[phenixbb] questions

Pavel Afonine pafonine at lbl.gov
Thu Dec 14 09:17:22 PST 2006

Hi Jianghi,

> 4) The refinement (TLS + ML + B individual) went through, I got  
> reasonable R, Rfree, rmsdBOND, rmsdANGLE.  But the B factors are  
> pretty low.  The B factor of the backbone is much lower than the side  
> chain, some have numbers like 4.  Some metal atoms also have B  
> factors around 4.  What did I do wrong?
- Low B-factors are common for high resolution models, like higher 1.0A.
- Also, you can get low B-factors at very low resolution, since in this 
case they are mostly modeled by overall B-factor (ether though TLS or by 
overall exponential scaling).
- In rare cases side chain atoms can have lower B than corresponding 
main chain atoms if they are involved in H-bonding.

I need more details for further diagnostics.


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