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 pipermailhttp://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