[phenixbb] modelling into positive densities

Sam Tang samtys0910 at gmail.com
Mon Apr 29 23:33:26 PDT 2019

Dear all

Thanks for all the advice and suggestions.

After multiple attempts I believe we were actually building too many
residues to the N-terminus (!). It also appeared the region is complicated
by extra density (seems to be EDO, likely degraded from PEG), which were
mis-treated as protein. Deleting the nearby mis-placed residues allowed the
green blobs to be fitted.

Thanks again!


On Mon, 29 Apr 2019 at 20:08, Grüne Tim (PSI) <Tim.Gruene at psi.ch> wrote:

> 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.
> Best,
> Tim
> ------------------------------
> *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
> 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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