<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Mohan,<div class=""><br class=""></div><div class=""> What you suggest is not correct. I don't know if your map is from x-ray crystallography or electron microscopy but in both cases the map values are not literally "density" (ie mass per unit volume). The processing of the maps often introduces negative values, and often puts the most common map value (peak histogram) at zero or even a negative value. As Elaine, suggested you would need to ask someone expert in the processing of maps. Chimera only uses the numeric values in the map file, it knows nothing about how those values relate to physical properties. I have never seen an attempt to quantify mass density with x-ray or EM of biological samples. X-ray researchers instead usually look at a iso-contour 1 or 1.5 or 2 standard deviations above the mean map value.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Sep 8, 2015, at 1:52 AM, Mohan Pradhan wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><div style="background-color: rgb(255, 255, 255); font-family: 'bookman old style', 'new york', times, serif; font-size: 16px;" class=""><div id="yui_3_16_0_1_1441700760653_6921" class="">Dear Chimera users,</div><div id="yui_3_16_0_1_1441700760653_6921" class=""><br id="yui_3_16_0_1_1441700760653_7031" class=""></div><div id="yui_3_16_0_1_1441700760653_6921" class="">I am using the Volume Viewer application in Chimera to visualize the solvent density around protein at a threshold value of 2.5 times of the bulk solvent density.</div><div id="yui_3_16_0_1_1441700760653_6921" class=""><br id="yui_3_16_0_1_1441700760653_7035" class=""></div><div id="yui_3_16_0_1_1441700760653_6921" class="">My understanding is that the iso value corresponding to the bulk solvent density is marked by the peak in the plot of the volume viewer. I am then multiplying the iso value of the peak by 2.5</div><div id="yui_3_16_0_1_1441700760653_6921" class="">Is this the right way of identifying regions in protein that have a solvent density of 2.5 times of the bulk solvent density?</div><div id="yui_3_16_0_1_1441700760653_6921" class=""><br id="yui_3_16_0_1_1441700760653_7040" class=""></div><div id="yui_3_16_0_1_1441700760653_6921" class="">Kindly suggest.</div><div id="yui_3_16_0_1_1441700760653_6921" class=""><br id="yui_3_16_0_1_1441700760653_7044" class=""></div><div id="yui_3_16_0_1_1441700760653_6921" class="">Thanks,</div><div id="yui_3_16_0_1_1441700760653_6921" dir="ltr" class="">Mohan</div></div></div>_______________________________________________<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=""></div></blockquote></div><br class=""></div></body></html>