Inter-residue bonds should not select residues

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.93 (2020-04-03)
Description
For a model with ligands covalently attached to the protein, if I run the command "select ~protein" then the protein residues bonded to the ligands appear in `selected_residues(session)` (presumably because the command also selects the protein-ligand bond). This messed me up in this particular case because the ligand-protein bonds shouldn't have actually been there, so I ran a loop over the selection to delete all bonds between the residues and their neighbors. All good now, but there was a bit of fiddling involved to put things right again!

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open Atval.pdb

Chain information for Atval.pdb #1  
---  
Chain | Description  
D E H I L M P Q | No description available  
F J N R | No description available  
G K O S | No description available  
  

> toolshed show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select ~protein

704 atoms, 752 bonds, 1 model selected  

> style sel stick

Changed 704 atom styles  

> show sel cartoons

> hide sel atoms

> select clear

> show cartoons

> hide atoms

> style stick

Changed 46072 atom styles  

> show cartoons

> dssp

> show ~protein

> select ~protein

704 atoms, 752 bonds, 1 model selected  

> select zone sel 3

Selected 216 atoms  

> show sel

> select up

1068 atoms, 980 bonds, 1 model selected  

> show sel

> select clear

> view sel

> color byhetero

> select clear

> view sel

> select clear

> view sel

> select clear

> view sel

> select clear

> view sel

Expected an objects specifier or a keyword  

> select ~protein

704 atoms, 752 bonds, 1 model selected  

> hide sel cartoons

> select clear

> hide cartoons

> show

> addh

Summary of feedback from adding hydrogens to Atval.pdb #1  
---  
warnings | Not adding hydrogens to /H LYS 390 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /H GLU 431 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /H LYS 434 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /H LYS 450 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /I LYS 390 CB because it is missing heavy-atom bond
partners  
27 messages similar to the above omitted  
notes | No usable SEQRES records for Atval.pdb (#1) chain D; guessing termini
instead  
No usable SEQRES records for Atval.pdb (#1) chain E; guessing termini instead  
No usable SEQRES records for Atval.pdb (#1) chain F; guessing termini instead  
No usable SEQRES records for Atval.pdb (#1) chain G; guessing termini instead  
No usable SEQRES records for Atval.pdb (#1) chain H; guessing termini instead  
11 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /D THR 86, /E THR 86, /F HIS
87, /G LEU 317, /H THR 86, /I THR 86, /J HIS 87, /K LEU 317, /L THR 86, /M THR
86, /N HIS 87, /O LEU 317, /P THR 86, /Q THR 86, /R HIS 87, /S LEU 317  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /D ARG 667, /E ARG 667, /F
MET 241, /G SER 475, /H ARG 667, /I ARG 667, /J MET 241, /K SER 475, /L ARG
667, /M ARG 667, /N MET 241, /O SER 475, /P ARG 667, /Q ARG 667, /R MET 241,
/S SER 475  
3580 hydrogen bonds  
/D ARG 667 is not terminus, removing H atom from 'C'  
/E ARG 667 is not terminus, removing H atom from 'C'  
/F MET 241 is not terminus, removing H atom from 'C'  
/G SER 475 is not terminus, removing H atom from 'C'  
/H ARG 667 is not terminus, removing H atom from 'C'  
11 messages similar to the above omitted  
46152 hydrogens added  
  

> select /I:416@CA

1 atom, 1 model selected  

> select /I:416@CA

1 atom, 1 model selected  

> select up

22 atoms, 21 bonds, 1 model selected  

> select clear

> select /B:729@C47

1 atom, 1 model selected  

> select up

85 atoms, 90 bonds, 1 model selected  

> select ~protein

1176 atoms, 1224 bonds, 1 model selected  

> select clear

> view sel

> hide H

> select clear

Expected an objects specifier or a view name or a keyword  

> view sel




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
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