[chimerax-users] select displayed atoms via command line / transfer saved views

[Elaine Meng]

Dear Helge,
For 1) yes, it would be command:

select @@display

...the @@ part means atom attribute, and the name of the boolean (on or off) attribute is "display", see:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes>
<https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#atom>

For 2) not exactly... if you haven't already made the new session,  I would start with the original session with the desired view and then open the data you want in the new session, fit/superimpose them on the original session contents, and close the parts you don't want, and then save the new session.  If you already made the new session with a lot of steps, however, it depends on whether you can use the same transformations as in the old session to generate that view.  (Whether the data you want to have the same view as the original data is already in coordinates that superimpose with it.)  You could try reporting the model transformations in the original session and then in the new session apply them.  Reporting/applying transformations would be done with the "view matrix" command, see

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix>

... or you could save to a "positions" file from the original session and apply that file in the new session:

<https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html>

That wouldn't include the clipping plane position(s), which can be reported with "clip list" and applied with "clip"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Nov 11, 2022, at 2:05 AM, Helge Paternoga via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX users,
> 
> I have to unrelated questions:
> 
> 
> 1) Is there a way to select displayed atoms via the command line?
> 
> 
> 2) Is it possible to transfer saved views from one session to another one?
> 
> 
> Many regards and thank you for reading,
> 
> Helge