Re: [Chimera-users] [chimera-dev] Auto set threshold boundaries and colors
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@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/f...)
"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
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@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@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/f...)
"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
participants (2)
-
Benjamin Looker -
Elaine Meng