--
Andrej Sali, Professor
Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and
California Institute for Quantitative Biomedical Research
Mission Bay Genentech Hall
600 16th Street, Suite N472D
University of California, San Francisco
San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier)
Tel +1 (415) 514-4227; Fax +1 (415) 514-4231
Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239
Email ; Web http://salilab.org
-----Original Message-----
From: Bozidar Yerkovich [">mailto:]
Sent: Wednesday, February 26, 2003 4:18 PM
To: Andrej Sali
Subject: Help - syntax problem (fwd)
---------- Forwarded message ----------
Date: Fri, 21 Feb 2003 19:17:52 +0100
From: Anita Bentley <>
To:
Subject: Help - syntax problem
Dear Modeller experts,
I have been trying to use Modeller for a very specific task. It
gives me really interesting answers and I would like to go a bit
further.
Here is what I do:
I have a PDB coordinate file for the N-terminus and a new X-ray
structure we have just solved for the C-terminus of another protein.
The homology is high, so that I can get a quite satisfactory model for
the "long" protein.
It turns out both domains contain a Zn ion, well characterised in the
coordinate files. I would like to model both ions in the target
structure. For the N-terminal part this involves slightly different
ligands in the target. I therefore prepared a list of added restraints
in order to ensure the ion stays in the right place. And this is where
things start going funny: the C-terminal zinc ligands stay bound to the
ion and all is fine. But the N-terminal zinc ligands move away, as if
the restraints were ignored!
Here is the file I use:
# PRIMER: STEP 5 #
INCLUDE # Include the predefined TOP
routines
SET ALNFILE = 'adca_2.ali' # alignment filename
SET KNOWNS = 'psa' 'yoda' # codes of templs
SET SEQUENCE = 'ADCA' # code of the target
#SET ATOM_FILES_DIRECTORY = '/home/users/anita/work/yoda' # directories
for input
SET TOPOLOGY_MODEL = 1, HETATM_IO = on
SET STARTING_MODEL= 1 # index of the first model
SET ENDING_MODEL = 2 # index of the last model
# (determines how many models to
calculate)
SET DEVIATION = 4.0 # have to be >0 if more than 1 model
SET RAND_SEED = -12312 # to have different models from another
TOP file
CALL ROUTINE = 'model' # do homology modelling
CALL ROUTINE = 'special restraints'
SUBROUTINE ROUTINE = 'special restraints'
ADD_RESTRAINT ATOM_IDS = 'NE2:42' 'ZN2:481'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1
ADD_RESTRAINT ATOM_IDS = 'NE2:119' 'ZN2:481'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1
ADD_RESTRAINT ATOM_IDS = 'NE2:183' 'ZN2:481'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1
ADD_RESTRAINT ATOM_IDS = 'OE1:258' 'ZN2:481'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.1 0.1
ADD_RESTRAINT ATOM_IDS = 'OE2:258' 'ZN2:481'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.1 0.1
ADD_RESTRAINT ATOM_IDS = 'NE2:431' 'ZN2:482'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1
ADD_RESTRAINT ATOM_IDS = 'NE2:440' 'ZN2:482'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1
ADD_RESTRAINT ATOM_IDS = 'NE2:442' 'ZN2:482'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.0 0.1
RETURN
It is the first 5 restraints that pose problems. Any suggestions?
Best regards,
Anita
Anita Lewit-Bentley
LURE
Bât. 209D, Centre Universitaire Paris-Sud
BP 34, 91898 Orsay Cedex
France
tel: (33-1) 64 46 80 50
fax: (33-1) 64 46 41 48
e-mail: