[chimerax-users] Feature Request: Named selections

[Jared Adolf-Bryfogle]

Hi Elaine,

Thanks for the response!  I remembered the aliases from Chimara, and they
were certainly useful.  I saw a ticket was opened up for this, and I'm very
excited about it.  A GUI component in the models tab, or as another tab
would we a great addition to extend functionality.

Link to ticket here: https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/838

Cheers,
-Jared


Jared Adolf-Bryfogle, Ph.D.
Research Associate
Lab of Dr. William Schief
The Scripps Research Institute



On Thu, Sep 14, 2017 at 12:15 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Jared,
> The short answer is that in ChimeraX, we do intend to have user-named sets
> of objects, but it hasn’t been implemented yet.
>
> In Chimera, there were two approaches:
> (1)  “alias” to make a simple string substitution, so it could be any atom
> specification string, like a list of residues, etc.  This command could
> also make action aliases, essentially macros to execute one or more
> commands, so it was dual purpose.
>
> (2) something called named selections, where the set actually had to be
> selected (with the green outlines) before you gave it a name. The set of
> objects was only evaluated at that time, unlike the string substitution.
> For example, if you used command “select protein” with a specific model
> open and then named the selection, it would only include the protein part
> of that model, not any other models, whereas if you’d used “alias blah
> protein” then “blah” would always mean the protein parts of whatever models
> were open at the time.
>
> Because of our “named selection” terminology, people who were familiar
> with Pymol gravitated toward approach #2  in Chimera.  Personally, I
> preferred approach #1 and thought it was easier to understand.
>
> ChimeraX does have an “alias” command, but it’s only for action aliases
> (macros).  We intend to have a command (not settled yet what the command or
> keywords would be) for object aliases with two options, evaluate-now (like
> Chimera's approach #2) and evaluate-when-used (like Chimera’s approach #1).
>
> Then they would be listed in the “rapid access” interface (what you get
> from clicking the lightning bolt icon on the bottom corner) and maybe in a
> menu.
>
> I don’t know the time frame, as unfortunately programmer time is limited,
> but we appreciate your comments — it’s good for users to speak up on what
> they feel are the most pressing needs!
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Sep 13, 2017, at 4:35 PM, Jared Adolf-Bryfogle <jadolfbr at gmail.com>
> wrote:
> >
> > Hi All!
> > I just started playing around with the alpha, and I’m very happy with it
> so far!  Really love to windows and the ability to easily select models.
> > One thing that is missing is a similar list of selections (yes, ala
> PyMol).  I find these to be extremely useful in a  long running session and
> I was wondering if something like that is planned.
> > It would be similar to the model window, where you could control each
> selection and maybe apply view controls to each selection as well - like
> having components that are cartoon and others stick, etc.
> > Thanks for any info!
> > Sincerely,
> > -Jared
>
>
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