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

Oliver Clarke olibclarke at gmail.com
Fri Aug 14 11:14:11 PDT 2015

Thanks Elaine, tricky! And very helpful, thank you - one of my aliases was breaking when I ran it with axes or planes selected, this fixed it.

So I now have the following aliases for hiding/showing selected axes (unselects everything that is not an axis first, then hides/shows using modeldisp):

#hide selected axes
#Usage: hide_axis
alias ^hide_axis ~sel; ~modeldisp sel

#show selected axes
#Usage: show_axis
alias ^show_axis ~sel; modeldisp sel

> On Aug 14, 2015, at 1:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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
> -----
> 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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