<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Would be nice to include B-factors in the molmap calculation of a density map from an atomic model. Currently adds a Gaussian for each atom and all Gaussians have the same width (standard deviation) computed from the specified resolution and sigmaFactor as described in the documentation.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</a></div><div class=""><br class=""></div><div class="">I’ve made a Chimera feature request for this — more likely to go into Chimera 2 than Chimera 1.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://plato.cgl.ucsf.edu/trac/chimera/ticket/14258" class="">https://plato.cgl.ucsf.edu/trac/chimera/ticket/14258</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 29, 2015, at 8:58 AM, Oliver Clarke <<a href="mailto:olibclarke@gmail.com" class="">olibclarke@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">Hi all,<br class=""><br class="">For the purposes of model validation, I’d like to analyze local correlation of my model with the experimental map (and color it on either/both the model or map). I figured the easiest way to do this is to use molmap to generate a synthetic map, then use vop local correlation to generate a correlation map which I can use to color either the model or map (using scolor or “Values at Atom Positions”). <br class=""><br class="">This works fine, and generates informative looking pictures, I just wanted to clarify exactly what molmap is doing, to make sure I understand it. <br class=""><br class="">Am I correct in thinking molmap does not use a per-atom temperature factor (or alter the width of the gaussian depending on the atomic B-factor)? <br class=""><br class="">Because if this is the case I guess the way I am doing things will exaggerate how bad the model is in regions where the B-factor is high and the density weak (which is not the worst thing in the world - better than having an unrealistically rosy view of one’s model!). <br class=""><br class="">Would it be possible to incorporate atomic B-factors into molmap calculations for Chimera 2? Or does anyone know of an external program that will perform a similar calculation (I know I can generate RSCC plots in Phenix which must be doing this internally, but I rather like displaying it on the model and map for ease of interpretation).<br class=""><br class="">Cheers,<br class="">Oliver.<br class="">_______________________________________________<br class="">Chimera-users mailing list<br class=""><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br class=""><br class=""></div></blockquote></div><br class=""></div></div></body></html>