[modeller_usage] Heterodimer modeling

[Xiongzhuo Gao <>]

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