Hi Eric,
This sounds great. I use aliases which are not commands also of
course. That’s why I suggested a setable flag as an option in the alias
command to indicate that “this” alias is a command and should go to
the menu. As I haven’t needed ‘^’ yet, using it as you
suggest would work for me.
Here is an example for highlighting a particular protein mutant
(we have many mutants we use for mapping. Some give positive results, some don’t).
General for all positive mutants:
alias pos_map_HSS color white $1; represent
stick $1; setattr m stickScale 3 $1; color blue $1@n=; color red $1@o=; color
green $1@s=; ribcol c_HSS $1;
Specific mutant:
alias HSS_987N #0:987.B
Highlight the mutant:
pos_map_HSS HSS_987N
New alias for new menu:
alias ^pos_HSS_987N pos_map_HSS HSS_987N
There can also be a paired alias to turn off the highlighting. Now
I can do all on or all off by typing, but having the menu with all the
individual mutants listed would be highly desirable.
Tim
From: Eric Pettersen
[mailto:pett@cgl.ucsf.edu]
Sent: Wednesday, 04 February 2009 20:06
To: Richmond Timothy J.
Cc: chimera-dev@cgl.ucsf.edu; chimera-users@cgl.ucsf.edu BB
Subject: Re: [chimera-dev] alias menu
On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote:
Dear Chimera Developers,
Perhaps I have missed it, but I would find a menu for selected
aliases very useful. Having returned to Chimera from PyMol recently, it would
be great to have an option for the alias command that allowed the particular
alias to be listed in a separate window and ran the alias by clicking on the
alias name listed there.
Best regards,
Tim
Hi Tim,
As
Elaine pointed out in her reply, aliases are frequently used as shorthands for
long atom specs rather than as replacements for complete commands.
However, the form of the alias command that uses '^' (so that matching
only occurs at the start of the line) typically is used to define full
command aliases.
So
my thinking is this: aliases defined with the '^' character would be placed in
an 'Aliases' top-level menu (created on the fly as needed). Such aliases
would automatically be remembered across Chimera invocations (and populate an
Aliases menu). The menu could be torn-off (except on Aqua) to make a
stand-alone window. Those aliases could be deleted as normal with the
~alias command (which would remove them from the menu and no longer remember
then in subsequent Chimeras).
Would
this be good enough?
--Eric