[phenixbb] Map after refinement

Pavel Afonine PAfonine at lbl.gov
Fri Feb 26 13:43:39 PST 2010


I heard about this scenario of getting a nonsensical map a couple of 
times before, however I was never able to reproduce this problem myself.

Could you please send me (to my email address, not to the whole bb) the 
phenix.refine inputs so I can reproduce this problem and fix it? 
Specifically, I need: model and data files, and the exact command that 
leads to bad maps. All files will be handled confidentially.

I guess the problem is in HL coefficients that are used by phenix.refine 
to output phase-combined map. model_vs_data does not use HL coefficients 
and this possibly explains the difference. If it is the case then we 
would need to figure out what happens to HL coefficients and this would 
require us to reproduce your Autosol run.


On 2/26/10 12:31 PM, Xuewu Zhang wrote:
> Hi Phenix developers/gurus,
> I got a SAD structure, the experimental map (overall_best_denmod..mtz) 
> from Autosol looks great. I then built the model and used 
> phenix.refine to refine the model using the "exptl_fobs....mtz", which 
> worked well as shown by the lowered Rfree. However, the map from the 
> refinement makes no sense at all, totally featureless. Using the same 
> refined model and mtz, phenix.model_vs_data did make the right map. I 
> have tried both phenix 1.5 and 1.6. Any clue?
> Thanks,
> Xuewu Zhang
> UT Southwestern Medical Center
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