[Chimera-users] Creating a Volume Viewer Preset

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 15 08:57:19 PDT 2020

Hi Michael,
Presets are not automatically applied when you open something.  Instead you have to apply them explicitly using the Presets menu or the "preset" command. 

First figure out what command(s) do what you want, then put them in a file to make a custom preset as explained here, using the Presets category of the Preferences:

Alternatively (but equivalently), you can make an alias command to execute the command(s).  Again you have to use that new command or the Aliases menu to actually run it after opening new volume data.

The command to do what you want might be something like this:

volume all style surface level 0.5 color blue level -0.5 color red

To make an alias, something like command:

alias ^mysurf volume all style surface level 0.5 color blue level -0.5 color red

Then you can enter command "mysurf" later to do it, or choose menu Aliases... mysurf

If you wanted that display automatically when you open a signed map, you would have to change the python code of the program; somebody else would have to advise on that.

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

> On Jul 15, 2020, at 8:01 AM, MICHAEL M ARISTOV <aristov at wisc.edu> wrote:
> Hello All,
> I’m hoping to get some inset in setting up a preset for New Surface.
> Ideally, I’d Like it to do the following:
> Firstly, I’d like to open the surface with a predefined Level -0.05 -> 0.05 (regardless of range) (The value set in volume viewer)
> Secondly, I’d like to set the color of the surface to Red for Negative and Blue for Positive
> Lastly, I’d like any additional surfaces opened in the same session to have the above parameters as well.
> If anyone could provide me some tips to make the above settings default, I would greatly appreciate it!
> Thank you for your time and insight.
> -Mike Aristov

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