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!
Sam
On Mon, 29 Apr 2019 at 20:08, Grüne Tim (PSI)
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:* [email protected] [ [email protected]] on behalf of Sam Tang [ [email protected]] *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