<div dir="ltr">Hi Pavel,<div><br><div>This R-value is quite different from a refinement R. Basically the statistical or maximum-likelihood density modification procedure allows calculation of each structure factor based on the values of all the other structure factors and the expectations about the map (i.e, flat solvent, distribution of density values in protein, ncs, etc.) These "map-phasing" structure factors are (at least in the first cycle) independent of the starting structure factors and can be compared with the measured data and an R-value obtained. The values of these R-values range from about 0.25 to 0.5 in most cases, and when the map is very good usually the R values are smaller. These R values do not involve any atomic model so they are quite unlike a refinement R.</div><div><br></div><div>As noted by Daniel, there is not much (or maybe any) discussion of these density modification R-values in the literature (I just looked quickly and didn't find anything really discussing this) although they are used in Resolve and related ones are used in dm and perhaps other software (if anyone knows of a relevant discussion, please let me know!). The closest I found was using a free R related to the one calculated by resolve for optimization of parameters: <a href="https://atbweb.stanford.edu/atb_publications/roberts_brunger_1995.pdf">https://atbweb.stanford.edu/atb_publications/roberts_brunger_1995.pdf</a></div><div><br></div><div>For discussion of how map-likelihood structure factors are calculated in Resolve, see "Map-likelihood phasing": <a href="https://journals.iucr.org/d/issues/2001/12/00/gr2165/">https://journals.iucr.org/d/issues/2001/12/00/gr2165/</a></div><div><br>I hope that helps!</div><div>All the best,</div><div>Tom T</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jun 10, 2022 at 2:06 PM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi Tom and Daniel,</p>
<p>I'm confused about what R factor we are talking about here? You
say "This R value describes the mismatch between measured and
map-based structure factor amplitudes. ", then questions I'd ask
are:<br>
</p>
<p>- what program was used to calculate it?</p>
<p>- Was all scaling between model and data generated Fs done
properly? Not treating solvent region (or whatever that is in
cryo-em) alone can result in large R factors.<br>
</p>
<p>- Was model refined properly (coordinates and B factors).
Unrefined B factors even for perfectly fitting model (coordinates
wise) can result in high R factors.</p>
<p>- Why we calculate and try to interpret R factors at all given it
is cryo-EM case (no Fobs)?</p>
<p>Pavel<br>
</p>
<div>On 6/9/22 05:56, Tom Terwilliger wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">Hi Daniel,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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).</div>
<div><br>
</div>
<div>All the best,</div>
<div>Tom T</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Jun 8, 2022 at 11:04
PM Daniel Larsson <<a href="mailto:daniel.larsson@icm.uu.se" target="_blank">daniel.larsson@icm.uu.se</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
Hi Tom,
<div><br>
</div>
<div>Thank you so much for the feedback.</div>
<div><br>
</div>
<div>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...</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Daniel</div>
<div><br>
</div>
<div>
<div><br>
<blockquote type="cite">
<div>On 8 Jun 2022, at 21:39, Tom Terwilliger <<a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a>>
wrote:</div>
<br>
<div>
<div dir="auto">Hi Daniel,</div>
<div dir="auto"><br>
</div>
<div dir="auto">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.</div>
<div dir="auto"><br>
</div>
<div dir="auto">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. </div>
<div dir="auto"><br>
</div>
<div dir="auto">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.)</div>
<div dir="auto"><br>
</div>
<div dir="auto">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.</div>
<div dir="auto"><br>
</div>
<div dir="auto">I hope that helps!</div>
<div dir="auto">All the best,</div>
<div dir="auto">Tom T</div>
<div><br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Jun
8, 2022 at 14:25 Daniel Larsson <<a href="mailto:daniel.larsson@icm.uu.se" target="_blank">daniel.larsson@icm.uu.se</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi all,<br>
<br>
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.<br>
<br>
Regards,<br>
Daniel<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">Thomas C
Terwilliger
<div>Laboratory Fellow, Los
Alamos National Laboratory</div>
<div>Senior Scientist, New
Mexico Consortium</div>
<div>100 Entrada Dr, Los Alamos,
NM 87544</div>
<div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">
tterwilliger@newmexicoconsortium.org</a></div>
<div>Tel: 505-431-0010</div>
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<div>
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<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">Thomas C Terwilliger
<div>Laboratory Fellow, Los Alamos National
Laboratory</div>
<div>Senior Scientist, New Mexico Consortium</div>
<div>100 Entrada Dr, Los Alamos, NM 87544</div>
<div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></div>
<div>Tel: 505-431-0010</div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Thomas C Terwilliger<div>Laboratory Fellow, Los Alamos National Laboratory</div><div>Senior Scientist, New Mexico Consortium</div><div>100 Entrada Dr, Los Alamos, NM 87544</div><div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></div><div>Tel: 505-431-0010</div><div><br></div></div></div></div></div></div></div></div></div></div>