<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Hi Ben, </div><div><br></div><div>EMDB map density values are generally passed without modification from the depositor's uploaded map (a rare exception is when values need to be inverted to make map object density positive). The variation you observe reflects the wide diversity of tools used by the 3DEM community.</div><div><br></div><div>The situation is similar to X-ray crystallography several decades ago, before the normalizing maps to statistical parameters became common practice.</div><div><br></div><div>HTH,</div><div><br></div><div>Cathy Lawson</div><div><br><br><br></div><div><br>On Jul 21, 2015, at 21:13, Benjamin Barad <<a href="mailto:ben.barad@ucsf.edu">ben.barad@ucsf.edu</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr">Hi everyone,<div><br></div><div>I wonder whether someone could comment on why the numeric voxel values of maps in the EMDB (or elsewhere) have such large differences in their range. Do the absolute values have physical meaning, and if so how should I interpret the vast ranges in scale? What units should be ascribed to them?</div><div><br></div><div>Even if they are not physically meaningful, why is there such a dramatic range in scaling? </div><div><br></div><div>For some examples, the map parameters for EMDB 5623 are as follows:</div><div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Minimum density:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">-0.555</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Maximum density:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">1.20</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Average density:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">-0.008</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Standard deviation:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">0.049</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Recommended contour level:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">0.25 (author)</span></div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>By comparison, the map parameters for EMDB 2278 are:</div><div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Minimum density:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">-9.453</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Maximum density:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">15.384</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Average density:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">0.048</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Standard deviation:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">1.252</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Recommended contour level:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">1.35 (emdb)</span></div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>And the map parameters for EMDB 6324 are:</div><div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Minimum density:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">-0.092</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Maximum density:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">0.139</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Average density:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">0.001</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Standard deviation:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">0.005</span></div><div class="" style="display:inline;float:left;margin-left:0px;margin-right:0px;width:637.28125px;font-family:Verdana,sans-serif;font-size:13px;line-height:19.9939994812012px;background-color:rgb(237,237,237)"><span class="" style="font-weight:bold;display:inline;float:left;margin-left:0px;margin-right:6.359375px;width:259.15625px">Recommended contour level:</span><span class="" style="display:inline;float:left;margin-left:6.359375px;margin-right:6.359375px;width:358.984375px">0.016 (emdb)</span></div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>Thanks,</div><div>Ben Barad</div><div><br></div></div>
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