[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage]molecular modelling with multiple chains

典范 wrote:
> Could you please tell me how to perform molecular modelling with
> multiple chains?   I get trouble in preparing the alignment file in
> this case.

Modeller should have no problem modeling a multiple-chain system. Simply
put the sequences of both chains in your alignment file, and use a chain
break character ('/') to separate them. So your template sequence would
look something like:

>P1;5fd1
structureX:5fd1:1:A:26:B::::
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD
SEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK/
KRRWKKNFIAVSAANRFKKISSSGAL*

Obviously you would change '5fd1' to the actual PDB code of your
template structure, and change the starting/ending residue IDs from 1:A
and 26:B if necessary.

	Ben Webb, Modeller Caretaker
-- 
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage