[Chimera-users] [chimera-dev] Chimera orbitals alias question

Tom Goddard goddard at sonic.net
Tue Oct 16 15:26:55 PDT 2018

Hi Benjamin,

  When you open a Gaussian cube file with multiple orbitals in Chimera it assigns them to be model numbers #0.1, #0.2, #0.3, ….  You can see these numbers in the Volume Viewer menu Data.  You can also see them in Model Panel (menu Favorites / Model Panel) — they will be grouped because they were read from one file so press the Group / Ungroup button on Model Panel to see them all.  Also all orbitals are shown at once initially — not too useful.  To hide them all (#0 refers to all #0.x models):

	volume #0 hide

To show the first orbital

	volume #0.1 show

To set the displayed surface level of the first orbital but not the others

	volume #0.1 level 0.001

To set the levels for the first 5 oribitals

	volume #0.1-5 level 0.002


> On Oct 16, 2018, at 10:38 AM, Elaine Meng wrote:
>> On Oct 13, 2018, at 2:34 PM, Benjamin Looker  wrote:
>> Hello!
>> My name is Benjamin Looker, I am a chemistry graduate student at Cornell University, and our group often uses Chimera to visualize the orbitals output from the DFT software ORCA. 
>> When these .cube files are opened in Chimera, the two phases of the wavefunction surface are given different colors and bars in the volume viewer. 
>> My question is, when using an alias command, how would one set the level and color of only one of these phases, ie: to perform actions on only one of the bars and colors, instead of homogenizing the whole function?
>> An alias such as:
>> alias ^orbitals volume all level 0.05 color #2d2d00000b0b style surface
>> Is great, but that pesky "all" undermines the point of the operation. I have tried referencing model numbers, such as #0, #1, and #2 instead of "all," but Chimera returns an error. I do not know the label of the object that I am trying to affect. 
>> Any help would be greatly appreciated!
>> Best, 
>> -- 
>> Benjamin G. Looker
>> Graduate Student 
>> Lancaster Group
> Hi Benjamin,
> I don't have an example cube file to test with, but from your description I'm guessing it has signed data and that is why Chimera automatically shows two isosurfaces when you open a single file.  The levels are the same magnitude, just the opposite signs.  How the initial display values are set is described in the “surface and mesh display” section of the Volume Viewer documentation:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
> "For unsigned data types, an initial threshold is set so that 1% of voxels (1% of the volume encompassed by the data region) lie above it; for signed data types, positive and negative thresholds are placed symmetrically about zero."
> In that case, there is no way to specify in the command line changing only one isosurface and not the other.  You can see in the Model Panel (open from Favorites) that the entire dataset is listed as one model.
> Although you could open the data twice and use your volume command on only one copy (specified by the model number as shown in the Model Panel) that would still leave both the isosurfaces on the other copy as initially shown.
> However, there is nothing magical about the initial display setting other than it is meant to be easily viewable.  There is no knowledge used about the type of data (i.e. it doesn’t care or know that orbitals are what you’re showing) so you may want to go ahead and set all the isosurfaces using your values rather than relying on initial display.  You can specify level and color multiple times in the volume command for multiple isosurfaces, e.g.
> volume #0 style mesh level 0.8 color red level 1.2 color 0,.5,.8
> This is one of the examples in the “volume” command manpage
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> P.S. for future reference, the chimera-dev list is mainly for programming questions.  General usage questions are better sent to chimera-users at cgl.ucsf.edu CC’d here
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