[modeller_usage] loop refinement with disulfide patch
Subject: [modeller_usage] loop refinement with disulfide patch
From: "M. Seigneuret" <>
Date: Wed, 27 Feb 2008 14:44:40 +0100
Dear Modeller Collegues,
After sticking for a long time to the old TOP language, I am trying to
switch to Python because I need to use some of the high-end Modeller
features such as dope_loopmodel. Here is my problem :
I want to refine several loops in an existing model using
dope_loopmodel. Some of the loops have disulfide bridges with the rest
of the model or between themselves (the disulfides do not exist in the
A previous case of using restraints or patches in loop refinement
already appeared in the discussion list but there, loopmodel was used
on the fly after automodel so that the redefined patches and restraints
automodel subclasses were active during loop refinement.
What happens when one uses only loopmodel or dope_loopmodel to refine an
existing model ? I suppose it is possible to import patches subclasses
from automodel. I tried to fiddle but got nowhere. Could somebody help me ?
To make myself clear, I am pasting below an example (on one loop) of
what I was doing with the old TOP language
(it worked, at least computationally).
Thanks in advance for your help.
Institut Cochin, U567-UMR8104
Département de Biologie Cellulaire
22 rue Méchain, 75014 Paris, France
Tel: 33 (0)1 40 51 64 50
Fax: 33 (0)1 40 51 64 54
SET SEQUENCE = 'mod2l34'
SET LOOP_MODEL = 'mod2f.B99990002.pdb'
# index of the first loop model:
SET LOOP_STARTING_MODEL = 20
SET LOOP_ENDING_MODEL = 30
SET LOOP_MD_LEVEL = 'refine_1'
CALL ROUTINE = 'loop'
SUBROUTINE ROUTINE = 'select_loop_atoms'
PICK_ATOMS SELECTION_SEGMENT = '59:' '61:', SELECTION_STATUS = 'initialize'
SUBROUTINE ROUTINE = 'special_patches'
PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '41' '60'