[Chimera-users] ~select doesn't work on axes?

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 14 10:28:03 PDT 2015

Hi Oliver,
Originally command-line specifications only pertained to sets of atoms.  As we added more and more functionality, other types of objects (nonmolecular surfaces, etc.) were shoe-horned into working with certain commands, but these are more the exception than the rule.  For example, distance and angle commands can take axis/plane/centroid identifiers, but most other commands do not…

However, I think what you want can be done:

(A) It is slightly distasteful (inelegant), but you can clear the selection, including any selected axes/planes/centroids, by using a specification that doesn’t specify anything.  For example, if there aren’t any residues named XYZ, you could use the command:

sel :xyz

(B) You can hide axes/planes/centroids that are selected with command:

~modeldisp sel

If you also had atoms selected, however, this will also undisplay the whole atomic model.  You can re-show the objects with “modeldisp sel” or all models with just “modeldisp” … this command works on whole models, even the nonatomic ones.  It doesn’t know about object identifiers (a1, p1, etc.) so you can only use it with “sel” to indicate specific axes/planes/centroids.

I hope this helps,
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 14, 2015, at 10:03 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> The command "~sel” does not unselect selected axes/planes/centroids - is this intended, and/or is there another way to unselect these objects from the command line? 
> Also, is there a command to undisplay selected axes/planes/centroids? I can only figure out how to do so from the GUI but I would like to do this from the command line, as when you have many axes defined and only want to hide a few it would be easier to have an equivalent of “~disp sel” rather than hunting for the specific axes in the Axes/Planes/Centroids list.
> Cheers,
> Oliver.

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