Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#3457 closed defect (fixed)

tape-measure mouse mode using dead MarkerSet

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

Description 

The following bug report has been submitted:
Platform:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-05-04)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.94.dev202005040453 (2020-05-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1xd2

Summary of feedback from opening 1xd2 fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 8303  
notes | Fetching compressed mmCIF 1xd2 from
http://files.rcsb.org/download/1xd2.cif  
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif  
  
1xd2 title:  
Crystal Structure of a ternary Ras:SOS:Ras*GDP complex [more info...]  
  
Chain information for 1xd2 #1  
---  
Chain | Description  
A | Transforming protein p21/H-Ras-1  
B | Transforming protein p21/H-Ras-1  
C | Son of sevenless protein homolog 1  
  
Non-standard residues in 1xd2 #1  
---  
MG — magnesium ion  
PO4 — phosphate ion  
  

> set bgColor white

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> show surfaces

> open 1xd2 format mmcif fromDatabase pdb

Summary of feedback from opening 1xd2 fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 8303  
  
1xd2 title:  
Crystal Structure of a ternary Ras:SOS:Ras*GDP complex [more info...]  
  
Chain information for 1xd2 #2  
---  
Chain | Description  
A | Transforming protein p21/H-Ras-1  
B | Transforming protein p21/H-Ras-1  
C | Son of sevenless protein homolog 1  
  
Non-standard residues in 1xd2 #2  
---  
MG — magnesium ion  
PO4 — phosphate ion  
  

> ui mousemode right clip

> ui mousemode right clip

> ui mousemode right "tape measure"

> toolshed show "Basic Actions"

> toolshed show "Command Line Interface"

> toolshed show "Model Panel"

> close #2

> toolshed show Clashes

> clashes

2 clashes  

> marker segment #2 position -4.694,42.78,56.38 toPosition -5.027,44.4,58.3
> color yellow radius 0.1 label 2.529 labelHeight 0.2529 labelColor yellow

> hide #!1 models

> show #!1 models

> marker segment #2 position 6.094,20.38,72.88 toPosition 11.92,18.41,66.2
> color yellow radius 0.1 label 9.079 labelHeight 0.9079 labelColor yellow

> close #2

> close #1

> open 4eah

Summary of feedback from opening 4eah fetched from pdb  
---  
note | Fetching compressed mmCIF 4eah from
http://files.rcsb.org/download/4eah.cif  
  
Fetching url http://files.rcsb.org/download/4eah.cif failed: <urlopen error
Got 142030 bytes when 583122 were expected>  

> open 1tub

Summary of feedback from opening 1tub fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 8458  
notes | Fetching compressed mmCIF 1tub from
http://files.rcsb.org/download/1tub.cif  
Fetching CCD GTP from http://ligand-expo.rcsb.org/reports/G/GTP/GTP.cif  
Fetching CCD TXL from http://ligand-expo.rcsb.org/reports/T/TXL/TXL.cif  
  
1tub title:  
Tubulin α-β dimer, electron diffraction [more info...]  
  
Chain information for 1tub #1  
---  
Chain | Description  
A | tubulin  
B | tubulin  
  
Non-standard residues in 1tub #1  
---  
TXL — taxotere  
  

> hide /A target abp

> hide /A target abp

> hide /A target abp

> hide /A target abp

> hide /A target abp

> hide /A target abp

> hide /A target abp

> show /A target abp

> show /A target abp

> show /A target abp

> hide /A target abp

> hide /A target abp

> hide /A target abp

> hide /A target abp

> hide /A target abp

> hide /A target c

> hide /A target c

> show /A target c

> close

> open 1tub

Summary of feedback from opening 1tub fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 8458  
  
1tub title:  
Tubulin α-β dimer, electron diffraction [more info...]  
  
Chain information for 1tub #1  
---  
Chain | Description  
A | tubulin  
B | tubulin  
  
Non-standard residues in 1tub #1  
---  
TXL — taxotere  
  

> marker segment #2 position -50.69,43.53,-33.09 toPosition
> -50.69,43.53,-33.09 color yellow radius 0.1 label 0 labelHeight 0.2
> labelColor yellow

> toolshed show "Basic Actions"

> toolshed show Shell

> close #1

> close

> open 6SWN

Summary of feedback from opening 6SWN fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GLU" near line 2127  
notes | Fetching compressed mmCIF 6swn from
http://files.rcsb.org/download/6swn.cif  
Fetching CCD LWB from http://ligand-expo.rcsb.org/reports/L/LWB/LWB.cif  
Fetching CCD EDO from http://ligand-expo.rcsb.org/reports/E/EDO/EDO.cif  
  
6swn title:  
N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH iBET-BD1 (GSK778) [more info...]  
  
Chain information for 6swn #1  
---  
Chain | Description  
AAA | Bromodomain-containing protein 4  
  
Non-standard residues in 6swn #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
LWB —
4-[2-(methoxymethyl)-1-[(1~{R})-1-phenylethyl]-8-[[(3~{S})-pyrrolidin-3-yl]methoxy]imidazo[4,5-c]quinolin-7-yl]-3,5-dimethyl-1,2-oxazole  
  

> rainbow

> open 6SWQ

Summary of feedback from opening 6SWQ fetched from pdb  
---  
warnings | Unable to fetch template for 'LW5': might be missing bonds  
Unable to fetch template for 'LW5': might be missing bonds  
Missing or invalid residue template for LW5 #204 in chain AAA  
note | Fetching compressed mmCIF 6swq from
http://files.rcsb.org/download/6swq.cif  
  
6swq title:  
N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH iBET-BD2 (GSK046) [more info...]  
  
Chain information for 6swq #2  
---  
Chain | Description  
AAA | Bromodomain-containing protein 4  
  
Non-standard residues in 6swq #2  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
LW5 —
4-acetamido-3-fluoranyl-~{N}-(4-oxidanylcyclohexyl)-5-[(1~{S})-1-phenylethoxy]benzamide  
  

> close #1

Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> close

> open 6SWQ

Summary of feedback from opening 6SWQ fetched from pdb  
---  
note | Fetching CCD LW5 from http://ligand-expo.rcsb.org/reports/L/LW5/LW5.cif  
  
6swq title:  
N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH iBET-BD2 (GSK046) [more info...]  
  
Chain information for 6swq #1  
---  
Chain | Description  
AAA | Bromodomain-containing protein 4  
  
Non-standard residues in 6swq #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
LW5 —
4-acetamido-3-fluoranyl-~{N}-(4-oxidanylcyclohexyl)-5-[(1~{S})-1-phenylethoxy]benzamide  
  

> rainbow

Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.5 (19F101)
      Kernel Version: Darwin 19.5.0
      Time since boot: 2 days 17:00

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.01.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Change History (3)

comment:1 by pett, 5 years ago

Component: Unassigned → Structure Analysis
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → tape-measure mode mode using dead MarkerSet

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Tape measure marker set was closed. Subsequent measurements recreated it, but a subsequent click and release on empty space which clears the marker set raised this error.

comment:3 by pett, 5 years ago

Summary: tape-measure mode mode using dead MarkerSet → tape-measure mouse mode using dead MarkerSet
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