[Chimera-users] [chimera-dev] Auto set threshold boundaries and colors

[Benjamin Looker]

Elaine,

Thank you so much for responding, the ability to create that alias in the
program will be very useful, thanks!

Best,

Ben Looker

On Mon, Sep 24, 2018 at 1:10 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Benjamin,
> This only refers to intiial display.  You can of course change the
> threshold (isosurface level) to whatever is appropriate for the specific
> data, by dragging the vertical bar in the Volume Viewer histogram or by
> using the “volume” command.
>
> It is not a preference, but you could create an alias that would be listed
> in the menu so that you could reapply it easily.  For example, command:
>
> alias ^orbitals volume all level 0.05 color pink style surface
>
> … or there could be multiple levels and colors specified in the same
> command.  Then your alias “orbitals” (or whatever you named it) would be
> listed in a top-level Aliases menu for easy reapplication to later
> datasets. I.e., choosing menu: Aliases… orbitals or typing the command
> “orbitals” would run it.  Aliases are saved in the preferences:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
>
> The volume command has many options:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>
>
> The 1% initial  display (rather than a specific threshold value) was most
> useful for the wide variety of volume data where people often do not know
> what threshold will be best for viewing.  It is surely adjustable by
> changing the code but others would have to advise on that matter.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Sep 23, 2018, at 10:18 AM, Benjamin Looker <bgl44 at cornell.edu> wrote:
> >
> > Hello!
> >
> > My name is Benjamin Looker, and I have recently become acquainted with
> your software for visualization of molecular orbital calculations that my
> group does with some regularity. I was wondering whether the statement on
> this page refers to a specific preferences file in the Chimera program
> files.  :
> >
> > (
> http://www.rbvi.ucsf.edu/chimera/1.8/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html)
>
> >
> > "For unsigned data types, an initial threshold is set so that 1% of
> voxels"
> >
> > The reason I ask is because it would be much simpler, given a known
> color code and level, to standardize the import of files into Chimera for
> any sort of publication, especially in the event that many molecular
> orbitals needed to be visualized at once for a project.
> >
> > Best,
> >
> > --
> > Benjamin G. Looker
> > Graduate Student
> > Lancaster Group
>
>

-- 
Benjamin G. Looker
Graduate Student
Lancaster Group
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