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

[Elaine Meng]

Hi James,
The CA atoms are shown when the side chain is shown, or else there would be a much bigger gap!  The tether is drawn between the CA and the ribbon.
Best,
Elaine

> On May 12, 2022, at 9:49 AM, JAMES MICHAEL S1JJRUdFUiA= <jmkrieger at cnb.csic.es> wrote:
> 
> Hi Elaine,
> 
> The CA tether sounds like a great way to deal with this kind of thing. Perhaps it would be helpful to show CA atoms along with the side chain or include CB tethers too.
> 
> Best wishes
> James
> 
> Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> escribió:
> 
>> Hi Jacob,
>> The topic of that post is slightly different, whether the CA is shown at all.  Now, whether the CA falls on the ribbon or not is another issue.  It can fall off the ribbon on beta-strands where the the ribbon path is smoothed (by default).  Also by default, there will be "tethers" displayed between the CA and the ribbon when the CA is not on the ribbon.  This is explained in the cartoon (ribbon) command help:
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>
>> 
>> See for example Lys 164 in 2mnr, where a tether is shown.
>> 
>> If you turn off smoothing the ribbon will always fall exactly on the CA positions:
>> 
>> cartoon smooth 0
>> 
>>  However, turning off smoothing makes the beta-strands very ripply, like some lasagna noodles, so you may not want to turn off smoothing entirely or on the whole ribbon.  Thus your options are to:
>> 
>> (A) use weaker smoothing overall, e.g.:
>> 
>> cartoon smooth 0.5
>> (default = 1.0)
>> 
>> - and/or -
>> 
>> (B) weaken or turn off smoothing only at the particular residue positions where you are seeing the problem, e.g.:
>> 
>> cartoon #1/A:164 smooth 0
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On May 12, 2022, at 8:32 AM, Anderson, Jacob via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> 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
>>> <image.png>
>>> 
>>> Two floating examples:
>>> <image.png>