[phenixbb] modelling into positive densities

Dorothee Liebschner dcliebschner at lbl.gov
Fri Apr 26 10:33:54 PDT 2019


Here are some suggestions:

1) For the offending residues, check the TLS groups. Maybe you can exclude
these residues from the TLS groups (using isotropic Bs for these residues
only) or come up with a better assignment.
2) From your description, it sounds like you refined XYZ, B, TLS and
occupancies right after MR. You could refine XYZ and B first, adding TLS
and occupancies later.
3) 1.5 Å resolution is typically the "border" for using individual
anisotropic ADP's. So you might want to try using anisotropic ADPs instead
of TLS. There is no guarantee that it'll work, but why not give it a try.
4) Unrelated to B or TLS: Check the distance between the oxygen of the
peptide unit (which is pushed out of density) and the nitrogen from the
symmetry related molecule. I circled the interaction in red in your figure.
The distance should be around 2.7-3.5 Å. I cannot tell from looking at the
screenshot. If it is shorter, nonbonded restraints could push the atoms

Best wishes,


[image: bolb.jpg]

On Fri, Apr 26, 2019 at 5:41 AM Sam Tang <samtys0910 at gmail.com> wrote:

> Hello,
> 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.
> Regards
> Sam
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Project Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
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Fax: (510) 486-5909
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