[phenixbb] B factor over 300

Pavel Afonine PAfonine at lbl.gov
Mon May 3 10:07:31 PDT 2010

Hi Daqi,

> I refined my structure (of which the data is very anisotropic) using 
> phenix.refine and with individual_sites, individual_adp, and tls 
> options turned on. From the refined coordinates, the highest B-factor 
> in the ANISO record (ie B_tls + B_individual) is 305.  This number 
> looks rather high. Is it something I should worry about? and is 
> there an easy way to compute the individual B-factor component?

- what is "high", what is "low", what is "acceptably high",... ? This 
was discussed many times on both phenixbb and ccp4bb.

- you can use phenix.tls
For usage information just type phenix.tls and hit Enter, then read 
message output to the screen.
Using this command you can go back and forth between total and local 
B-factors, as defined here:

see slides #30-36.

Note 1) going from individual components Utls, Uatom to Utotal is the 
exact operation (numbers are computed exactly by the formula), while 
going back: splitting Utotal into Utls  and Uatom is an approximate 
operation, since Utls is obtained as a least-squares fit of Utls to 
Utotal (Utls_fit), and the Uatom then is Utotal - Utls_fit.

Note 2) Uatom may be positive as well as negative or zero.

Please let me know if you have any questions or need help with this.


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