create a disulphide in a protein

[Giulio Rastelli <>]

Dear Modellers,

Starting from a Xray structure of a protein where the 2 cysteines are far
apart, I would like to model the *same* protein with a disulphide.
I tried manual patching of disulphides in 2 ways, but none seems to work:

1) 

INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE  = '/lab/giulio/cu/homology/align.pir' 
SET KNOWNS   = 'alr2'
SET SEQUENCE = 'dis' 
SET ATOM_FILES_DIRECTORY = '/lab/giulio/cu/homology'
SET STARTING_MODEL= 1
SET ENDING_MODEL  = 12
SET DEVIATION     = 4.0
SET RAND_SEED     = -12312
SET HETATM_IO = on
CALL ROUTINE = 'model'
STOP
SUBROUTINE ROUTINE = 'special_patches'
 PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '298' '303'
 RETURN
END_SUBROUTINE

2)

READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'
SET HETATM_IO = on
READ_MODEL FILE = 'alr2'
SEQUENCE_TO_ALI ATOM_FILES = 'alr2', ALIGN_CODES= 'alr2'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 'alr2.ini', ;
                ALIGN_CODES = ALIGN_CODES 'alr2-ini'
GENERATE_TOPOLOGY SEQUENCE = 'alr2-ini'
PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '298' '303'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ= off
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'
ENERGY

Any suggestions? Thank you very much for your help
(PS I'm using Modeller 6)

Giulio