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