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

Tom Goddard goddard at sonic.net
Fri Nov 18 12:40:58 PST 2011

Hi Claudius,

   I added the "measure center" command to Chimera which will be in 
tonight's daily builds.  For example,

     measure center #0 mark true

will place a marker at the center of map #0 and report the grid index of 
the center position on the status line and in the reply log.  Here's a 
fancier example

     me cen #0,1 level 0.15 mark true radius 10 color red model 2

that places markers at the centers of maps #0 and #1 above contour level 
0.15 with marker radius 10 Angstroms and color red, and both markers 
will be in the marker model with id number 2.


-------- Original Message --------
Subject: Re: [Chimera-users] Calculating and showing the Mass center of 
Volume Segments
From: Tom Goddard
To: Schmidt, Claudius
Date: 11/15/11 10:22 AM
> Hi Claudius,
>   My previous script to place a marker and the volume center of mass 
> had a bug as you noticed.  It placed the marker in the global 
> coordinate system but calculated it in the volume coordinate system.  
> These are different if you move or rotate the view before using the 
> script.
>   Here's the fixed volumecenter.py script.  I changed a few lines at 
> the end.  It now makes a new model for each center marker you create 
> and the coordinates are correct.  You still need to choose the volume 
> data set in the volume dialog before running the script.
>     Tom
>> Hello Tom,
>> I'm very sorry to bother you again, but the Script only works fine if 
>> I only load one map. As soon as I got another MRC loaded, it sets the 
>> marker on absurd positions no matter what I selected in volume viewer 
>> or anywhere else.
>> With best regards
>> Claudius
>> *Von:*Tom Goddard
>> *Gesendet:* Dienstag, 15. November 2011 02:36
>> *An:* Schmidt, Claudius
>> *Cc:* 'chimera-users at cgl.ucsf.edu'
>> *Betreff:* Re: [Chimera-users] Calculating and showing the Mass 
>> center of Volume Segments
>> 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).
>> 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
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