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From: "Thorsten Schweikardt" <>
To: <>
Subject: More weight for user distance restraints
Date: Thu, 28 Aug 2003 16:28:34 +0200
Hi to all,
I have a problem with user defined distance restraints, I want
to model the n-terminus of a protein that's available as pdb
with the help of measured distances. So far, it works, but
one little problem remains: the distance-requirements
are not met entirely, because modeller does not distort
the rest of the protein at all, is there a possibility to force it
to add more weight to these distance restraints, even if
it means distorting the template protein?
Thanks,
Thorsten
University of Mainz
My Top-File:
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INCLUDE
SET ALNFILE = 'alignment.ali'
SET KNOWNS = 'protein1'
SET SEQUENCE = 'protein1plusnterm'
SET ATOM_FILES_DIRECTORY = './'
SET STARTING_MODEL= 1
SET ENDING_MODEL = 20
SET LIBRARY_SCHEDULE = 4
SET FINAL_MALIGN3D = 1
CALL ROUTINE = 'model'
SUBROUTINE ROUTINE = 'special_restraints'
SET ATOM_IDS = 'OG:3' 'OG:169'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 30.0 10.0
SET ATOM_IDS = 'OG:116' 'OG:169'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 0.0
SET ATOM_IDS = 'CA:42' 'CA:169'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 1.0
SET ATOM_IDS = 'CA:3' 'CA:42'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 21.0 4.0
SET ATOM_IDS = 'CA:3' 'CA:116'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 50.0 1.0
RETURN
END_SUBROUTINE
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