Re: [modeller_usage]molecular modelling with multiple chains

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
-- 
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