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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