[phenixbb] modelling into positive densities

Sam Tang samtys0910 at gmail.com
Fri Apr 26 05:38:33 PDT 2019


I am refining a structure solved to 1.5A by MR. Rw/Rf were 0.17/0.22 which
seem acceptable to me. At the very beginning part of the protein the
electron density is a bit wobbly. I am able to build the residues into the
positive densities. But after phenix.refine the chain always shifts away a
bit and leaves the green blobs there.

(Photo: https://drive.google.com/open?id=1UngAJuEUt1S0LwPybMJLw2E1xA4cNM3R)

I am thinking if this can be solved by adjusting the target weights. Or can
I apply certain restraints only to those few residues?

I refined XYZ (reciprocal space), XYZ (real space), individual B-factors,
TLS and occupancies.

Thanks in advance.


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