[phenixbb] Need help with atom selection for anisotropic refinement

Nathaniel Echols nechols at lbl.gov
Wed Oct 16 13:54:27 PDT 2013

I think the problem is with the boolean logic ("and"/"or").  First, the

optional (element H or element D or resname HOH or chain E or chain F or
> chain A or chain B)

This will be processed okay but it's going to select all atoms in chains
A/B/E/F in addition to all H/D and waters, which probably isn't what you
really want since the anisotropic selection includes chains A and B.  I'm
not sure what will actually happen here, but it's better not to rely on the
atom selections being processed in a particular order (and better not to
rely on the code automatically handling the problem of overlapping

chain A and chain B and not (element H or element D or resname HOH or chain
> E or chain F or chain A resseq 5:11 or chain A resseq 66:72 or chain A
> resseq 117:138 or chain A resseq 152:184 or chain A resseq 196:210 or chain
> A resseq 249:251 or chain B resseq 3:6 or chain B resseq 66:72 or chain B
> resseq 166:210 or chain B resseq 249:251)

The problem here is that you have specified that the atoms match "chain A
and chain B", which is impossible.  You probably want this:

(chain A or chain B) and not (....)

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