
# you need to change this to point to your local copy of the PDB,
PDBDIR="/projects/biodata/pdb/data/structures/all/pdb"
for p in `ls -1 $PDBDIR`
do
y=`basename $p .ent.Z`;
if [[ $p != $y ]]; then
echo READ_MODEL FILE = \'$PDBDIR/$p\' > make_chains_.top
echo MAKE_CHAINS MINIMAL_CHAIN_LENGTH = 30, \
MINIMAL_RESOLUTION = 2.0, MINIMAL_STDRES = 30, \
CHOP_NONSTD_TERMINII = on, \
STRUCTURE_TYPES =\'structureN structureX\' >> make_chains_.top
mod7v7 make_chains_.top
cat ${y/pdb/\.\/}.*.chn >> pdb_seq.chn
rm ${y/pdb/\.\/}.*.chn
fi
done;
After that, which will take some time to run, pdb_seq.chn will contain
a
subset of all the PDB chains, in a similar form to the CHAINS_all.seq
file.
You should, then, be able to read this new database in, apply SEQFILTER
(see the example/command/seqfilter.top) , and write out the list of
chain representatives (at 95%, for instance). For best use, you should
rewrite the database (via READ_SEQUENCE_DB and WRITE_SEQUENCE_DB) in
binary format and limit it to just the representative sequences
generated by SEQFILTER (by specifying the CHAINS_LIST option on
READ_SEQUENCE_DB).
Enjoy!
j.
_______________________________________________________________________
Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics
Hamburg http://www.zbh.uni-hamburg.de/staff.php
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