[modeller_usage] Bug in user distance restraints ?

["Thorsten Schweikardt" <>]

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