[Chimera-users] volume viewer - planes

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 23 10:12:54 PDT 2016

Hi Michael,
You can do it with the “volume” command, using “all” to specify all volume models.  For example, to show as transparent solids and only the 20th Z plane:

volume all style solid
volume all planes z,20


There are additional options to “planes” for synchronized playback, and if it’s only specific models that you want (not “all”) you can specify a range or comma-separated list of model numbers instead of “all”.  I guess the drawback is that the indices would have to be the same for the different datasets.

If indices were different, you can still synchronize display by concatenating multiple commands together with semicolons, e.g. something like:

volume #2 planes z,18,28; volume #3 planes z,20,30

I  hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 23, 2016, at 9:17 AM, Michael Elbaum <michael.elbaum at weizmann.ac.il> wrote:
> Hi.    I'm using the volume viewer and the Planes function is extremely useful in order to see a subsection of the volume. Often I want to compare different processing or filtering of the same dataset. When I load several datasets, all the visualization parameters are set individually. Normally this is good, for example in setting different colors, but for Planes it's problematic. In order to switch among the various representations and see the same section of the volume I have to scan them individually, and when two are visible I can move only one. Is there a way to link the Planes among the maps? Perhaps there's a command line trick?
> thanks,
> Michael

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