[phenixbb] a few questions
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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