[phenixbb] Excluding atoms from coordinate refinement ignored
eozkan at stanford.edu
Fri Dec 21 16:55:15 PST 2012
Hi Phenix developers,
I have an issue using 1.8.1 (1168) with excluding atoms from coordinate
refinement. I have defined a certain residue to be excluded from
coordinate refinement, as can be seen in the .eff file produced by this
strategy = *individual_sites individual_sites_real_space rigid_body \
*individual_adp group_adp *tls *occupancies group_anomalous
individual = not (resseq 60 and resname PHE)
torsion_angles = not (resseq 60 and resname PHE)
rigid_body = None
However, this gets ignored, and this residue and its NCS-related
brethren get moved into nondescript electron density on a symmetry axis.
This residue was just fine in an earlier version of Phenix, but when I
switched to 1.8.1, it started moving into this density. So, I thought
excluding it from xyz refinement, which is a dirty trick in my opinion,
would fix this problem. Not so.
I have the feeling that this is due to rotamer corrections as part of
the torsion NCS implemented in 1.8.1 now. Sticking a zero occupancy
dummy atom in the density did prevent this residue from moving in.
Turning off torsion NCS also fixed it. By the way, I have "fix rotamer
sidechains" off, as I am yet to see it improve things (at medium or low
Thanks and happy holidays!
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