[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 

Please let me know if you have any questions.

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
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