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