Hi Uma,
How different are your NADs optimised in Refmac and Coot? Are you sure you are
using the same geometric restraints? Coot has to know where Refmac's restraint
files are. This info is passed through an environment setting on your computer
(I don't know the name by hart. Anyone?). Are you using Windows, Linux or OSX
or something else?
You can try to find more details about geometric outliers by checking Refmac's
log file. That way you may find which specific bond/angle is the problem.
Cheers,
Robbie
Date: Sat, 28 Apr 2012 11:47:58 -0400
From: rosiso2...@gmail.com
Subject: [ccp4bb] Ligand geometry
To: CCP4BB@JISCMAIL.AC.UK
Dear All:
I use Refmac5 to refine my model. After the run, I check the model quality by
Coot.
Here is the problem:
In Coot, the ligand - NAD, has bad geometry as indicated by a big red bar.
While the geometry of NAD fit nicely with the electron density.
If I use refine tools (i.e. regularize Zone or real space refine zone), the
geometry of NAD turns to perfec with bond, angle and so on. But the ligand
slightly turn away from the electron density map.
If I run Refmac5 again with this modified model, the NAD turns back, fit nice
to electron density, but gives red bar in coot geometry.
The Refinment Parameters in Refmac5 is set @ "use automatic weight" and "use
experinmental sigmals to weight X-ray terms".
Thank you for advice and comments
Ros
