[phenixbb] modelling into positive densities

Grüne Tim (PSI) Tim.Gruene at psi.ch
Mon Apr 29 05:08:56 PDT 2019

Dear Sam,

at 1.5A you might expect to see holes in the aromatic rings and at least a den in the proline residue.
The region of your screen shot is quite noisy - either you integrated your data too far into the noise, or there is more than one conformation of the side chain. You can split the range of offending residues, including 1-2 either side, and see if coot models the second one reasonably.

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Sam Tang [samtys0910 at gmail.com]
Sent: Friday, April 26, 2019 2:38 PM
To: PHENIX user mailing list
Subject: [phenixbb] modelling into positive densities


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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