[phenixbb] map to model fsc did not start from 1

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Wed Dec 11 13:12:08 PST 2019

Hi Yangqi,
There was a bug in mtriage in a few versions that did lead to this behavior
of the FSC not being 1 at low-res.  You could try a nightly build and see
if this is the cause (or perhaps it really should be lower but that is not

In principle at least you should be able to use the helical symmetry for
creation of a complete model from a protomer (if that is what you are
asking)  You can try phenix.map_symmetry and see if that finds the NCS.
Otherwise, you can input your NCS with helical symmetry to
phenix.map_symmetry and it should check that ncs.  The most likely problem
is if the helical axis is not along (0,0,1).

Let me know if that doesn't work,
All the best,
Tom T

On Wed, Dec 11, 2019 at 2:04 PM Yangqi Gu <yangqi.gu at yale.edu> wrote:

> Dear Phenix developer,
> I have a question regarding the map to model fsc. I have a filament map
> and a model with arbitrary copy of the protomer ( I built them in Chimera),
> then I used the filament model to refine against my map. But I
> encountered an issue is that the reported FSC (map to model) did not start
> from 1 but rather 0.8. I am wondering if there is anyway to fix it. Also,
> in the case of a filament, how do I use NCS operator to refine rather than
> manual building the filament model? I tried specifying NCS with helical
> symmetry, but it did not work.
> Best,
> Yangqi
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Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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