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Here is a Python script to place a marker at the center of mass of a
map at points above the displayed contour level. You open your map
and then open the script (menu File / Open) to create the marker.
For marking more than one map, just highlight the map in the volume
dialog by clicking on its histogram or name and open the script.
The grid index of the center point will be reported in the reply log
(menu Favorites / Reply Log).<br>
<br>
I will make the Chimera "measure" command do this calculation and
marker placement in the future. This is a busy month so it will be
some time before I get to that.<br>
<br>
I've attached the script and also put it on the Chimera Python
scripts web page:<br>
<br>
<a class="moz-txt-link-freetext" href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a><br>
<br>
Tom<br>
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There isn't any Chimera command to identify the center of mass or
a density map or place a marker/atom there. But that seems
useful. A Python script can easily do it. I'll see if I can give
you a Python script at the end of today, or maybe add an operation
to the Chimera "measure" command to do this job.<br>
<br>
Tom<br>
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<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I got a volume map that I segmented in 4
parts. Now I wanted to measure how the parts are coordinated
to each other. As the Axes/Planes/Centroids menu can only
create planes by atoms I wanted to place atoms in the mass-
center of each segment. Is there any way to realize that?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Or do you have any other way to measure
the angles. To explain what I’m trying to measure: Example
you have 4 segments, I call them a b c d. I want to measure
how the axis that is formed by a and b, forms an angle to c
and d, or how ist he angle of the plane formed by a b and c
compared to ab and d . All for segments are basically the
same objects just turned and rotated.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">With best regards<o:p></o:p></p>
<p class="MsoNormal">C. Schmidt<o:p></o:p></p>
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