# [Chimera-users] Calculating and showing the Mass center of Volume Segments

Tom Goddard goddard at sonic.net
Mon Nov 14 17:35:40 PST 2011

```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 /

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.

I've attached the script and also put it on the Chimera Python scripts
web page:

http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts

Tom

> 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.
>
>     Tom
>
>> Hello,
>>
>> 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?
>>
>> 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.
>>
>> With best regards
>>
>> C. Schmidt
>>
>>
>>
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20111114/f3513712/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: volumecenter.py
Type: text/x-python-script
Size: 1094 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20111114/f3513712/attachment.bin>
```