3D labels: name 'session' is not defined

[ubaumann@…]

The following bug report has been submitted:
Platform:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.1.dev202007121748 (2020-07-12 17:48:02 UTC)
Description
(Describe the actions that caused this problem to occur here)

I try to measure distances
Thak you!

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.1.dev202007121748 (2020-07-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ubaumann/Sync/Geteilt-mit-Lena/hsp47_rgf_refine_32.pdb

Summary of feedback from opening /Users/ubaumann/Sync/Geteilt-mit-
Lena/hsp47_rgf_refine_32.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2020-06-21 Time 13:35:18 CEST +0200 (1592739318.65 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/home/abraham/Storage/projects/hsp47/client/rgf/cryst1/phenix/refine/Refine_31/hsp47_rgf_refine_31.mtz  
  
68 messages similar to the above omitted  
  
Chain information for hsp47_rgf_refine_32.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E G | No description available  
F | No description available  
H | No description available  
  

> hide atoms

> show cartoons

> select /B:35-414

2938 atoms, 2997 bonds, 2 pseudobonds, 2 models selected  

> select /C:0-20

134 atoms, 146 bonds, 1 model selected  

> select /D:0-19

126 atoms, 137 bonds, 1 model selected  

> select /E:0-19

126 atoms, 137 bonds, 1 model selected  

> select /G:0-19

126 atoms, 137 bonds, 1 model selected  
Drag select of 412 residues, 2 pseudobonds  

> select up

3320 atoms, 3412 bonds, 2 pseudobonds, 2 models selected  

> hide (#!1 & sel) target a

> cartoon hide (#!1 & sel)

> open /Users/ubaumann/Documents/Papers/Hsp47-HisMutants/complex-klmno.pdb

Summary of feedback from opening
/Users/ubaumann/Documents/Papers/Hsp47-HisMutants/complex-klmno.pdb  
---  
warning | CONECT record for nonexistent atom: 2958  
  
Chain information for complex-klmno.pdb #2  
---  
Chain | Description  
K | No description available  
  

> close #2

> open /Users/ubaumann/Documents/Papers/HSp47-Clients/3zha-complex.pdb

Summary of feedback from opening
/Users/ubaumann/Documents/Papers/HSp47-Clients/3zha-complex.pdb  
---  
warnings | Cannot find LINK/SSBOND residue ACE (0 )  
Cannot find LINK/SSBOND residue ACE (0 )  
Cannot find LINK/SSBOND residue ACE (0 )  
Cannot find LINK/SSBOND residue ACE (0 )  
Cannot find LINK/SSBOND residue ACE (0 )  
4 messages similar to the above omitted  
  
3zha-complex.pdb title:  
Molecular basis for the action of the collagen-specific chaperone HSP47
SERPINH1 and its structure-specific client recognition. [more info...]  
  
Chain information for 3zha-complex.pdb #2  
---  
Chain | Description  
C D | No description available  
H I J | No description available  
  
Non-standard residues in 3zha-complex.pdb #2  
---  
ACE — acetyl group  
SIN — succinic acid  
  

> hide sel cartoons

> select clear

Drag select of 6247 atoms, 6 pseudobonds, 7 bonds  

> hide sel atoms

> show sel cartoons

> select clear

> mmaker #2 to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker hsp47_rgf_refine_32.pdb, chain A (#1) with 3zha-complex.pdb, chain
D (#2), sequence alignment score = 1908.9  
RMSD between 357 pruned atom pairs is 0.612 angstroms; (across all 368 pairs:
0.859)  
  

> save /Users/ubaumann/Documents/Papers/Hsp47-Elena/overlay-rgf-3zha_klmno.cxs

> show atoms

> style stick

Changed 13296 atom styles  

> hide cartoons

Drag select of 2462 atoms, 2420 bonds  

> select up

2510 atoms, 2426 bonds, 1 model selected  

> select up

2708 atoms, 2646 bonds, 1 model selected  

> select up

3298 atoms, 3272 bonds, 1 model selected  

> hide sel target a

Drag select of 53 atoms, 51 bonds  

> select up

57 atoms, 52 bonds, 1 model selected  

> select up

81 atoms, 79 bonds, 1 model selected  

> select up

137 atoms, 136 bonds, 1 model selected  

> select up

3299 atoms, 2997 bonds, 1 model selected  

> hide sel target a

> hide :HOH

> color sel byhetero

> color sel byhetero

> select clear

> color byhetero

> ui tool show "Side View"

> ui mousemode right pivot

> mmaker #2/K to #1/A

No molecules/chains to match specified  

> mmaker #2/C to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker hsp47_rgf_refine_32.pdb, chain A (#1) with 3zha-complex.pdb, chain
C (#2), sequence alignment score = 1904.1  
RMSD between 362 pruned atom pairs is 0.527 angstroms; (across all 371 pairs:
0.768)  
  

> hide #!2 models

> select #1/A:385@OD2

1 atom, 1 model selected  

> distance #1/A:385@OD2 #1/C:11@NE

Distance between hsp47_rgf_refine_32.pdb #1/A ASP 385 OD2 and /C ARG 11 NE:
2.767Å  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/dist_monitor/monitor.py", line 104, in _changes_handler  
self._update_distances(pseudobonds=[pb])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/dist_monitor/monitor.py", line 130, in _update_distances  
settings=label_settings)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 361, in add_labels  
ol[o] = lo = label_class(o, view, **settings)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 815, in __init__  
size=size, height=height, font=font)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 619, in __init__  
has_graphics = session.main_view.render is not None  
NameError: name 'session' is not defined  
  
Error processing trigger "changes":  
NameError: name 'session' is not defined  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 619, in __init__  
has_graphics = session.main_view.render is not None  
  
See log for complete Python traceback.  
  

> select #1/A:385@OD1

1 atom, 1 model selected  

> distance #1/A:385@OD1 #1/C:11@NH2

Distance between hsp47_rgf_refine_32.pdb #1/A ASP 385 OD1 and /C ARG 11 NH2:
2.881Å  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/dist_monitor/monitor.py", line 104, in _changes_handler  
self._update_distances(pseudobonds=[pb])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/dist_monitor/monitor.py", line 130, in _update_distances  
settings=label_settings)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 361, in add_labels  
ol[o] = lo = label_class(o, view, **settings)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 815, in __init__  
size=size, height=height, font=font)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 619, in __init__  
has_graphics = session.main_view.render is not None  
NameError: name 'session' is not defined  
  
Error processing trigger "changes":  
NameError: name 'session' is not defined  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 619, in __init__  
has_graphics = session.main_view.render is not None  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GTX 775M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac14,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      Boot ROM Version: 143.0.0.0.0
      SMC Version (system): 2.15f7

Software:

    System Software Overview:

      System Version: macOS 10.15.5 (19F101)
      Kernel Version: Darwin 19.5.0
      Time since boot: 1 day 20:37

Graphics/Displays:

    NVIDIA GeForce GTX 775M:

      Chipset Model: NVIDIA GeForce GTX 775M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 2 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x119d
      Revision ID: 0x00a2
      ROM Revision: 3782
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9

[pett]

Reported by Ulrich Baumann

[Greg Couch]

Fixed.