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

pramod kumar promarksn at gmail.com
Wed Oct 23 12:06:54 PDT 2019

Dear Pavel,

Thank you so much for the consideration, I have shared the file with you.

Best regards,

On Tue, Oct 22, 2019 at 7:26 PM Pavel Afonine <pafonine at lbl.gov> wrote:

> 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
> files.
> Pavel
> 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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