[chimerax-users] I suggest the addition of a "Automatic Styling (Smart Initial Display)" button

[Conrad Huang]

We have some limited undo capability in ChimeraX.  (It doesn't work with 
surfaces yet, but does work with atoms, bonds, and ribbons.)  So, after 
you click on the "Show atoms" button, you should be able to return to 
the previous state by typing "undo" on the command line.  It's certainly 
not ideal, but we're working on some ideas.

As for copying from the browser, after you highlight the text, 
right-clicking should pop up a context menu with "Copy" and "Unselect" 
as options.

Hope this helps.

Conrad

On 3/29/2018 11:17 AM, JEAN-YVES SGRO wrote:
> Greetings,
> 
> 
> thank you for your quick reply about the "non-bug" request relating to 
> the initial display and the explanation. After your reply I searched 
> more intensely in the documentation and indeed found page 
> help:user/autostyle.html with these details about the number of chains.
> 
> 
> As I am preparing to demonstrate ChimeraX in the department (tutorial I 
> find that some inherent aspect of the Automatic Styling (Smart Initial 
> Display)  is very quickly lost. /e.g./ simply by clicking on the "Show 
> atoms" button in the Molecular display toolbar and then the "Hide atoms".
> 
> 
> I found commands for selection at 
> http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html which 
> are useful and one can reconstruct the initial display.
> 
> 
> As I example I am using myoglobin (1mbo.) The molecule opens as a 
> ribbon, heteroatoms as stick models, the iron ion as sphere, and AA 
> close to the ligands as sticks as well.
> 
> 
> Simply pressing the "Show atoms" button will display all water molecules 
> as small spheres.
> 
> But now if I click "Hide atoms" only the ribbon is left.
> 
> 
> Yesterday I tried to find a way to select /heteroatoms/ in general and 
> use the sel ~ sel selection inversion found on the pipermail 
> <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html> 
> but that was not the best solution.
> 
> 
> Today I could reconstruct the initial display with these commands if all 
> I did was to toggle the "Show atoms" and "Hide atoms" buttons:
> 
> 
> show ions
> 
> show ligand
> 
> select ligand:<3.8 & protein
> 
> show selAtoms
> 
> 
> For novices this is a bit complicated to understand.
> 
> 
> Therefore I would like to suggest the addition of a "Automatic Styling 
> (Smart Initial Display)" button, perhaps at the First position in the 
> Molecular display toolbar.
> 
> 
> I firmly believe that this would avoid lots of frustration for many new 
> users!
> 
> 
> P.S. One more thing: would it be possible to Copy from the built-in 
> browser to Paste elsewhere as I am trying to do with the email address?
> 
> 
> Sincerely,
> 
> Jean-Yves Sgro
> 
> 
> 
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