Hi,
It is tested by distance criteria.
Please send your top, ali and coordinate files to me, we will take a look.
I will reply here with the conclusion.
Andras
Dr Nicolas Le Novere wrote:
>
> 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:
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras