On 1/28/10 1:48 AM, Armin Meier wrote: > where can I find the maximal length of CACA, NO, SCMC and SCSC distance, > for which restraints are yet generated by Modeller, i.e. there must be a > cutoff for e.g. CACA distances, which - when exceeded - determines that > no restraint is generated. What are these cutoffs?
You can tell by looking at the automodel.py Python code, or by adding some print statements to your script, e.g.:
a = automodel(env, alnfile=...) print a.max_ca_ca_distance print a.max_n_o_distance print a.max_sc_mc_distance print a.max_sc_sc_distance
would print 14.0 11.0 5.5 5.0
If you call a.very_fast(), however, it reduces these distances slightly to increase the speed of the optimization.
Documentation for these parameters appears to be missing from the manual, so I will add some for the next Modeller release.
Ben Webb, Modeller Caretaker