Opened 6 years ago

Closed 6 years ago

#2582 closed defect (fixed)

Non-ASCII to log produces error

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Logging Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-862.14.4.el7.x86_64-x86_64-with-centos-7.5.1804-Core
ChimeraX Version: 0.9 (2019-06-06)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /mol/ban/letea/Kraken-Tea/Manuscript-prep/Figures/pdbs/Derived-from-
Krak-B-Complete_RSR-RealSpaceRefine_17/B-IF5-GTPcoord-afterRSR2.pdb
/mol/ban/letea/Kraken-Tea/Manuscript-prep/Figures/pdbs/Derived-from-Krak-B-
Complete_RSR-RealSpaceRefine_17/B-SAF3.pdb /mol/ban/letea/Kraken-
Tea/Manuscript-prep/Figures/pdbs/Derived-from-Krak-B-Complete_RSR-
RealSpaceRefine_17/B-RNA2.pdb /mol/ban/letea/Kraken-Tea/Manuscript-
prep/Figures/pdbs/Derived-from-Krak-B-Complete_RSR-
RealSpaceRefine_17/B-HD2.pdb /mol/ban/letea/Kraken-Tea/Manuscript-
prep/Figures/pdbs/Derived-from-Krak-B-Complete_RSR-
RealSpaceRefine_17/B-HC2.pdb /mol/ban/letea/Kraken-Tea/Manuscript-
prep/Figures/pdbs/Derived-from-Krak-B-Complete_RSR-
RealSpaceRefine_17/B-Unk2.pdb /mol/ban/letea/Kraken-Tea/Manuscript-
prep/Figures/pdbs/Derived-from-Krak-B-Complete_RSR-
RealSpaceRefine_17/B-BD2.pdb /mol/ban/letea/Kraken-Tea/Manuscript-
prep/Figures/pdbs/Derived-from-Krak-B-Complete_RSR-
RealSpaceRefine_17/B-BC2.pdb

  
  
  
  
  
  
  
  
Chain information for B-IF5-GTPcoord-afterRSR2.pdb #1.1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for B-SAF3.pdb #1.2  
---  
Chain | Description  
7 | No description available  
O | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
  
Chain information for B-RNA2.pdb #1.3  
---  
Chain | Description  
A | No description available  
  
Chain information for B-HD2.pdb #1.4  
---  
Chain | Description  
B | No description available  
C | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
T | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
  
Chain information for B-HC2.pdb #1.5  
---  
Chain | Description  
C | No description available  
I | No description available  
J | No description available  
N | No description available  
R | No description available  
S | No description available  
g | No description available  
i | No description available  
k | No description available  
  
Chain information for B-Unk2.pdb #1.6  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
  
Chain information for B-BD2.pdb #1.7  
---  
Chain | Description  
A | No description available  
D | No description available  
I | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
U | No description available  
Z | No description available  
a | No description available  
  
Chain information for B-BC2.pdb #1.8  
---  
Chain | Description  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
K | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
U | No description available  
a | No description available  
b | No description available  
d | No description available  
j | No description available  
m | No description available  
n | No description available  
p | No description available  
q | No description available  
r | No description available  
v | No description available  
  

> set bgColor white

> set silhouettes true

> lighting soft

> hide atoms

> hide cartoons

> show #1.1 cartoons

> dssp #1.1

> show #1.2/g cartoons

> show #1.3 atoms

> style #1.3 sphere

Changed 13122 atom styles  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #1.3 cartoons

> hide #1.3 cartoons

> hide #1.3 atoms

> show #1.3 atoms

> style #1.3 stick

Changed 13122 atom styles  

Expected a keyword  

> hide

> hide #1.3 cartoons

> hide #1.3 atoms

> show #1.3 atoms

> nucleotides selAtoms atoms

Expected a keyword  

> style #1.3 sphere

Changed 13122 atom styles  

> color #1.3 "lavender blush"

> color #1.3 "lavender blush" transparency 0.80

> lighting soft

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> view matrix camera
0.18561,0.23726,0.95355,1367.5,-0.98038,-0.02079,0.19601,413.89,0.066331,-0.97123,0.22875,524.88

> lighting soft

> cartoon style modeHelix tube radius 2 sides 24 thickness 0.9

> color #1.3 "lavender blush" transparency 80

> color #1.1/A "medium orchid"

> color #1.1/B "cadet blue"

> view matrix camera
0.18561,0.23726,0.95355,1367.5,-0.98038,-0.02079,0.19601,413.89,0.066331,-0.97123,0.22875,524.88

> hide #1.1/B

> hide #1.1/B cartoons

> toolshed show "Side View"

> save image /mol/ban/letea/Kraken-Tea/Manuscript-prep/Figures/AP-site-
occupation/AP-site-IF-RNA-SAFhelp_1.png width 1099 height 696

> color #1.1/A "olive drab"

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/log/tool.py", line 218, in cm_save  
self.log.save(filename)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/log/tool.py", line 430, in save  
f.write(self.page_source)  
UnicodeEncodeError: 'ascii' codec can't encode character '\xa9' in position
375: ordinal not in range(128)  
  
UnicodeEncodeError: 'ascii' codec can't encode character '\xa9' in position
375: ordinal not in range(128)  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/log/tool.py", line 430, in save  
f.write(self.page_source)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 396.26
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Logging
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Non-ASCII to log produces error

comment:2 by Eric Pettersen, 6 years ago

Resolution: → fixed
Status: assigned → closed

I believe this was fixed on August 13th by c2d6b7fac29e625abbb53bb75011710296e6c9b5

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