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