Bond connectivity changes don't update ribbon

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3.dev202110120902 (2021-10-12 09:02:44 UTC)
Description
Also noticed while reporting #5432: the `bond` and `~bond` commands don't properly update the cartoon. If I delete a N-C backbone bond the cartoon remains connected even after a new call to `cartoon`; if I create a bond between previously-disconnected backbone atoms the cartoon doesn't update without a new explicit `cartoon` command.

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3.dev202110120902 (2021-10-12)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3io0

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #1  
---  
Chain | Description | UniProt  
A | EtuB protein | A5N734_CLOK5  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open 3io0

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #2  
---  
Chain | Description | UniProt  
A | EtuB protein | A5N734_CLOK5  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> delete #2&~:268-273

> delete #1:268-273

> ui tool show Shell

Shell commands:  
from chimerax.atomic import AtomicStructure  
m1, m2 = session.models.list(type=AtomicStructure)  
m1.combine(m2, {},m1.position)  

> hide #2 models

> save test.pdb #1

> save test.cif #1

> open test.pdb

Chain information for test.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open test.cif

Chain information for test.cif #4  
---  
Chain | Description  
A | EtuB protein  
  
test.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> save test_session.cxs

> hide #!3 models

> hide #4 models

> ~cartoon

> cartoon

> bond #1:267@C|#1:268@N

Created 1 bond  

> bond #1:273@C|#1:274@N

Created 1 bond  

> ~cartoon

> cartoon

> close #4#3

> save test.pdb #1

> save test.cif #1

> open test.pdb

Chain information for test.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open test.cif

Chain information for test.cif #4  
---  
Chain | Description  
A | EtuB protein  
  
test.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> hide #3 models

> select #4:272

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select clear

> save test_session.cxs

> hide #1 models

> show #1 models

> hide #!4 models

> show #1

> select #1/A:137

7 atoms, 6 bonds, 1 residue, 1 model selected  

> ~cartoon sel

> select #1/A:136

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

94 atoms, 94 bonds, 14 residues, 1 model selected  

> select down

4 atoms, 3 bonds, 1 residue, 1 model selected  

> ~cartoon sel

> select clear

> cartoon

> ~bond sel

> cartoon

> select #1/A:136

4 atoms, 2 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select add #1/A:137

11 atoms, 8 bonds, 1 pseudobond, 2 residues, 2 models selected  

> ~cartoon sel

> select clear

> cartoon

> ~cartoon

> select #1/A:136@CA

1 atom, 1 residue, 1 model selected  

> select add #1/A:136@C

2 atoms, 1 residue, 1 model selected  

> bond sel

Created 1 bond  

> ~bond sel

> cartoon

> select clear

> ~cartoon

> cartoon




OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         14G         22G        444M         25G         47G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
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[Eric Pettersen]

I wouldn't expect deleting an N→C backbone bond to disconnect the ribbon. That bond should automatically be replaced with a missing-structure pseudobond and the chain remains connected, and therefore the ribbon remains unchanged.

You are correct about the cartoon not updating on bond formation. The cartoon code needs to react to the 'chains' part of the atomic changes trigger, specifically ChangeTracker::REASON_RESIDUES. I'm switching the ownership of this ticket to Tom for this.

[Tom Goddard]

The graphics updating does not monitor ChangeTracker. The C++ code should call the ribbon graphics changed method structure.set_gc_ribbon().

[Eric Pettersen]

Adding chain-forming bond now updates ribbons.