[phenixbb] Phenix TLS refined model feeding into next round of refinement

Daqi Tu daqi.tu at gmail.com
Wed Jul 20 15:34:57 PDT 2011


Thanks. This answered my concern. I wanted to use TLS, just not 
anisotropic INDIVIDUAL B factor refinement, which at my resolution is 
not high enough. I was just worried the ANISOU record will fool the 
program into anisotropic individual B factor refinement. But clearly 
when TLS is still requested, Phenix knows what to do.


On 7/20/2011 5:39 PM, Pavel Afonine wrote:
> Hi,
>> I used to think after one round of Phenix TLS refinement, if I need 
>> to do further refinements after correcting couple residues, I need to 
>> take out the ANISOU records from the pdb file. The reason is if not, 
>> all protein atoms might be applied anisotropic individual B factor 
>> refinement in the next round. Yesterday, I made a "mistake" directly 
>> feeding the pdb file from the previous TLS refinement into the next 
>> one. Seems it is fine. Is that true Phenix automatically recognize 
>> what I wanted, that is, TLS only, not anisotropic individual B factor 
>> refinement?
> - it seems to me extremely weird if you do one refinement run with TLS 
> and then the next one without TLS. I can't see a reason for this.
> - by removing ANISOU records you completely invalidate the results of 
> previous TLS refinement;
> - phenix.refine tries to decide automatically where the input ANISOU 
> come from. If input file contains ANSIOU and resolution is low enough 
> and TLS refinement is not requested then phenix.refine simply removes 
> ANISOU and continues. Obviously, this means the previous results of 
> TLS refinement are all completely invalidated.
> More details:
> 1) http://www.phenix-online.org/newsletter/
> articles "TLS for dummies" and "On atomic displacement parameters 
> (ADP) and their parameterization in PHENIX".
> 2) 
> http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf
> 3) 
> http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf
> Pavel.
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