[phenixbb] low resolution secondary structure refinement
Pavel Afonine
PAfonine at lbl.gov
Wed Apr 7 17:29:22 PDT 2010
> it would probably be a day or two of work for Pavel or me.
Actually, in rigid body refinement atoms do not move w.r.t. each other -
the rigid body groups move as a whole, so I don't understand why one may
need to use secondary structure restraints.
The only restraints that make sense to use are those that would prevent
rigid bodies from running one into another, but this is definitely more
than a couple of days of work (for me, at least) -:)
Simple geometry non-bonded restraint term is a possibility and
easy-to-add-now option but not a good idea: one or two ideally
coinciding atoms may throw the whole rigid body miles away from its
original position (because non-bonded term grows exponentially as atoms
get closer to each other). Possibly better is to use overlap functions
(computed based on calculated density map, for example - so-called "soft
non-bonded restraints") - but this is a little project for someone who's
ready to jump into it -:)
Pavel.
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