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Re: [modeller_usage] MODELLER BASIC HELP

bharat lal wrote:
> 1) It's written in the manual that the sequences should be in PIR format
> .. but for the template sequence I am not getting the second line ,
> about the structure ?? from where I can get it ??
> and whats the actual way for obtaining PIR sequences and with the
> structure details required  as required for the template??

See http://salilab.org/modeller/9v7/manual/node445.html for a
description of the alignment file format. When Modeller reads a template
structure (one marked as structureX, for example, on the second line) it
gets the corresponding PDB file to read also from the second line,
immediately after the structureX: part. In the case at that URL, it
reads the '5fd1' PDB file. It will automatically try adding ".pdb" to
the end of the file name, but you can certainly put a full file name
there if you want.

> 2)How to align the two sequences in PIR foramat .. since I aligned the
> sequences in FASTA format I am not getting the same structure given in
> the manual as an example ??

I don't understand this question - aligning sequences is independent of
the file format you read or write them in.

> 3) Where do I have to save the .pdb file of the template in modeller and
> the code that is given for homology modeling , there is nothing
> mentioned about the .pdb file being used ??

I think this should be covered above. You can put your PDB files in the
same directory as your script and alignment file, or you can set
env.io.atom_files_directory to a list of other directories to look in
for PDB files. See the many examples in the manual.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage