[phenixbb] ligand refinement

xinghuaqin at 126.com xinghuaqin at 126.com
Mon Aug 10 19:42:39 PDT 2015

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
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