Is there any way to import alignment created without using modeller. Do I have to manual make a new ali file in the pir format for modeller. Could you please calarify the how the alignment was imported into modeller in the difficult example from http://bioinf.cs.ucl.ac.uk/psipred/
Knut J _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969
On 2/18/10 5:32 AM, Knut J Bjuland wrote: > Is there any way to import alignment created without using modeller. Do > I have to manual make a new ali file in the pir format for modeller. > Could you please calarify the how the alignment was imported into > modeller in the difficult example from http://bioinf.cs.ucl.ac.uk/psipred/
Modeller needs both sequence and structure information in order to do comparative modeling; thus the PIR format as used by Modeller contains a header line that maps the sequence to a matching PDB structure. A typical alignment format (e.g. FASTA) contains only sequence information, so there is no way to automatically add this structural information - you will have to add the PIR header line manually, and that was what was done for the difficult example.
As an aside, Modeller can convert FASTA format to PIR with a script similar to
from modeller import * e = environ() a = alignment(e, file='my.fasta', alignment_format='FASTA') a.write(file='my.pir', alignment_format='PIR')
Note, however, that because FASTA does not contain structural information, each sequence in my.pir will have a simple "sequence:::::::::" PIR header, and you'll have to go in and change this if it corresponds to a template structure.
If, of course, your external alignment already contains the structural information somehow, you could write your own automatic conversion, e.g. with some Perl or Python scripting.
Ben Webb, Modeller Caretaker