[phenixbb] Problem with rotamer refinement
pafonine at lbl.gov
Tue Jul 11 10:10:34 PDT 2017
could you please send me files that are sufficient to reproduce this?
On 7/11/17 10:06, Renato Ferras wrote:
> Dear all,
> I am refining a protein structure at 1.74 A resolution with
> phenix.refine (version 1.10.1_2155) and I have noticed that some side
> chains don't remain in the electronic density even after careful hand
> adjustment in which they are almost perfect. It seems pretty clear
> where the side chain should (must) be located, moreover it is
> consistent with two rotamers (either rotamer tp60 - #4 in coot - or
> rotamer tp-100 - #9 in coot -, which are approx. at 180 deg for chi3).
> In spite of that, after reciprocal space refinement, I observe that
> the end of side chain rotates chi3 angle and both N and O gets far
> from where they started (there is this difference in the chi3 angle).
> My concerns are about the proper interpretation of geometrical
> restraints listed in .geo file, specially what the ideal value is, how
> weights are applied to ideal value and why phenix doesn't reach
> convergence in reciprocal space refinement. Below are the values from
> .geo for the referred Gln:
> dihedral pdb=" CB GLN B 21 "
> pdb=" CG GLN B 21 "
> pdb=" CD GLN B 21 "
> pdb=" OE1 GLN B 21 "
> ideal model delta sinusoidal sigma weight residual
> 0.00 23.41 -23.41 2 3.00e+01 1.11e-03 8.42e-01
> is there a description for us to interpret what these numbers are? To
> my understanding, the ideal values are established as being either 0
> or 180 degrees (yet sinusoidal 2). I cannot say about how heavy the
> weights are on these (in fact, I left my refinement to optimize
> weights), but anyway, if I understand correctly, the ideal value (for
> chi3) should be rotamer dependent. Taking Gln as an example, I see
> several rotamers do have values close to either 0 or 180 degree, but
> what about rotamers 4 and 9? I might imagine a similar situation for
> residues like Asn and His, though I have not searched deep for these yet.
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