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.