[chimerax-users] Showing CA atoms along with ribbon

[Elaine Meng]

Hi Samuel,
This is likely because you are showing ribbons.  By default, ribbons (aka cartoons) suppress backbone atom display, although if you show the CB it will then show the CA because it needs to draw a bond instead of having the sidechain floating in space.  If you look closely at strands, the CA might also be slightly off of the ribbon and attached to it with a conical "tether."

Your choices are to either not show cartoons at the same time, or if you want to show cartoons at the same time, then turn off backbone-atom suppression.  This is the "suppressBackboneDisplay" option of the cartoon command.  For example:

cartoon suppress false

See the cartoon command documentation:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>

Another approach is to just open an extra copy, one to show ribbons and one to show atoms, but that  is usually not a great solution because then you have to worry about specifying only the copy you want in various commands, and it can cause confusion when running calculations.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 27, 2021, at 4:25 AM, Samuel Haysom via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> i want to show just the CA atoms of a selection of residues (starting with the rest of the model shown as a cartoon). To do this I am trying to use a command like this:
> 
> show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799 at CA target a
> 
> But this doesn't do anything. If I take off the @CA bit I can show all the atoms in the residue.
> 
> Full .cxc is as follows:
> 
> open 5ljo
> open 5d0o
> 
> hide #1,2 atoms
> show #1,2/A cartoons
> 
> color #1,2/A rgb(0.252,0.680,1.000)
> color #1,2/B rgb(0.000,0.831,0.321)
> color #1,2/C rgb(1.000,0.861,0.137)
> color #1,2/D rgb(1.000,0.400,0.100)
> color #1,2/E rgb(0.780,0.000,0.400)
> 
> ### Align barrels ###
> # mmaker #2/A:435-810 to #1/A:435-810
> view matrix model #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> 
> 
> ### Color EPR regions ###
> color #1,2/A:424-447 green
> color #1,2/A:454-518 red
> color #1,2/A:348-423 dark orange
> 
> ### Create Morph ###
> morph #1,2 frames 40
> 
> ### Show single mutant CA ###
> ### New positions ###
> show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799 at CA target a
> color #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799 magenta
> 
> ### Existing Positions ###
> show #3/A:435,499,501,535,564,751,793 target a
> color#3/A:435,499,501,535,564,751,793 purple
> 
> Log:
> Startup Messages  
> ---  
> note | available bundle cache has not been initialized yet  
> 
> UCSF ChimeraX version: 1.3.dev202110261153 (2021-10-26)  
> © 2016-2021 Regents of the University of California. All rights reserved.  
> How to cite UCSF ChimeraX  
> 
>> open 5ljo
> 
> Summary of feedback from opening 5ljo fetched from pdb  
> ---  
> warnings | Atom H is not in the residue template for LEU /B:22  
> Atom H is not in the residue template for CYS /C:25  
> Atom H is not in the residue template for GLU /D:26  
> Atom H is not in the residue template for GLU /E:24  
> Atom H is not in the residue template for PHE /A:24  
> 
> 5ljo title:  
> E. coli BAM complex (BamABCDE) by cryoEM [more info...]  
> 
> Chain information for 5ljo #1  
> ---  
> Chain | Description | UniProt  
> A | Outer membrane protein assembly factor BamA | BAMA_ECO45  
> B | Outer membrane protein assembly factor BamB | BAMB_ECOLI  
> C | Outer membrane protein assembly factor BamC | BAMC_ECOLI  
> D | Outer membrane protein assembly factor BamD | BAMD_ECO57  
> E | Outer membrane protein assembly factor BamE | BAME_ECOL6  
> 
> 
>> open 5d0o
> 
> 5d0o title:  
> BamABCDE complex, outer membrane β barrel assembly machinery entire complex
> [more info...]  
> 
> Chain information for 5d0o #2  
> ---  
> Chain | Description | UniProt  
> A | Outer membrane protein assembly factor BamA | BAMA_ECOLI  
> B | Outer membrane protein assembly factor BamB | BAMB_ECOLI  
> C | Outer membrane protein assembly factor BamC | BAMC_ECOLI  
> D | Outer membrane protein assembly factor BamD | BAMD_ECOLI  
> E | Outer membrane protein assembly factor BamE | BAME_ECOLI  
> 
> 
>> hide #1,2 atoms
> 
>> show #1,2/A cartoons
> 
>> color #1,2/A rgb(0.252,0.680,1.000)
> 
>> color #1,2/B rgb(0.000,0.831,0.321)
> 
>> color #1,2/C rgb(1.000,0.861,0.137)
> 
>> color #1,2/D rgb(1.000,0.400,0.100)
> 
>> color #1,2/E rgb(0.780,0.000,0.400)
> 
>> view matrix models
>> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> 
>> color #1,2/A:424-447 green
> 
>> color #1,2/A:454-518 red
> 
>> color #1,2/A:348-423 dark orange
> 
>> show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799 at CA target a
> 
> _