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: nl223@cus.cam.ac.uk
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: nl223@cus.cam.ac.uk
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Andras Fiser -
Dr Nicolas Le Novere