[Chimera-users] Using marker files to place oriented density maps inside a tomogram

Daniel Castano Diez daniel.castano at unibas.ch
Wed Nov 14 13:28:57 PST 2012

Hi Tom,

thanks for the answer. Actually I already wrote some scripts for  
placing each different copy of the density map as an individual model,  
but this is not practical for placing hundreds of copies (as it's the  
case with tomograms).  I will try your python script.

I was under the impression that a .cmm markerfile was a better  
approach, as I though that one could define a marker with more  
attributes as in the example:

<marker id="1" x="-6.1267" y="17.44" z="-3.1338"  radius="0.35217"/>

I mean, something like:

<marker id="1" x="-6.1267" y="17.44" z="-3.1338"  map ="my_map.em"   
matrix = "my_matrix.txt" />

or similar with quaternions or euler angles... but I guess that was  
wrong? That'll be a pitty,  as I am interfacing Chimera with the  
subtomogram averaging package Dynamo and the most stable way seemes to  
be having Dynamo converting its "table" files (lists of positions and  
angles) into .cmm files that could then be directly fed into Chimera.



> Hi Daniel,
>   Take a look at the placem.py script which can place copies of maps  
> or molecules at specified positions.
>     http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts
> It specifies the rotation as a quaternion which is close to a  
> rotation axis and angle description.  I could show you how to adapt  
> it to use Euler angles or a 3x3 rotation matrix if you like.
>     Tom
>> Hi,
>> I'd like to use a Chimera marker file to place multiple copies of a  
>> density map in different spatial positions inside a tomogram. My  
>> input is thus a single map file a set of 3d locations, each  
>> attached to an euler triplet (or a rotation matrix)
>> With the documentation I could find
>> http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html it is explained how to place spheres without orientation in a volume, but I was not able to figure out how to place a density map at those locations, and also how to impart a different orientation to the density map located at each  
>> position.
>> My question is: where could I find a description of the marker file  
>> syntax that describes this functionality?
>> thanks,
>> Daniel
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