Dear Users,
recently we got several questions personaly or on the list about the same
problem:
Modeller crashes because the template structures are not overlapping. This
happens when for instance one tries to model a dimer using two different
template structures for each of the domains and without any structural overlap
between them.
When the program starts, Modeller tries to superpose the two or more templates
according to the alignmnet which does not work in these cases, of course, then
stops with error.
Despite of the missing information about the structural orientation of the
templates you can do the modeling if you include in your top file the following
modified subroutine, just as you see below:
SUBROUTINE ROUTINE = 'transfer_xyz'
# SET ALIGNMENT_FORMAT = 'PIR'
## READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS
## MALIGN3D FIT = off, GAP_PENALTIES_3D = 0 4
READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE
READ_TOPOLOGY FILE = TOPLIB
READ_PARAMETERS FILE = PARLIB
CALL ROUTINE = 'create_topology'
TRANSFER_XYZ CLUSTER_CUT = -1.0
BUILD_MODEL INITIALIZE_XYZ = OFF
WRITE_MODEL FILE = MODEL
RETURN
END_SUBROUTINE
Modeller will create models, but in case of insufficient implicit structural
restraints (as e.g. bulkiness of the structures) the orientation of the
individual, not overlapping parts of the model (as defined by the not
overlapping templates) and the confomation of the interconnecting segments may
be not accurate.
Users may impose some knowledge for the orientation of the domains, by
orienting the structures prior to the modelling, or if they can introduce
explicit restraints in between the independent structural parts (e.g.
catalytic site between units: upper limit distance restraints among catalytic
residues etc.)
Also, at the end of modelling , if the orientation of the templates was dubios
one should not force the overall final superposition :
set FINAL_MALIGN3D = 0
best wishes,
Andras
--
,
Andras Fiser, PhD # phone: (212) 327 7206
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras