[phenixbb] Phenix-RSR model fit issue in CS-Map

Pavel Afonine pafonine at lbl.gov
Tue Oct 22 17:26:42 PDT 2019

Hi Pramod,

I need to see the map and models before and after refinement to diagnose 
the issue. Can you share the files? I will have a look once I have the 


On 10/22/19 10:34, pramod kumar wrote:
> Dear Experts,
> I have a map generated through cryosparc (ab initio-reconstr and 
> homo-refine at 3.7A* FSC and sharpened in Scipion and separately in 
> EMAN2). I have build the initial pdb through BALBES which has perfect 
> validation parameters and nice fitting in the map (with the mtz 
> output) but the co-ordinates are shifted from the true origin of 
> CS-map. I used phenix-RSR to fit and refine, but validation results 
> remained too far to accept the model as good solution and also a small 
> region entered in wrong nearyby densities.
> So far following independent and downstream approaches I have taken:-
> In phenix; dock in map, map to model, rigid body refine followed by 
> real space refine (with both .map and converted .mtz), using only 
> chain A-map boxing and model generation through NCS.
> I have tried chimera fit for entire assembly and also only one chain 
> in boxed map and full map but still the validation remained far from 
> acceptable values and a small region in wrong neighboring density.
> Please help.
> -- 
> Best regards,
> Promod

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