[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
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20061214/cc93329e/attachment-0004.htm>
More information about the phenixbb
mailing list