Atoms/Bonds→Delete deletes all atoms if non-empty selection has no atoms/bonds

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.3.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-02-05)
Description
I selected a single distance pseudobond and used Actions / Atoms / Delete and it delete all my structures.  I expected it to probably do nothing since a distance is a pseudobond, and was surprised when it deleted every atom and bond.  I think it should delete no atoms and bonds if something is selected.


Log:
UCSF ChimeraX version: 0.92 (2020-02-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3jc1

3jc1 title:  
Electron cryo-microscopy of the IST1-CHMP1B ESCRT-III copolymer [more info...]  
  
Chain information for 3jc1 #1  
---  
Chain | Description  
Aa Ac Ae Ag Ai Ak Am Ao Aq As Au Aw Ay Ba Bc Be Bg Bi Bk Bm Bo Bq Bs Bu Bw By
Ca Cc Ce Cg Ci Ck Cm Co | Increased Sodium Tolerance 1 (IST1)  
Ab Ad Af Ah Aj Al An Ap Ar At Av Ax Az Bb Bd Bf Bh Bj Bl Bn Bp Br Bt Bv Bx Bz
Cb Cd Cf Ch Cj Cl Cn Cp | Charged multivesicular body protein 1b  
  
  

> select /Aa:6-187

1466 atoms, 1484 bonds, 1 model selected  

> usage select

select [objects] [residues true or false] [polymer an atoms specifier]
[minimumLength a number] [maximumLength a number] [sequence a text string]  
— select specified objects  
Subcommands are:

  * select add
  * select clear
  * select down
  * select intersect
  * select subtract
  * select up
  * select zone

  

> select polymer /Aa

49844 atoms, 1 model selected  

> select polymer /Ab

42262 atoms, 1 model selected  

> delete sel

> open 3jc1

3jc1 title:  
Electron cryo-microscopy of the IST1-CHMP1B ESCRT-III copolymer [more info...]  
  
Chain information for 3jc1 #2  
---  
Chain | Description  
Aa Ac Ae Ag Ai Ak Am Ao Aq As Au Aw Ay Ba Bc Be Bg Bi Bk Bm Bo Bq Bs Bu Bw By
Ca Cc Ce Cg Ci Ck Cm Co | Increased Sodium Tolerance 1 (IST1)  
Ab Ad Af Ah Aj Al An Ap Ar At Av Ax Az Bb Bd Bf Bh Bj Bl Bn Bp Br Bt Bv Bx Bz
Cb Cd Cf Ch Cj Cl Cn Cp | Charged multivesicular body protein 1b  
  
  

> select polymer /Ab

42262 atoms, 1 model selected  

> delete sel

> align #2/Co toAtoms #1/Co

RMSD between 1466 atom pairs is 0.000 angstroms  

> align #2/Co toAtoms #1/Bg

RMSD between 1466 atom pairs is 0.001 angstroms  

> usage align

align atoms toAtoms an atoms specifier [move move] [each each] [matchChainIds
true or false] [matchNumbering true or false] [matchAtomNames true or false]
[cutoffDistance a number] [reportMatrix true or false]  
— Align one set of atoms to another  
move: one of atoms, chains, nothing, residues, structure atoms, or structures  
each: one of chain, coordset, or structure  

> align #2/Co toAtoms #1/Bg reportMatrix true

Alignment matrix in structure 3jc1 coordinates  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 -0.00000000  
-0.00000000 1.00000000 0.00000000 -0.00000000  
-0.00000000 -0.00000000 1.00000000 0.00000000  
Axis -0.65396826 0.09270011 -0.75082102  
Axis point -1501.20331751 772.31679296 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis -0.00000000  
  
RMSD between 1466 atom pairs is 0.001 angstroms  

> align #2/Co toAtoms #1/Co

RMSD between 1466 atom pairs is 0.000 angstroms  

> align #2/Co toAtoms #1/Bg reportMatrix true

Alignment matrix in structure 3jc1 coordinates  
Matrix rotation and translation  
0.99931157 -0.03709981 -0.00001219 8.03229319  
0.03709980 0.99931153 -0.00027861 -7.89792385  
0.00002252 0.00027796 0.99999996 -50.24771427  
Axis 0.00750080 -0.00046778 0.99997176  
Axis point 217.64698710 222.61206895 0.00000000  
Rotation angle (degrees) 2.12621037  
Shift along axis -50.18235209  
  
RMSD between 1466 atom pairs is 0.001 angstroms  

> hide #2 models

> show #2 models

> view position #2 sameAsModels #1

> move z -50.18 models #2 coordinateSystem #2

> turn z 2.126 models #2 coordinateSystem #2

> move z -50.18 models #2 coordinateSystem #2

> turn z 2.126 models #2 coordinateSystem #2

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> ui mousemode rightMode distance

> distance #1/Bu:130@CD #1/Am:158@CG

Distance between 3jc1 #1/Bu LYS 130 CD and /Am PRO 158 CG: 40.399Å  

> color #1/Bu:130@CD #1/Am:158@CG pink

> select #1/Bu:164@CD

1 atom, 1 model selected  

> distance #1/Bu:130@CD #1/Am:164@CD

Distance between 3jc1 #1/Bu LYS 130 CD and /Am ARG 164 CD: 33.847Å  

> delete atoms

> delete bonds




OpenGL version: 4.1 ATI-3.5.5
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.