[chimerax-users] Showing Bond/PBond to Cartoon/Ribbons

[JAMES MICHAEL S1JJRUdFUiA=]

I think this is related to the way the ribbon/cartoon smooths over  
secondary structures. Beta strands are wavy not flat, for example.  
There is a similar problem in PyMOL. If we want to show a whole  
residue then the best way to do that is to turn off the flat strands  
and the idealisation of helices.

PyMOL also has a feature called "side chain helper" where the bonds  
are connected to the idealised calpha location rather than the actual  
calpha atom location, which may be a nice feature to have in chimerax  
too.

Best wishes
James

"Anderson, Jacob via ChimeraX-users" <chimerax-users at cgl.ucsf.edu> escribió:

> There has been a prior post on this problem, but I wanted to ask  
> about some asymmetry I see in ChimeraX when displaying residues  
> emanating from ribbons/cartoons.
>
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html
>
> For example, sometimes when I select a residue on a ribbon/cartoon  
> and write "show sel atoms,bonds", I get a floating residue. However,  
> other times I get a nice connection between the beta carbon and the  
> ribbon (the desired behavior).
>
> How can users get a consistent behavior where there is a connection  
> from the beta carbon to the ribbon?
>
> Good Example - connected to ribbon
> [cid:6ddcc2ee-f9b2-4060-8e3f-fde8ccc74881]
>
> Two floating examples:
> [cid:46516984-036d-4a39-9713-9056a161548a]