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
Nick Fusseder wrote: > 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?
CHAINS_all.seq holds the sequences from PDB (although it is not kept up to date, obviously). It's only used for searching. I don't know what made you think you need to put your own sequences in there (perhaps our documentation is misleading?).
> 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?
It's very easy to create a sequence file from a structure - use alignment.append_model(). One example is in http://salilab.org/modeller/FAQ.html#19
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Nick Fusseder