Re: [modeller_usage] Fwd: PIR file format

On 9/21/12 11:44 AM, Nanda Pandey wrote: > I have read in the forum that one needs to input PDB structure details > also while changing the format, Please let me know if this is required > for query sequence also or only while submitting the alignment as input > (changed to PIR).

The file format is fully described at http://salilab.org/modeller/9.11/manual/node476.html

You can also find several example alignments in the manual and tutorial.

You need to tell Modeller which part of the PDB file corresponds to the sequence, but of course this is usually only for the templates (since you don't have a PDB file for your query sequence).

Ben Webb, Modeller Caretaker