[phenixbb] TLS refinement

Pavel Afonine pafonine at lbl.gov
Sun Oct 5 14:38:20 PDT 2008


Hi Hua,

once you used TLS refinement option, please make sure you use it in all 
subsequent runs. In the case where your R increased to 36% did you use 
TLS refinement option? If you didn't then it explains the increase in 
R-factors.

Please let me know if you have any questions.
Pavel.


On 10/5/2008 2:18 PM, HUA YUAN wrote:
> Dear Phenix community members,
>  
> I have a molecular replacement solution refined agains a twinned 2.7 
> angstrom data to Rfree as 33%, with TLS and twin-law and others as 
> default.  The map looks good and shows extra map for my flavin 
> ligand.  Then I manually rebuild the model, fixing some obvious 
> off-map residues and put a flavin molecule into the model.  After 
> this, I used the *def file from previous run to do another round of 
> refinement.  This time the Rfree increased to 36%.  I realized that it 
> has something to do with the TLS, isotropic and aniostropic B factor.  
> However, I don't know exactly what's the reason and what to do at this 
> stage.  Any comments or suggestions?  Should I do TLS refinement at 
> the last step?
>  
> Thanks and Best Wishes for all,
>  
> Hua
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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/20081005/e92541b1/attachment-0003.htm>


More information about the phenixbb mailing list