[Chimera-users] [chimera-dev] alias menu

Richmond Timothy J. richmond at mol.biol.ethz.ch
Wed Feb 4 13:29:01 PST 2009

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


General for all positive mutants:

alias pos_map_HSS  color white $1; represent stick $1; setattr m
stickScale 3 $1; color blue $1 at n=; color red $1 at o=; color green $1 at 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.






From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] 
Sent: Wednesday, 04 February 2009 20:06
To: Richmond Timothy J.
Cc: chimera-dev at cgl.ucsf.edu; chimera-users at 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,




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 Pettersen

                        UCSF Computer Graphics Lab




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