[phenixbb] ligand refinement

Schubert, Carsten [JRDUS] CSCHUBER at its.jnj.com
Tue Aug 11 05:59:56 PDT 2015


A couple of questions you might ask before reverting to drastic measures:
Can you exclude a covalent bond to the protein?
How confident are you about the fit, orientation and nature of the ligand?
Do you see the same phenomenon in a different dataset, i.e. is it reproducible?

It is better to look for an explanation of your experimental findings than to tweak/restrain the refinement to conform to your expectations.

At this resolution the occupancy will be tightly coupled to B-factors. You could try and refine an overall occupancy for the ligand. What makes you believe that you have partial occupancy? Residual fofc density?


From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of xinghuaqin at 126.com
Sent: Monday, August 10, 2015 10:43 PM
To: phenixbb
Subject: [phenixbb] ligand refinement

Hi everyone,

I am refining a structure of protein/ligand complex (2.75 Å) almost to the last stage. However, I found that some atoms of the ligand is too close to the protein (1.2 or 1.3 Å) after refinement.
How should I avoid this? Should I use the "nonbonded_distance_cutoff" parameter? What the value should be set to?

Another question is that at this resolution is it possible for  me to refine the occupancy?

Any suggestion is appreciated.



Xinghua Qin Ph.D

Department of Physiology
The Fourth Military Medical University
169# Changlexi Road
Xi'an 710032, China
Tel. 86-29-84772779

E-mail: xinghuaqin at 126.com<mailto:xinghuaqin at 126.com>
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