I suggest the addition of a "Automatic Styling (Smart Initial Display)" button
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
Hi Jean-Yves, Thanks for the suggestion! I think we were planning to have some easily accessible display presets that would include something similar, but (as you found) it hasn’t been done yet.
In the meanwhile, note that for basic changes in atomic and cartoon (ribbon) display, coloring, and style you can use “undo”, as command or in the Edit menu, but that goes only 1 step at a time, and only includes those few most basic actions.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/undo.html
In the built-in browser, I can highlight some text and then right-click into it to get context menu that includes “Copy” which could then be pasted. At least if you’re in the Contact Us page, the email address is already a mailto link so that just clicking it should start a message in your email app,
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 29, 2018, at 11:17 AM, JEAN-YVES SGRO jsgro@wisc.edu 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 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
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%C2%A0whic... 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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participants (3)
-
Conrad Huang -
Elaine Meng -
JEAN-YVES SGRO