<html><body><div style="color:#000; background-color:#fff; font-family:bookman old style, new york, times, serif;font-size:16px"><div id="yui_3_16_0_1_1441901665262_3420" dir="ltr"><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3466" class="">Dear Tom and Elaine,</span><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3468" class=""><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3470" class=""> Thank you both for your response. I think I was not very clear with my question. Let me rephrase my query here again in more detail.</span><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3472" class=""><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3474" class=""><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3476" class="">I have done Molcular Dynamics simulation of my protein in explicit solvent. Following which I calculated the water density from the trajectory using grid-based approach with grid cells of size 0.5 X 0.5 X 0.5 Å. A sample of the grid-based density output file is attached here for your reference.</span><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3478" class=""><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3480" class=""><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3482" class="">We then used Chimera to visualize the map using the volume viewer menu. We are attaching two image files here at two different isocountor threshold cutoff. One which was set to the isovalue at which we observe the maximum value of the historgram at an isovalue of 37. (image-1)</span><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3484" class=""><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3486" class=""><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3488" class="">Second we set it to 2.5 times that isovalue 2.5 X 37 ~ 93) (Image-2).</span><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3490" class=""><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3492" class=""><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3494" class="">The issue we wanted to clarify was what do these histogram actually depict with regard to the input grid file?</span><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3496" class=""><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3498" class=""><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3500" class="">What is the histogram depicting at an iso-value of zero?</span><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3502" class=""><br style="padding: 0px; margin: 0px; color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3504" class=""><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" id="yui_3_16_0_1_1441901665262_3506" class="">Why is there a sinusodial curve for the histogram towards the lower isovlaue?</span><span></span></div><div id="yui_3_16_0_1_1441901665262_3420" dir="ltr"><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" class=""><br></span></div><div id="yui_3_16_0_1_1441901665262_3420" dir="ltr"><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" class="">Thanks,</span></div><div id="yui_3_16_0_1_1441901665262_3420" dir="ltr"><span style="color: rgb(51, 51, 51); font-family: Menlo, Consolas, 'Lucida Console', 'DejaVu Sans Mono', monospace; font-size: 12px;" class="">Mohan</span></div> <br><div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: bookman old style, new york, times, serif; font-size: 16px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"> <font size="2" face="Arial"> On Wednesday, September 9, 2015 4:07 AM, Tom Goddard <goddard@sonic.net> wrote:<br> </font> </div> <br><br> <div class="y_msg_container"><div id="yiv3245520120"><div>Hi Mohan,<div class="yiv3245520120"><br clear="none" class="yiv3245520120"></div><div class="yiv3245520120"> 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="yiv3245520120"><br clear="none" class="yiv3245520120"></div><div class="yiv3245520120"><span class="yiv3245520120Apple-tab-span" style="white-space:pre;"> </span>Tom</div><div class="yiv3245520120"><br clear="none" class="yiv3245520120"><div><blockquote class="yiv3245520120" type="cite"><div class="yiv3245520120yqt3988349418" id="yiv3245520120yqt04698"><div class="yiv3245520120">On Sep 8, 2015, at 1:52 AM, Mohan Pradhan wrote:</div><br clear="none" class="yiv3245520120Apple-interchange-newline"><div class="yiv3245520120"><div class="yiv3245520120"><div class="yiv3245520120" style="background-color:rgb(255, 255, 255);font-family:'bookman old style', 'new york', times, serif;font-size:16px;"><div class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_6921">Dear Chimera users,</div><div class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_6921"><br clear="none" class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_7031"></div><div class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_6921">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 class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_6921"><br clear="none" class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_7035"></div><div class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_6921">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 class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_6921">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 class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_6921"><br clear="none" class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_7040"></div><div class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_6921">Kindly suggest.</div><div class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_6921"><br clear="none" class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_7044"></div><div class="yiv3245520120" id="yiv3245520120yui_3_16_0_1_1441700760653_6921">Thanks,</div><div class="yiv3245520120" dir="ltr" id="yiv3245520120yui_3_16_0_1_1441700760653_6921">Mohan</div></div></div>_______________________________________________<br clear="none" class="yiv3245520120">Chimera-users mailing list<br clear="none" class="yiv3245520120"><a rel="nofollow" shape="rect" class="yiv3245520120" ymailto="mailto:Chimera-users@cgl.ucsf.edu" target="_blank" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br clear="none" class="yiv3245520120">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br clear="none" class="yiv3245520120"></div></div></blockquote></div><br clear="none" class="yiv3245520120"></div></div></div><br><br></div> </div> </div> </div></div></body></html>