pafonine at lbl.gov
Wed Mar 23 14:39:54 PDT 2011
you are asking the right question.
We discussed the issue of residue side chains partially or fully lacking
density at PHENIX developers meeting last week. This was brought up by
an industrial consortium user.
Some people tend to chop them off (which I do not not not like), some
let the refinement programs do what they want, and the programs stupidly
tends to stick these sidechains in whatever density is available around
(this is bad too).
I think we decided that I have to do something about it, probably the
- if a side chain lacks the density and the full rotamer search does not
find any density, then a) set occupancies of affected atoms to zero, and
b) move the side chain to the highest probable rotameric state that
generates least clashes with surrounding atoms and may be still have
some good density fit (even though it is a bad density). I will work on
this. That's for sure.
> Does refine restrains side chain rotamers to, say, the closest one from
> the rotamer dictionary or, perhaps, the starting coordinates (I find
> this less likely, of course)? I am particularly interested in what
> would happen if a side chain is disordered and there is no strong
> electron density to support a specific conformation. Do I understand
> correctly that the real-space refinement for the side chains is on by
> default, which means that disordered side chains would tend to stay
> within their biased density?
> I apologize if I missed the description of this in the manual, just
> point me to the right section then.
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