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can't get disulfides bonds



Dear modellers,

[modeller6a]

My template contains two disulfides bonds, and the cysteines are 
conserved in the protein I want to model. Hence, PATCH_SS_TEMPLATE, 
automatically run by the routine 'model' is suppose to take care of 
the bonds. It doesn't. Hence my first question:

How MODELLER detect SS bonds in templates: SSBOND in the HEADER or 
CONECT at the end of the PDB file?

Then I decided to patch the disulfides manually with

INCLUDE                             # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 1     # uncomment to produce a large log file
SET ALNFILE  = 'a7ggmono2.ali'      # alignment filename
SET KNOWNS   = 'mono2'               # codes of the templates
SET SEQUENCE = 'a7gg'               # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files
SET STARTING_MODEL= 1               # index of the first model 
SET ENDING_MODEL  = 1               # index of the last model
                                    # (determines how many models to calculate)

CALL ROUTINE = 'model'              # do homology modelling
STOP
SUBROUTINE ROUTINE = 'special_patches'
       PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '127' '141'
       PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '189' '190'
       RETURN
END_SUBROUTINE

It did not work either.

Any ideas?

--
Dr Nicolas Le Novère                    http://www-alt.pasteur.fr/~lenov
Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK
tel: +44 1223 336623  fax: +44 1223 336676   e-mail: