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

pramod kumar promarksn at gmail.com
Tue Oct 22 10:34:09 PDT 2019

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

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,
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