[phenixbb] Where is phenix.refine finding starting r values?

Pavel Afonine PAfonine at lbl.gov
Mon Jan 18 23:12:50 PST 2010

Hi Aaron,

this is because Refmac reports residual B-factors in ATOM records and 
the TLS component is stored in PDB file header that is ignored when you 
run phenix.refine (slides #30-36):

It is not a problem if you run an equivalent refinement in 
phenix.refine, since within a macro-cycle or two it will be equilibrated.


On 1/18/10 6:47 PM, Bart, Aaron G wrote:
> Greetings,
> I am fairly new to crystallography, and have just started to use Phenix for structural refinement. I am currently working on a 2.8A structure that was run through multiple rounds of rigid body refinement via Refmac and manual revision using Coot. I eventually got stuck where large portions of my molecule had very poor density and the rwork and rfree stayed around 0.3. I then performed a TLS refinement which resulted in better density, and tried running it through phenix.refine with default ADP settings, as well as simulated annealing. It worked beautifully, however when I looked at the log file for the refinement, phenix was reporting a starting rwork and rfree that represented my first stage of refinement in refmac, 0.38/0.44. My question is, is phenix somehow neglecting the refinement that was done in refmac?   
> Regards
> -Aaron
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