[phenixbb] high R-value with resolve_cryo_em

[Tom Terwilliger]

Hi Daniel,

Oops...way too much jargon in my reply.  "Cut the resolution" means "Use a
lower resolution cutoff".  Of course that could mean a bigger or smaller
number.  It means "Use a bigger number for the value of resolution"  The
idea here is to select a resolution range in which most of the data are
reasonably accurate, where the estimated correlation of Fourier terms with
the true ones is something like 0.5 (the standard half-map correlation
cutoff of 0.143), but it is not obvious exactly what quality cutoff and
therefore what resolution cutoff should be used, so a few tries never hurt.

You might try boxing your map yourself, using varying values for the buffer
around the model (from 5 to 10 A). Then tell resolve_cryo_em not to box the
incoming map. This way you can actually vary the solvent content.

Using the model in density modification could help but keep in mind that
you should always also do it without the model so that you have some map
that you know does not have any model bias. (The model-based density
modification does not seem to have model bias in my experience but it
always could).

All the best,
Tom T

On Wed, Jun 8, 2022 at 11:04 PM Daniel Larsson <daniel.larsson at icm.uu.se>
wrote:

> Hi Tom,
>
> Thank you so much for the feedback.
>
> By “cutting the resolution” does that mean that I should put a smaller or
> higher number for the density modification resolution? I guess I should try
> both lower and higher...
>
> The solvent content using default settings is very high, more than 97%. My
> guess is that this is because there is a lot of nucleic acid and perhaps
> the density is being more localized (e.g. to the phosphate groups) than
> what is normal for proteins. I tried to force a lower solvent content, such
> as 90%, but that did not change the R-value. I will try with model-based
> density modification and see if that helps.
>
> Regards,
> Daniel
>
>
> On 8 Jun 2022, at 21:39, Tom Terwilliger <
> tterwilliger at newmexicoconsortium.org> wrote:
>
> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
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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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