Session close/reset: NameError: name 'task' is not defined

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-18.5.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-09)
Description
command "close session" gives  NameError: name 'task' is not defined

... I think it is only after webservice usage, e.g. running Modeller even if it has finished running

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> open presets.cxc

> alias cardef car style modeh def arrows t arrowshelix f arrowscale 2 wid 2
thick 0.4 sides 12 div 20; car style ~(nucleic|strand) x round; car style
(nucleic|strand) x rect

> alias nospheres style (protein|nucleic|solvent) & @@draw_mode=0 stick

> alias nucrib cardef; car style nucleic x round width 1.6 thick 1.6

> alias cylinders cardef; car style protein modeh tube rad 2 sides 24 thick
0.6

> alias licorice cardef; car style protein modeh default arrows f x round
width 1 thick 1

> alias cartoon1 surf hide; nospheres; cartoon; cardef; nuc tube/slab shape
box

> alias cartoon2 surf hide; nospheres; cartoon; cylinders; car style nucleic x
round width 1.6 thick 1.6; nuc stubs

> alias cartoon3 surf hide; nospheres; cartoon; licorice; car style nucleic x
round width 1.6 thick 1.6; nuc tube/slab shape ellipsoid

> alias surfw nospheres; surface; color white targ s trans 80

> alias surfat nospheres; surface; color fromatoms targ s trans 70

> alias surfc nospheres; surface; color bychain targ s trans 0

> alias surfm nospheres; surface; color bymodel targ s trans 0

> alias pub set bgcolor white silhouettes t

> alias unpub ~set bgcolor; set silhouettes f

executed presets.cxc  
executed startup.cxc  
UCSF ChimeraX version: 0.9 (2019-04-09)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd /Users/meng/demo/mavdemo

Current working directory is: /Users/meng/demo/mavdemo  

> open peclyase.msf

Summary of feedback from opening peclyase.msf  
---  
note | Alignment identifier is peclyase.msf  
  
Opened 7 sequences from peclyase.msf  

> open 1bn8

Summary of feedback from opening 1bn8 fetched from pdb  
---  
note | Fetching compressed mmCIF 1bn8 from
http://files.rcsb.org/download/1bn8.cif  
  
1bn8 title:  
Bacillus subtilis pectate lyase [more info...]  
  
Chain information for 1bn8 #1  
---  
Chain | Description  
A | protein (pectate lyase)  
  
Non-standard residues in 1bn8 #1  
---  
CA — calcium ion  
  
Associated 1bn8 chain A to PEL_BACSU with 0 mismatches  
  

> open 1jta

Summary of feedback from opening 1jta fetched from pdb  
---  
note | Fetching compressed mmCIF 1jta from
http://files.rcsb.org/download/1jta.cif  
  
1jta title:  
Crystal Structure of Pectate Lyase A (C2 form) [more info...]  
  
Chain information for 1jta #2  
---  
Chain | Description  
A | pectate lyase A  
  
Non-standard residues in 1jta #2  
---  
SO4 — sulfate ion  
  
Associated 1jta chain A to PELA_ERWCH with 0 mismatches  
  

> toolshed show '"Modeller Comparative"'

> modeller comparative peclyase.msf:1 combineTemplates true numModels 1 fast
true hetPreserve false hydrogens false waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1554845604605-1109522449  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1554845604605-1109522449  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1554845604605-1109522449 finished  
Matchmaker 1bn8, chain A (#1) with PELC_ERWCH, chain (blank) (#), sequence
alignment score = 358.3  
RMSD between 183 pruned atom pairs is 0.926 angstroms; (across all 315 pairs:
9.380)  
  
Associated PELC_ERWCH chain (blank) to PELC_ERWCH with 0 mismatches  
Chain information for PELC_ERWCH  
---  
Chain | Description  
3.1/  | No description available  
  

> mmaker #2 to #1

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 1bn8, chain A (#1) with 1jta, chain A (#2), sequence alignment
score = 813.4  
RMSD between 273 pruned atom pairs is 0.843 angstroms; (across all 347 pairs:
2.376)  
  

> toolshed show '"Modeller Comparative"'

No target sequence chosen for alignment peclyase.msf  

> modeller comparative peclyase.msf:1 combineTemplates true numModels 1 fast
true hetPreserve false hydrogens false waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service15548456956651203543089  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service15548456956651203543089  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service15548456956651203543089 finished  
Matchmaker 1bn8, chain A (#1) with PELC_ERWCH, chain (blank) (#), sequence
alignment score = 348.1  
RMSD between 183 pruned atom pairs is 0.934 angstroms; (across all 315 pairs:
9.379)  
  
Associated PELC_ERWCH chain (blank) to PELC_ERWCH with 0 mismatches  
Chain information for PELC_ERWCH  
---  
Chain | Description  
4.1/  | No description available  
  

> view

> toolshed show '"Modeller Comparative"'

No target sequence chosen for alignment peclyase.msf  

> modeller comparative peclyase.msf:1 combineTemplates false numModels 1 fast
true hetPreserve false hydrogens false waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1554845795173366598689  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1554845795173366598689  
stdout.txt = standard output  
stderr.txt = standard error  

> toolshed show '"Modeller Comparative"'

Modeller job ID appModeller9v8Service1554845795173366598689 finished  
Matchmaker 1bn8, chain A (#1) with PELC_ERWCH, chain A (#), sequence alignment
score = 145.9  
Matchmaker 1jta, chain A (#2) with PELC_ERWCH, chain B (#), sequence alignment
score = 100.6  
Matchmaker PELC_ERWCH, chain (blank) (#3.1) with PELC_ERWCH, chain C (#),
sequence alignment score = 1496.3  
Matchmaker PELC_ERWCH, chain (blank) (#4.1) with PELC_ERWCH, chain D (#),
sequence alignment score = 1490.3  
RMSD between 154 pruned atom pairs is 1.486 angstroms; (across all 1358 pairs:
15.007)  
  
Associated PELC_ERWCH chain A to PELC_ERWCH with 0 mismatches  
Associated PELC_ERWCH chain B to PELC_ERWCH with 0 mismatches  
Associated PELC_ERWCH chain C to PELC_ERWCH with 0 mismatches  
Associated PELC_ERWCH chain D to PELC_ERWCH with 0 mismatches  
Chain information for PELC_ERWCH  
---  
Chain | Description  
5.1/A 5.1/B 5.1/C 5.1/D | No description available  
  

> close session

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 253, in execute  
cmd.run(cmd_text)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2628, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/close.py", line 60, in close_session  
session.reset()  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 411, in reset  
sm.reset_state(container, self)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 421, in reset_state  
task.terminate()  
NameError: name 'task' is not defined  
  
NameError: name 'task' is not defined  
  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 421, in reset_state  
task.terminate()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.8.38
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Conrad Huang]

Fixed in 1922f9e15

Fix multiple bugs introduced by f06fb63.