lf of Tereza Skalova
Reply-To: Tereza Skalova
Date: Friday, March 8, 2019 at 3:08 AM
To: "CCP4BB@JISCMAIL.AC.UK"
Subject: [ccp4bb] Ramachandran outliers
Dear all,
I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers.
Do you have any idea how to reduce the numb
Dear Tereza,
First, a shameless plug for ISOLDE (https://isolde.cimr.cam.ac.uk). It’s built
specifically for working with models around your resolution.
Other than that, I’d suggest having a close look at the corresponding sites in
your high-resolution reference models as a sanity check.
Dear Tereza,
In certain cases it could be better to do a step back to be able to
rebuild properly.
Did you look carefully in the real-space the agreement between your
model and the visible density.
If you "over"refined your model in reciprocal space only you can loose
some information.
Thank you for your comments.
1) manual correction in Coot does not work - the density is too weak
2) manual NCS is substantially better than automatic local NCS in this case
3) CPP4i2 might be good idea
4) PDB REDO is great, however no more help in this case
5) Prosmart - I use "prosmart -id -p1
Dear Tereza,
It is highly recommended that you do not attempt to directly optimise the
Ramachandran plot during refinement. Doing so would not guarantee you a better
model, and would mean that you could no longer use the Ramachandran plot for
validation purposes.
I suggest that you inspect
board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tereza
Skalova
Sent: Friday, March 08, 2019 10:08
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Ramachandran outliers
Dear all,
I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers.
Do you have any idea how to reduce the number
Dear all,
I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers.
Do you have any idea how to reduce the number?
I refine in Refmac, using h-bond based Prosmart restraints based on PDB
structures (identical molecules with high resolution) and I use NCS, medium
between AB
Dear all,
Picking up from the earlier thread about Ramachandran outliers, how would
these outliers (Ramachandran as well as rotamer) affect the surface
electrostatic calculations e.g by APBS, especially when the number of such
outliers is very large.
Sincerely,
Asma
Dear Misbah,
Please don't give up on Crystallography for the poor attitude of one senior
PI. Not
all of us have the same way of helping beginners.
Michael James
