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Re: [modeller_usage] Cutoff for distance restraints

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
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage