[Chimera-users] Calculating and showing the Mass center of Volume Segments
goddard at sonic.net
Fri Nov 18 12:40:58 PST 2011
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
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
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
> 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.
>> 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
>> *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:
>> 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.
>> 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 <mailto:Chimera-users at cgl.ucsf.edu>
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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