Mensur Dlakic wrote:
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 changefor (dmodel, maxdis, rsrrng, rsrsgn, rsrgrp, typ2, typ3, stdev) in \((5, self.max_ca_ca_distance, (2, 99999), True, 9, 'CA', 'CA', (0, 1.0)), tofor (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?
Yes, like I said, these i,i+1 restraints are excluded because they would conflict with the stereochemical backbone restraints. See the description of 'DISTANCE' restraints at http://salilab.org/modeller/manual/node160.html and follow the link to energy_data.excl_local, which excludes restraints which conflict with bonded atoms.
In order to generate these restraints, you would have to set the third element (dihedrals) of energy_data.excl_local to False (by default all four elements are True). But I wouldn't recommend that, as unless you are very careful this will also change the behavior of nonbond interactions.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage