[chimerax-users] ChimeraX bug report submission

[Samuel Haysom]

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