[chimerax-users] Suggestion - add shortcuts for Ca trace, Ca+sidechains

[Tom Goddard]

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 at sonic.net <mailto:goddard at 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>
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> 
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