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

Tom Goddard goddard at sonic.net
Wed Nov 14 10:17:29 PST 2012

Hi Daniel,

   Take a look at the placem.py script which can place copies of maps or 
molecules at specified positions.


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.


> 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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