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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