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Hi Ben.
<div class="">If CTF correction and reconstruction have been completed accurately, then the absolute density values should be linearly related to the potential, which most people refer to slightly incorrectly as the electron density. That is to say there is
an arbitrary linear transform applied to these values. Different packages use different conventions. In EMAN, for example, we typically normalize the data such that the mean solvent density is set to zero and the scaling is adjusted such that an isosurface
containing some specified volume corresponds to an isosurface threshold of 1.0. The zero solvent density simplifies solvent flattening and some other common tasks, but is really just a convenience. Other packages use completely different conventions.</div>
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<div class="">Bottom line is, no, you cannot trust that the numbers you find in the maps have any meaning in an absolute sense.<br class="">
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Steven Ludtke, Ph.D.</div>
<div style="margin: 0px; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Courier; " class="">
Professor, Dept of Biochemistry and Mol. Biol. (<a href="http://www.bcm.edu/biochem" class="">www.bcm.edu/biochem</a>)</div>
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Co-Director National Center For Macromolecular Imaging <span class="Apple-converted-space"> </span>(<a href="http://ncmi.bcm.edu" class="">ncmi.bcm.edu</a>)</div>
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Co-Director CIBR Center <span class="Apple-converted-space"> </span>(<a href="http://www.bcm.edu/research/cibr" class="">www.bcm.edu/research/cibr</a>)</div>
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Baylor College of Medicine<span class="Apple-converted-space"> </span> <span class="Apple-converted-space"> </span></div>
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<a href="mailto:sludtke@bcm.edu" class="">sludtke@bcm.edu</a></div>
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<div class="">On Jul 21, 2015, at 8:13 PM, Benjamin Barad <<a href="mailto:ben.barad@ucsf.edu" class="">ben.barad@ucsf.edu</a>> wrote:</div>
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<div class="">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>
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<div class="">Even if they are not physically meaningful, why is there such a dramatic range in scaling? </div>
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<div class="">For some examples, the map parameters for EMDB 5623 are as follows:</div>
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<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>
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<div class="">By comparison, the map parameters for EMDB 2278 are:</div>
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<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>
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<div class="">And the map parameters for EMDB 6324 are:</div>
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<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>
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<div class="">Thanks,</div>
<div class="">Ben Barad</div>
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