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Hi Claudius,<br>
<br>
I added the "measure center" command to Chimera which will be in
tonight's daily builds. For example,<br>
<br>
measure center #0 mark true<br>
<br>
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<br>
<br>
me cen #0,1 level 0.15 mark true radius 10 color red model 2<br>
<br>
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.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] Calculating and showing the Mass center
of Volume Segments<br>
From: Tom Goddard <br>
To: Schmidt, Claudius<br>
Date: 11/15/11 10:22 AM<br>
<blockquote cite="mid:4EC2ADF1.6030603@sonic.net" type="cite">
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Hi Claudius,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Tom<br>
<br>
<br>
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<p class="MsoNormal"><span style="color:#1F497D">Hello Tom,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">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. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">With best
regards<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Claudius <o:p></o:p></span></p>
<p class="MsoNormal"><a moz-do-not-send="true"
name="_MailEndCompose"><span style="color:#1F497D"><o:p> </o:p></span></a></p>
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<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext;mso-fareast-language:DE">Von:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext;mso-fareast-language:DE">
Tom Goddard <br>
<b>Gesendet:</b> Dienstag, 15. November 2011 02:36<br>
<b>An:</b> Schmidt, Claudius<br>
<b>Cc:</b> '<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>'<br>
<b>Betreff:</b> Re: [Chimera-users] Calculating and
showing the Mass center of Volume Segments<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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 moz-do-not-send="true"
href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a><br>
<br>
Tom<br>
<br>
<br>
<br>
<o:p></o:p></p>
<p class="MsoNormal">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>
<br>
<br>
<o:p></o:p></p>
<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>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
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<br>
<o:p></o:p></span></p>
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<br>
<br>
<br>
<o:p></o:p></span></p>
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