"mc" accelerator equivalent

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-05)
Description
Would it be possible to add an equivalent to the "mc" accelerator in Chimera, which places a dummy atom at the center of rotation and selects it? This is very useful for making simple scripts - e.g. to make a zone around the center of rotation in an alias. I couldn't find it in the "Markers and Links" section of the docs, apologies if I missed it.

Cheers
Oli

Log:
> camera ortho

> cofr centerOfView

> alias crosshairs_on cofr centerofview showpivot 10,0.3

> alias crosshairs_off cofr centerofview showpivot false

UCSF ChimeraX version: 0.9 (2019-06-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/oliverclarke/apocam_masks/tmp_post.mrc

Opened tmp_post.mrc, grid size 512,512,512, pixel 1.06, shown at level 0.0113,
step 2, values float32  

Unknown command: measure cofr mark true  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

This feature should be part of "marker" command. That command does not exist yet. The marker command will do other things that marker mouse mode enables and will be a way of logging what the mouse mode did. Developing this command is not currently a priority.

There is a "measure center" ChimeraX command that can place a marker at the center of mass of a density map or atomic model. That sounds more appropriate for the use you describe and perhaps solves your problem.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#center

[olibclarke@…]

Fair enough - I looked at measure center, but  it doesn’t place an atom at the center of rotation, just the center of a selection, and doesn’t select the resulting atom, which was the usefulness of the “mc” accelerator - it gives an easy way to select and manipulate an atom at the center of rotation within an alias.

Cheers
Oli

[olibclarke@…]

Hi Tom,

The marker command now exists, but does not have an option to place a marker at the center of rotation as far as I can tell (except by explicitly specifying the x,y,z coords of the CofR) - would it be possible to add this at some point?

Cheers
Oli

[pett]

The "position" arg to the marker command takes a "point-spec". One of the legal values for "point-spec" is "cofr".

[Tom Goddard]

As Eric points out in the previous comment, to make a marker at the center of rotation use

marker #3 position cofr

The model #3 need is a current marker model or if there is no #3 it creates a marker model.

[Tom Goddard]

Most commands that take an argument that is a 3D position will accept "cofr" as described in the documentation here

​https://www.cgl.ucsf.edu/chimerax/docs/user/commands/pointspec.html#point

[olibclarke@…]

Ah apologies, I did read the docs for \u201cmarker\u201d but couldn\u2019t find mention of the center of rotation or \u201ccofr\u201d, clearly I should have read more carefully, sorry!

Cheers
Oli

[Tom Goddard]

The marker command "position cofr" option does this.

[pett]

Yeah, you have to click on the "point-spec" link in the marker help page to see what the possibilities are.