Dear Modellers,

I'm building a heterodimer with a homodimer template. I have the template pdb file (dimer.pdb) and the sequence file of the heterodimer (hetero.ali).

Here is the hetero.ali file:

>P1;hetero sequence:to_model:1:A:859:B:853::: AAAAAAAAAAAAAAAAAAAAA/BBBBBBBBBBBBBBBBB

There are 859 a.a. in one chain and 853 a.a. in the other chain. I didn't type the exact number of a.a. here.

The following is the script I used for alignment:

from modeller import *

env = environ() aln = alignment(env) mdl = model(env, file='dimer', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='dimerAB', atom_files='dimer.pdb') # I used "dimerAB" to point out both chain A and chain B for alignment. I don't know whether it is correct. aln.append(file='hetero.ali', align_codes='hetero') aln.align2d() aln.write(file='hetero-dimerAB.ali', alignment_format='PIR') aln.write(file='hetero-dimerAB.pap', alignment_format='PAP')

The script running result showed the two chain of the heterodimer aligned to one chain of the template. Would you kindly tell me how I can get the correct alignment? Thank you.

Xiongzhuo Gao

BMCB Department University of New Hampshier Durham, New Hampshire 03824