[phenixbb] Refinement and Density modification

Pavel Afonine pafonine at lbl.gov
Mon Sep 8 23:14:49 PDT 2014

Hi Ashu,

2mFobs-DFmodel synthesis that phenix.refine outputs is not sharpened. 
High overall atomic B (maximal common B-factor that can be subtracted 
from all individual atomic B-factors that will still leave them 
non-negative) is what makes the map blurred.
If we subtract this common B from individual atomic B-factors, recompute 
Fcalc and then recompute Fmodel, which is

Fmodel = k_total * (Fcalc + Fbulk)

and then compute the new synthesis with amplitudes 
(2mFobs-DFmodel)/k_total it will be sharpened (and likely similar to 
what you used to build the model). Note, noise will be upscaled too 
(this is the main reason why it is not done by default!).

We are thinking of making this map available as part of phenix.refine 

For now try this:

phenix.pdbtools shift_b_iso=SOME_NEGATIVE_VALUE model.pdb

where SOME_NEGATIVE_VALUE is negative B-factor, like -10 or so, chosen 
such that subtracting it from atomic B will not leave them negative.

Then compute maps using modified PDB file:

phenix.maps model.pdb data.mtz


On 9/8/14 7:57 AM, Ashu S wrote:
> Dear all,
> I am working on a 3.6A Se SAD data. Autosol followed by autobuild gave 
> a decent map (as expected at this resolution) with a moderate trace. 
> After building poly ala trace and assigning few resides in and around 
> Se positions when I refine the model, all the sharp features of the 
> electron density map are lost. For example, a nice looking helical 
> density becomes a tube. I presume that this happens because wilson B 
> is high (~110 A2) and the map requires modification, sharpening etc. 
> Is there a way to get the map with similar sharp features after model 
> building  and refinement as auto build gives? How could I follow 
> exactly the same steps of density modification etc which auto build does?
> Thanks,
> Ashu
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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