[Chimera-users] volume viewer - planes

Tom Goddard goddard at sonic.net
Tue Aug 23 10:50:40 PDT 2016

Hi Michael,

  It would be nice if moving the slider updated the shown plane for all the volumes.  I couldn’t think of a trick to do that.  But here is a Python script syncregion.py that does it.  You open this file in Chimera when you have your volumes open and whenever the active one (one highlighted in volume viewer dialog) changes its displayed region, the other are updated to use the same region.


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> On Aug 23, 2016, at 10:42 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Michael,
> You will still be able to move them with the slider, but the problem is that the slider is only connected to one data set at a time.  So you’d have to click on one histogram to make that set “active” and connected to the slider, then click the other histogram to connect the other set to the slider instead.
> Elaine
>> On Aug 23, 2016, at 10:32 AM, Michael Elbaum <michael.elbaum at weizmann.ac.il> wrote:
>> Thanks. It helps a lot! Normally indices are the same. Will it still be possible to move them with the slider? I use mostly the nice gui interface, as you can tell...
>> Michael
>>> On 23 באוג׳ 2016, at 20:12, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 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
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes>
>>> 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
>>> ----------
>>> 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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