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

[Tom Terwilliger]

Hi Yangqi,
Oh I'm sorry, I didn't read carefully enough.  For a map-model FSC, these
normally do not go to 1.  A value of 0.8 is fine at low -res.  Half-map FSC
values should go to 1.
All the best,
Tom T

On Wed, Dec 11, 2019 at 2:28 PM BuddySphinx <yangqi.gu at yale.edu> wrote:

> Hi Tom,
>
> Thanks for your reply. I am wondering to get FSC starting from 1, does it
> require the model and map to be perfectly matching? I mean, my model is not
> built to every density (extra density for extra copy of the protomer, but I
> did not build the model on these density, since they are not complete).
> Which means there is more density than model, does it matter or do you
> think this is more likely to be the bug of the phenix version.
>
> Best,
>
> Yangqi
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Tom Terwilliger <tterwilliger at newmexicoconsortium.org>
> *Sent: *Wednesday, December 11, 2019 4:12 PM
> *To: *Yangqi Gu <yangqi.gu at yale.edu>; PHENIX user mailing list
> <phenixbb at phenix-online.org>; Thomas Charles Terwilliger
> <tterwilliger at newmexicoconsortium.org>
> *Subject: *Re: [phenixbb] map to model fsc did not start from 1
>
>
>
> 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 likely).
>
>
>
> 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
>
>
>
>
>


-- 
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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