[phenixbb] questions

Pavel Afonine pafonine at lbl.gov
Thu Dec 14 09:50:12 PST 2006


Hi Jianghai,

could you please send us .log file from your refinement run, so we can 
analyze what's going on.

In general, "bad" B-factors can be:
- misplaced model;
- inadequate TLS model (= domains chosen for TLS do not correspond to 
the reality).

If you are using like 2 months old or older version of phenix.refine, 
you may want to get the latest CCI APPS since we made lots of 
improvements. Just goto http://www.phenix-online.org/download/cci_apps/

Pavel.


Jianghai Zhu wrote:
> The resolution is 2.5 A.  The wilson B is about 50.  I know B factor 
> of the backbone is lower than that of the sidechian.  But a B factor 
> like 4 is definitely wrong.
>
> Jianghai
>
>
> On Dec 14, 2006, at 12:11 PM, Peter Zwart wrote:
>
>>
>>>> 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.
>>
>> HTH
>>
>> Peter
>>
>>
>>
>>
>>
>>
>>
>>
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