Thanks for your prompt response. I have already played with automodel.py,
although by changing different parameters, and could not get this to work.
In automodel.py, when I change
for (dmodel, maxdis, rsrrng, rsrsgn, rsrgrp, typ2, typ3, stdev) in \
((5, self.max_ca_ca_distance, (2, 99999), True, 9, 'CA', 'CA',
(0, 1.0)),
to
for (dmodel, maxdis, rsrrng, rsrsgn, rsrgrp, typ2, typ3, stdev) in \
((5, self.max_ca_ca_distance, (1, 99999), True, 9, 'CA', 'CA',
(0, 1.0)),
the program still makes the restraints only for i, i+2 CA atoms. Is there
an additional over-ride for this setting in a different script? Or is it by
now hard-coded into the program regardless of the script setting?
I just tried changing these numbers in Modeller 6v2, still makes the
restraints only for i, i+2 CA atoms.
Thanks,
Mensur
At 11:40 AM 5/9/2006, you wrote:
Mensur Dlakic wrote:
Is there any way to force Modeller to generate restraints for consecutive
CA atoms instead for every other one? What is the reason for excluding i,
i+1 restraints for CA atoms?
The i, i+1 CA-CA restraint (also the N-O and sidechain-sidechain
restraint) is excluded because it would conflict with the stereochemical
backbone restraints, but you can certainly turn it back on. Just modify or
override the mkhomcsr method in the automodel class
(modlib/modeller/automodel/automodel.py). The ranges for all three of
these restraint types are currently set to (2, 99999). Just change them to
(1, 99999).
Ben Webb, Modeller Caretaker
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| Mensur Dlakic, PhD | Tel: (406) 994-6576 |
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