Hi Alexis, The "name" option of "define" gives the model name as shown in the Model Panel (not a named selection), as described here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#options> E.g. if you open PDB 2gbp the model name is 2gbp but you can't use that in commands. You can use the separate "name" command to create a named selection that can be used in the command line: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Best, Elaine
On Nov 17, 2023, at 8:31 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks Elaine,
Indeed, the workaround works fine: I can use "defined axis #4" and "define axis #5" and then "angle #4.1 #5.1".
What I find confusing is that if I do "defined axis #4 name foo" and "define axis #5 bar", then "angle foo bar" doesn't work. I guess "foo" and "bar" are not names of selections like I'm used to.
Anyway, I think I've got what I need working now.
And thanks Tom, your explanation makes sense. You wouldn't want to break existing use cases.
Cheers, Alexis
On Thu, Nov 16, 2023 at 5:35 PM Tom Goddard <goddard@sonic.net> wrote: Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis