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: