<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">daniel.larsson@icm.uu.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<br>
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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>
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Regards,<br>
Daniel<br>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="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>