[phenixbb] high R-value with resolve_cryo_em

[Tom Terwilliger]

Hi Daniel,

We don't have a standard way to interpret the R value for density
modification...hence the rough guide of "0.25 is good and 0.5 is poor" but
no documentation.  This applies to both X-ray and cryoEM density
modification.

This R value describes the mismatch between measured and map-based
structure factor amplitudes.  Usually these match pretty well in cases
where the map is improved a lot and not when the map does not improve, but
there is no obvious and simple relationship.

My recommendation would be to use the estimate of map resolution and visual
quality as your guide as to whether it has improved your map, and the R
value in density modification as a possible indication that some change of
parameters might help if things are not going well (not that it tells you
what to change, but a good one is always resolution and another is solvent
content.)

In your case I might try cutting the resolution or randomly changing
solvent content and testing...but as the map looks ok I would not try too
hard.

I hope that helps!
All the best,
Tom T

On Wed, Jun 8, 2022 at 14:25 Daniel Larsson <daniel.larsson at icm.uu.se>
wrote:

> Hi all,
>
> I tried to do density modification using the resolve_cryo_em tool. The
> resolution improves quite a lot from around 2.60 to around 2.35 and the
> density looks significantly better than the autorefined original map.
> However, the R-values is close to 0.5, which seems very high. How should
> the R-value generated by this tool be interpreted? It is very poorly
> documented and not mentioned in the paper or on the manual page, but Tom
> Terwilliger mentioned in a workshop that “low number is good” and “point
> two-four is a very good number, point five is not a good number”, which
> makes me worried.
>
> Regards,
> Daniel
>
>
>
>
>
>
>
>
>
> När du har kontakt med oss på Uppsala universitet med e-post så innebär
> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>
> E-mailing Uppsala University means that we will process your personal
> data. For more information on how this is performed, please read here:
> http://www.uu.se/en/about-uu/data-protection-policy
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20220608/e8a6b328/attachment.htm>