Hi Jianghai,

Thanks for the .log  file ! I looked at it and now I think I now what's the problem: this is the bug in phenix.refine that we will fix for the next release. The bug arises when you try to refine using TLS and NCS at once. Sorry for this.

The possible solution is to split your refinement into 2 parts:
1) First, refine coordinates and isotropic B-factors. Use NCS restraints. DO NOT refine TLS.
2) At the end, as the final tune up, refine ONLY isotropic B-factors + TLS and do not refine coordinates. For this run, please REMOVE all NCS information (NCS selections) from the command file. This refinement run should be the final one.

Once again, sorry for the inconvenience. This will be fixed in the next release of CCI APPS and PHENIX. Once this fixed, you will be able to run everything in "one go" and in any combination.

Please let me know if what I suggested helped you. Any further questions are welcome!

Cheers,
Pavel.


Jianghai Zhu wrote:
Here is the log file.  Thanks.

Jianghai

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On Dec 14, 2006, at 12:50 PM, Pavel Afonine wrote:

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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