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@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@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