-- 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 sali@salilab.org; Web http://salilab.org

-----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] 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 anita.bentley@lure.u-psud.fr To: bozidar@salilab.org 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: anita.bentley@lure.u-psud.fr