[chimera-dev] a more logical command for atom view

[Elaine Meng]

Hi Jakob,
We appreciate your input, and have actually have come to some similar conclusions while hashing out command “designs” for our next-generation program, ChimeraX.   Everything is still in flux, and the command set is still quite limited, but our current scheme includes “show”  and “hide” which could work on atoms, ribbons, and/or surfaces.  We are planning to have an initial release sometime in 2016.

I don’t know if you would like that better… it kind of goes the opposite way from your suggestion.  As we have found out by discussions amongst ourselves, not everyone thinks in the same way.  One guiding principle is that we have tried to make commands make more “English” sense.  (What is the simplest term for what a user is trying to do?  He or she is trying to show or hide something.)

In Chimera, there is already a “show” command that undisplays the non-specified atoms in the same model as the specified atoms, so we couldn’t use it as a synonym without breaking some older scripts.  

You can create your own aliases (alias atom display; alias ~atom ~display), but your point is taken in that it would not help to soften the learning curve for others.
Thanks,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Apr 4, 2016, at 12:21 AM, Jakob Suckale <jakob.suckale at uni-tuebingen.de> wrote:
> 
> Dear Chimera dev't team,
> 
> As a new user to Chimera, I always found the command to show atoms
> counterintuitive and I would like to suggest to add a synonym that is
> logically consistent with the other options to show a molecule.
> 
> How about "atom achain"? If you asked any new user to complete the
> following series, the answer would not be "display" - surface achain,
> ribbon achain, ? achain. This is probably not something that veterans
> of Chimera still notice but it's illogical to new users and could be
> easily remedied with a synonym in addition to "disp". This wouldn't
> affect any old users while being consistent and logical.
> 
> All the best,
> 
> Jakob