Re: [modeller_usage] Cutoff for distance restraints
To: Armin Meier <>
Subject: Re: [modeller_usage] Cutoff for distance restraints
From: Modeller Caretaker <>
Date: Thu, 28 Jan 2010 08:07:36 -0800
Cc:
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.