Re: [modeller_usage] Bug in user distance restraints ?
To: Thorsten Schweikardt <>,
Subject: Re: [modeller_usage] Bug in user distance restraints ?
From: Oliver Hucke <>
Date: Tue, 28 Oct 2003 10:34:02 -0800
Hi Thorsten,
at least with the SGI version of modeller6v2 the addition of restraints
by redifining the 'special_restraints' subroutine leads to different
optimization traces. I started the calculation of a model with and
without additional restraints and inspected the time course of the
optimization in the *.D* file. At a certain point during the VTFM
optimization the optimization traces start to diverge.
Please let me know what you find out about the Linux and Windows
versions of modeller.
Schoene Gruesse nach Mainz,
Oliver
Thorsten Schweikardt wrote:
Hello to all,
I am having problems to use the user distance restraints, they are
ignored completely by Modeller 6v1/6v2latest, Windows and Linux-
versions: at first I thought they were not met entirely, but then
I ran some tests, with and without the restraints:
The 50 models I get when using the restraints are identical to those
that are modeled using no restraints at all...
Modeller really reads the commands (because using a "0.0" as standard
deviation crashes it), but it does not seem to incorporate the distances
into the model.
Changing the form of the restraints (gaussian, LJ, cosine etc) or using
different atoms (CA instead of OG) did not help.
My goal is to model the n-terminus of a protein that's available
as pdb with the help of measured distances from Electron Spin Resonance.
Could you please tell me whether I am doing something wrong (syntax?) or
if there is a bug of some kind? I would be very grateful for an answer.
Thanks again for listening,
Thorsten Schweikardt
University of Mainz
My Top-File:
-----------------------------
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'
#eg. Distance Serine-OH AA3 to Serine-OH AA169: 30Angstrom
SET ATOM_IDS = 'OG:3' 'OG:169'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 30.0 1.0
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
--
_______________________________________
Oliver Hucke (PostDoc)
Biomolecular Structure Center
Dept. of Biochemistry
University of Washington
Health Sciences Building K-418C
1959 NE Pacific St
Seattle, WA 98195
T:(206)685-7046
_______________________________________