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Hi Tom,
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<div class="">Thank you so much for the feedback.</div>
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<div class="">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>
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<div class="">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>
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<div class="">Regards,</div>
<div class="">Daniel</div>
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<div class="">On 8 Jun 2022, at 21:39, Tom Terwilliger <<a href="mailto:tterwilliger@newmexicoconsortium.org" class="">tterwilliger@newmexicoconsortium.org</a>> wrote:</div>
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<div dir="auto" class="">Hi Daniel,</div>
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<div dir="auto" class="">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>
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<div dir="auto" class="">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>
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<div dir="auto" class="">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>
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<div dir="auto" class="">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>
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<div dir="auto" class="">I hope that helps!</div>
<div dir="auto" class="">All the best,</div>
<div dir="auto" class="">Tom T</div>
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<div dir="ltr" class="gmail_attr">On Wed, Jun 8, 2022 at 14:25 Daniel Larsson <<a href="mailto:daniel.larsson@icm.uu.se" class="">daniel.larsson@icm.uu.se</a>> wrote:<br class="">
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Hi all,<br class="">
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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 class="">
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Regards,<br class="">
Daniel<br class="">
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<div dir="ltr" class="">Thomas C Terwilliger
<div class="">Laboratory Fellow, Los Alamos National Laboratory</div>
<div class="">Senior Scientist, New Mexico Consortium</div>
<div class="">100 Entrada Dr, Los Alamos, NM 87544</div>
<div class="">Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank" class="">
tterwilliger@newmexicoconsortium.org</a></div>
<div class="">Tel: 505-431-0010</div>
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