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

Eric Pettersen pett at cgl.ucsf.edu
Thu Feb 5 17:06:49 PST 2009

Hi Tim,
	Though this is an excellent idea, it is competing with a lot of other  
projects I'm already working on.  It might make it into our next  
release (middle of this year) but the following release is more  
likely.  I'm going to open a feature-request for this in our Trac  
database, with you on the recipient list so that you will get mail  
when it gets done.


On Feb 4, 2009, at 1:29 PM, Richmond Timothy J. wrote:

> 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 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.
> Tim
> 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,
> 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
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
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> Chimera-users at cgl.ucsf.edu
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