[phenixbb] questions

Peter Zwart PHZwart at lbl.gov
Thu Dec 14 09:11:42 PST 2006

>> 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?

What is the resolution of your data?

Backbone B-s usually are lower than the main chain.

What is the Wilson B value reported by phenix.refine?
You could re-refine and randomize all B-values and see what happens (I 
have to get back to you to to get the exact command for this). Maybe it 
is useful to obtain a copy of the latest verison of phenix.refine by 
downloading cci_apps from our server http://www.phenix-online.org.

If your B-values still come out lowish, try growing crystals that do not 
diffract very well, that usually does the trick.



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