Re: [modeller_usage] Disulfide bonds in dimer

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

Vladimir Chupakhin wrote:
> I have a script question for you:
> I want tom model dimer from homopentamer, how is correctly define 
> disulfide bonds
> *like this*
> CALL ROUTINE = 'model'              # do homology modelling
> STOP
> SUBROUTINE ROUTINE = 'special_patches'
> PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '166' '180'
> RETURN
> SUBROUTINE ROUTINE = 'special_patches'
> PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '160' '174'
> RETURN
> END_SUBROUTINE
>
> *or I need to define smthing like this*
> RESIDUE_IDS = 'A:166' 'A:180'
> RESIDUE_IDS = 'B:160' 'B:174'

See http://salilab.org/modeller/manual/node64.html

In short, the first approach will work if your system has only one 
chain. If it has multiple chains, you need:
RESIDUE_IDS = '166:A' '180:A'
RESIDUE_IDS = '160:B' '174:B'

Also, you should put both of the PATCH commands within the same 
'special_patches' routine. You have two routines, both called 
'special_patches'; in this case, only one of them will get called.

	Ben Webb, Modeller Caretaker
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