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FW: Help - syntax problem (fwd)




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Andrej Sali, Professor
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    California Institute for Quantitative Biomedical Research
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-----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

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