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. Thanks! Daniel
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/volumepathtr... 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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