[phenixbb] a few questions

Jianghai Zhu jzhu at cbr.med.harvard.edu
Sun Aug 6 08:50:17 PDT 2006


> However, I would  try different refinement strategy, for example:
> 1) you do SA refinement first;
> 2) then you do regular refinement + TLS.

How to do SA refinement only?

>> The RMSD of bonds and angles after either SA or combined  
>> refinement are about 0.006 and 0.851 respectively.  Don't you guys  
>> think the geometry restraints are too tight?
> At 2.5A resolution I wouldn't worry about these values. The  
> resolution is low enough to keep the geometry tight.

I thought the goal of the refinement for geometry is 0.02 and 2 for  
rmsd bonds and angle.

Another questions.  After SA or refinement, the B factors vary a  
lot.  In the same residue, B factors jump from 5 to 70.  and  for the  
next residue, B factors are from 40 to 90.  The B factors don't look  
like well restrained.  Are these numbers normal?  I don't see this  
kind behavior of B factor in other refinement programs.

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