Re: [chimerax-users] Suggestion - add shortcuts for Ca trace, Ca+sidechains
It seems that ChimeraX does not display CA traces — it shows just the atoms with no bonds between them. I see that CA-only structures do draw dashed lines between the CA atoms. I’ll have to ask Eric Pettersen on Tuesday what the plan is for depicting CA traces — apparently the mechanism that creates the pseudobonds between CA atoms automatically as is done in Chimera is not in ChimeraX.
Tom
On May 26, 2017, at 10:03 AM, Oliver Clarke wrote:
Sounds great!!
Alternative - have a C-alpha trace button and show/hide side-chain/base button?
That way if you do all atoms, you could quickly hide/show side chains, or if you’re displaying C-alpha trace and you want to quickly pop on side chains you can do so also? (Could also add this as a custom button of course)
Cheers Oli
On May 26, 2017, at 1:00 PM, Tom Goddard wrote:
Yes a C-alpha trace toolbar button would be nice — I’ll add that. The random atom color toolbar button is just for laughs — I’ll retire that one when I add C-alpha trace. The C-alpha trace plus side-chain doesn’t seem too different from full backbone + side chain in visual complexity, and backbone + sidechain already has a toolbar button (show all atoms). I’m thinking maybe that would be a toolbar button you could add as a customization. I plan to add a command soon where you can add new toolbar buttons (you specify and image file for icon and the command to execute using a command e.g. "toolbar add “CA trace” icon iconfile.png command "show selAtoms & @CA” shortcut ca” and it would be remembered in a preference file. Another useful one would be your thick backbone and thin side-chain sticks.
Tom
On May 26, 2017, at 7:35 AM, Oliver Clarke wrote:
Hi,
Frequently when looking at models in medium resolution maps (~4-5 Å), it is valuable to view the C-alpha trace when assessing model map fit (or making figures to show such).
At slightly higher resolution, where side chains are obvious but backbone torsions cannot be modeled based on the map alone, representing the C-alpha trace with sidechains displayed is often desirable (examples of both attached).
It looks like there is space in the upper toolbar for additional buttons - perhaps adding a button for a Calpha trace representation (equivalent would be P for nuclei acids) and one for a Calpha+sidechain/base representation may be worth considering? (I’m also not convinced of the value of the random atom colors representation as a shortcut, but maybe there is a use case I’m missing?)
Cheers Oli <Screenshot 2017-05-26 10.34.38.png><Screenshot 2017-05-26 10.34.25.png> <Screenshot 2017-05-26 10.23.18.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I made a ticket to be able to show C-alpha traces.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/694#comment:1 https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/694#comment:1
There are many approaches (use ribbons, use pseudobonds, automatic display, require command…). I think I favor a special command that adds pseudobonds because it is simplest. Realistically this feature is not likely to be implemented within 6 months.
Tom
On May 26, 2017, at 2:24 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
It seems that ChimeraX does not display CA traces — it shows just the atoms with no bonds between them. I see that CA-only structures do draw dashed lines between the CA atoms. I’ll have to ask Eric Pettersen on Tuesday what the plan is for depicting CA traces — apparently the mechanism that creates the pseudobonds between CA atoms automatically as is done in Chimera is not in ChimeraX.
Tom
On May 26, 2017, at 10:03 AM, Oliver Clarke wrote:
Sounds great!!
Alternative - have a C-alpha trace button and show/hide side-chain/base button?
That way if you do all atoms, you could quickly hide/show side chains, or if you’re displaying C-alpha trace and you want to quickly pop on side chains you can do so also? (Could also add this as a custom button of course)
Cheers Oli
On May 26, 2017, at 1:00 PM, Tom Goddard wrote:
Yes a C-alpha trace toolbar button would be nice — I’ll add that. The random atom color toolbar button is just for laughs — I’ll retire that one when I add C-alpha trace. The C-alpha trace plus side-chain doesn’t seem too different from full backbone + side chain in visual complexity, and backbone + sidechain already has a toolbar button (show all atoms). I’m thinking maybe that would be a toolbar button you could add as a customization. I plan to add a command soon where you can add new toolbar buttons (you specify and image file for icon and the command to execute using a command e.g. "toolbar add “CA trace” icon iconfile.png command "show selAtoms & @CA” shortcut ca” and it would be remembered in a preference file. Another useful one would be your thick backbone and thin side-chain sticks.
Tom
On May 26, 2017, at 7:35 AM, Oliver Clarke wrote:
Hi,
Frequently when looking at models in medium resolution maps (~4-5 Å), it is valuable to view the C-alpha trace when assessing model map fit (or making figures to show such).
At slightly higher resolution, where side chains are obvious but backbone torsions cannot be modeled based on the map alone, representing the C-alpha trace with sidechains displayed is often desirable (examples of both attached).
It looks like there is space in the upper toolbar for additional buttons - perhaps adding a button for a Calpha trace representation (equivalent would be P for nuclei acids) and one for a Calpha+sidechain/base representation may be worth considering? (I’m also not convinced of the value of the random atom colors representation as a shortcut, but maybe there is a use case I’m missing?)
Cheers Oli <Screenshot 2017-05-26 10.34.38.png><Screenshot 2017-05-26 10.34.25.png> <Screenshot 2017-05-26 10.23.18.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Tom Goddard