[modeller_usage] using BLAST to find templates for modelling

["Nick Fusseder" <>]

Hi all,

I have been dwelling over the following problems and simply do not know how
to continue. Any help would be greatly appreciated.

My scenario:
I am running a BLAST search against PDB sequences in order to find suitable
templates to model my target protein. I have all PDB structures locally
installed and the atom_files variable pointing to this directory in my .py
scripts.

I basically have 2 questions:

1. From what I understand the modlib/CHAINS_all.seq is used to store the
sequences for the PDB structures. Now if I want to use a novel PDB structure
as a template which is not included in this list, will I have to manually
create the chain sequence in PIR format (with commands/make_chains.py) and
append it to the modlib/CHAINS_all.seq file?
ALso is there a way to create a CHAIN_all.seq file from all PDB structure
files in one go?

2. Since I am already running a BLAST search to find my template structures,
I won't be using search.py. In order to create the .ali alignment file which
is neccessary for the computation of the final structure prediction of my
target sequence, i will need to run malign.py. The problem is, malign takes
a .seg file as input. I have not yet found an automated method to generate
such a .seg file from a target sequence and template structures found by
BLAST. Will I have to create the .seg file manually? 

Maybe I am just missing the point and the solution to all my problems is in
fact really easy. I guess my main problem boils down to which files can be
created by modeller for me and which files need to be generated or edited by
hand. 

I would greatly appreciate any help.

Regards,

nick

-- 
Echte DSL-Flatrate dauerhaft für 0,- Euro*!
"Feel free" mit GMX DSL! http://www.gmx.net/de/go/dsl