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

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jan 29 11:27:16 PST 2007

Hi Jeff,

   I understand your problem.  I think you can handle the large data 
sets interactively using the "precomputed subsample" feature of the 
volume dialog.  As you mentioned you need to create smaller binned 
versions of your data.  Then you open your full size map in Chimera but 
do not display it.  Then you use Features / Precomputed Subsamples and 
add the binned file (ie. subsampled data).  Then when you display the 
data with step sizes larger than 1 where it can use the binned data it 
will use the binned data.  In this way Chimera never needs to open the 
full data if you only display at binned step sizes.  You can then use 
the zone or subregion box tools to specify a smaller piece of the map 
and then use the volume dialog "File / Save map as" menu entry.  That 
always says at full resolution, so the needed part of the full size map 
will be read when you do that.  There is a Chimera script for creating 
the binned data (chimera/share/VolumeProcessing/downsize.py) described 
in the Volume Viewer documentation in the Chimera User's Guide:


   Another useful tool for handling tomograms that are too large to 
display in Chimera at full resolution is the Volume Planes module that 
can be downloaded from the Chimera experimental features page


When you display just one plane at a time, Chimera only loads that plane 
from the map file (for most map file formats, e.g. MRC).  This can allow 
you to flip through the planes at full resolution while having just a 
limited amount of data in memory at any one time.


Date: Jan 29, 2007

hi Tom,

is it possible for me to use a (previously generated) chimera marker 
file to zone and save a region from a volume map from a python prompt, 
without launching chimera?

A lot of volumes I use are simply too big to handle in chimera, and if I 
chop up large volumes, I might have filaments running across the borders 
that I cut, etc. When I have done such 'chopping out' of subvolumes, it 
is often difficult for me to figure out which filaments I care about (or 
where they are ...) a priori. One solution I was thinking of is to use a 
several-times binned file to generate a marker file using chimera, and 
then to use the zone tool from a python prompt on the unbinned volume, 
without having to launch chimera and try to actually visualize the full, 
unsegmented volume.

can I do this? (or, does this question make sense?)



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