Opened 5 years ago

Closed 5 years ago

#3727 closed defect (fixed)

Swapaa mouse mode using deleted residue

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202009150003 (2020-09-15 00:03:23 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.dev202009150003 (2020-09-15)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Bruce/Desktop/ADAM17/6M17 6M18/6m17_with_leucine.pdb"

6m17_with_leucine.pdb title:  
The 2019-ncov RBD/ACE2-B0AT1 complex [more info...]  
  
Chain information for 6m17_with_leucine.pdb #1  
---  
Chain | Description  
A C | sodium-dependent neutral amino acid transporter B(0)AT1  
B D | angiotensin-converting enzyme 2  
E F | sars-cov-2 receptor binding domain  
  
Non-standard residues in 6m17_with_leucine.pdb #1  
---  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
ZN — zinc ion  
  

> ui tool show Toolbar

> hide cartoons

> hide cartoons

> hide surfaces

> select /A:5-609

4799 atoms, 4942 bonds, 605 residues, 1 model selected  

> hide sel surfaces

> select /D:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> select /C:5-609

4799 atoms, 4942 bonds, 605 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> hide sel surfaces

> show sel cartoons

> hide sel atoms

> ui mousemode right "translate selected models"

> select clear

> ui mousemode right select

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select ~sel

25335 atoms, 26074 bonds, 4 pseudobonds, 3127 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> save "/Users/Bruce/Desktop/ADAM17/ADAM17 PDB
> 3LGP/Leucine_707_extracted_from_6m17.cxs" includeMaps true

> select ::name="LEU"

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right swapaa

> swapaa mousemode /C:707 LEU

swapaa: Cannot swap non-protein residues "/C LEU 707"  

> ui tool show "Show Sequence Viewer"

> ui tool show "Show Sequence Viewer"

> ui tool show "Show Sequence Viewer"

> select clear

> save "/Users/Bruce/Desktop/ADAM17/ADAM17 PDB
> 3LGP/Leucine_707_extracted_from_6m17.pdb" relModel #1

> swapaa mousemode /C:707 LEU

swapaa: Cannot swap non-protein residues "/C LEU 707"  

> swapaa mousemode /C:707 CYS

swapaa: Cannot swap non-protein residues "/C CYS 707"  

> swapaa mousemode /C:707 CYS

swapaa: Cannot swap non-protein residues "/C CYS 707"  

> swapaa mousemode /C:707 CYS

swapaa: Cannot swap non-protein residues "/C CYS 707"  

> swapaa mousemode /C:707 CYS

swapaa: Cannot swap non-protein residues "/C CYS 707"  

> swapaa mousemode /C:707 CYS

swapaa: Cannot swap non-protein residues "/C CYS 707"  

> close session

> open "/Users/Bruce/Desktop/ADAM17/ADAM17 PDB
> 3LGP/Leucine_707_extracted_from_6m17.pdb" format pdb

Leucine_707_extracted_from_6m17.pdb title:  
The 2019-ncov RBD/ACE2-B0AT1 complex [more info...]  
  

> ui mousemode right swapaa

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 529, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 48, in mouse_up  
self._unlabel()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 125, in _unlabel  
objects, otype = self._label_objects(r)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 110, in _label_objects  
la = [a for a in r.atoms if a.name == self._label_atom_name]  
File "cymol.pyx", line 940, in chimerax.atomic.cymol.CyResidue.atoms.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 940, in chimerax.atomic.cymol.CyResidue.atoms.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 48, in mouse_up  
self._unlabel()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 125, in _unlabel  
objects, otype = self._label_objects(r)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 110, in _label_objects  
la = [a for a in r.atoms if a.name == self._label_atom_name]  
File "cymol.pyx", line 940, in chimerax.atomic.cymol.CyResidue.atoms.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 940, in chimerax.atomic.cymol.CyResidue.atoms.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 529, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 48, in mouse_up  
self._unlabel()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 125, in _unlabel  
objects, otype = self._label_objects(r)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 110, in _label_objects  
la = [a for a in r.atoms if a.name == self._label_atom_name]  
File "cymol.pyx", line 940, in chimerax.atomic.cymol.CyResidue.atoms.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 940, in chimerax.atomic.cymol.CyResidue.atoms.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 636, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 44, in mouse_drag  
if self._swap_residue_step(r, rstep):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 85, in _swap_residue_step  
rname = r.name  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1160, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 48, in mouse_up  
self._unlabel()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 125, in _unlabel  
objects, otype = self._label_objects(r)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swapaa/mouse_swapaa.py", line 110, in _label_objects  
la = [a for a in r.atoms if a.name == self._label_atom_name]  
File "cymol.pyx", line 940, in chimerax.atomic.cymol.CyResidue.atoms.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 940, in chimerax.atomic.cymol.CyResidue.atoms.__get__  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel Iris OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Macmini7,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 249.0.0.0.0
      SMC Version (system): 2.24f32

Software:

    System Software Overview:

      System Version: macOS 10.15.6 (19G2021)
      Kernel Version: Darwin 19.6.0
      Time since boot: 1:00

Graphics/Displays:

    Intel Iris:

      Chipset Model: Intel Iris
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0a2e
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        DELL U3014:
          Resolution: 2560 x 1600
          UI Looks like: 2560 x 1600 @ 60 Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: J3Y9N63G634L
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.8.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202009150003
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Cc: Eric Pettersen added
Component: Unassigned → Structure Editing
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Swapaa mouse mode using deleted residue

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

This is a weird rare case. Leucine 707 of 6m17 is a HETATM residue with no label_seq_id so the ChimeraX reader is confused by it issuing the warning "Unable to infer polymer connectivity due to unspecified label_seq_id for residue "LEU" near line 27962" and considers is a non-protein residue because it does not belong to a chain and so has polymer_type = PT_NONE. When swapaa mouse mode is used it gives an error for this residue when the mouse button is released and it tries to run the swapaa command (to get a good rotamer). That UserError exception caused the residue attribute of the mouse mode not to be cleared on mouse up. The user then closed the structure and tried to use the mouse mode which used the dead residue.

I made sure the residue attribute is None even if the error occurs.

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