Quiliano Mesa, Miguel Angel wrote: > I have several sequences in FASTA format so I would like to do the > same process such as the basic tutorial with the database "95.pir", > my question is... how to convert to PIR format.. should I use a > program for this? there is a program for this? anyone have a scritp?
Converting the file formats is straightforward - simply read in the FASTA file with alignment.read() or (better) sequence_db.read() - see http://salilab.org/modeller/9v7/manual/node369.html - and then write out with alignment.write() or (better) sequence_db.write(). But that only solves part of your problem - PIR format contains more information than FASTA format (the header line contains the name of the corresponding PDB file and the range of residues to read). Since Modeller cannot invent this information from nothing, you will have to fill in this extra information yourself. If you have the original PDB files corresponding to these sequences, it may be easier just to rebuild your sequence database in PIR format starting from the PDBs. See http://salilab.org/modeller/wiki/Rebuilding%20sequence%20databases for an example.
Ben Webb, Modeller Caretaker