[Chimera-users] using a marker file to zone a volume from python prompt

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jan 29 19:32:48 PST 2007

Hi Jeff,

   I've attached a script that opens a density map and a Chimera marker 
file and writes a new volume corresponding to a zone around the markers. 
  It does not require showing the Chimera user interface to do this. 
Perhaps you don't need this now (I just got your follow-up email.) but 
perhaps you will find it useful in writing other scripts.

   Karin Gross at Max Planck Institute of Biochemistry has written a 
Chimera extension to slice tomograms at arbitrary angles.  I saw it when 
I visited Munich in December.  They also were planning on allowing 
marker placement on those planes.

   The volume planes tool could be made to average neighboring planes. 
Currently it simply displays a NxMx1 subvolume in solid rendering mode. 
  Since there is no existing code in Chimera to support averaging 
adjacent planes that would have to be added.  Probably the easiest 
solution is to add the adjacent planes in Python and create a new single 
plane volume on the fly.


Jeff wrote:
> thanks Tom,
> I will try that. alongside that, is there a way for me to run a 'zone' 
> function and save a subregion from a python command line (no chimera 
> launched, just import a library?)?
> I have used the volume planes tool to generate a marker set of a 
> membrane, it was handy. But, it only handles orthogonal directions, it 
> can't provide an arbitrary interpolant (which is a large reason I rely 
> heavily on IMOD's slicer tool); this functionality would be very useful. 
> A second addition to the volume planes tool would simply be allowing 
> averaging several slices together (reduces noise) in the direction 
> normal to the planes, which may already be there (the documentation 
> online said something about this feature, but it wasn't clear to me)
> it the volume planes tool were able to handle an arbitrary 
> view/interpolant, then I wouldn't have to depend on the slicer tool, and 
> the previous request about rotating markers that was related to that 
> requirement (different features available in different slicer 
> orientations in IMOD, necessitating a rotation prior to visualization 
> with the volume planes tool in chimera, thus requiring old marker set 
> from original volume to be rotated to be used in new volume, etc) would 
> effectively be voided
> -Jeff
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