Help Viewer: _generate_index() missing 1 required positional argument: 'logger'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-17.5.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-12-11)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-12-11)  
How to cite UCSF ChimeraX  

> open 6ek0 fromDatabase pdb

6ek0 title:  
High-resolution cryo-EM structure of the human 80S ribosome [more info...]  
  
Chain information for 6ek0 #1  
---  
Chain | Description  
L5 | 28S ribosomal RNA  
L7 | 5S ribosomal RNA  
L8 | 5.8S ribosomal RNA  
LA | 60S ribosomal protein L8  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6  
LF | 60S ribosomal protein L7  
LG | 60S ribosomal protein L7a  
LH | 60S ribosomal protein L9  
LI | 60S ribosomal protein L10-like  
LJ | 60S ribosomal protein L11  
LL | 60S ribosomal protein L13  
LM | 60S ribosomal protein L14  
LN | 60S ribosomal protein L15  
LO | 60S ribosomal protein L13a  
LP | 60S ribosomal protein L17  
LQ | 60S ribosomal protein L18  
LR | 60S ribosomal protein L19  
LS | 60S ribosomal protein L18a  
LT | 60S ribosomal protein L21  
LU | 60S ribosomal protein L22  
LV | 60S ribosomal protein L23  
LW | 60S ribosomal protein L24  
LX | 60S ribosomal protein L23a  
LY | 60S ribosomal protein L26  
LZ | 60S ribosomal protein L27  
La | 60S ribosomal protein L27a  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L35a  
Lg | 60S ribosomal protein L34  
Lh | 60S ribosomal protein L35  
Li | 60S ribosomal protein L36  
Lj | 60S ribosomal protein L37  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | Ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41  
Lo | 60S ribosomal protein L36a  
Lp | 60S ribosomal protein L37a  
Lr | 60S ribosomal protein L28  
Lz | 60S ribosomal protein L10a  
S2 | 18S ribosomal RNA  
S6 | Human initiator Met-tRNA-i  
SA | 40S ribosomal protein SA  
SB | 40S ribosomal protein S3a  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15a  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
Sf | Ubiquitin-40S ribosomal protein S27a  
Sg | Receptor of activated protein C kinase 1  
  
Non-standard residues in 6ek0 #1  
---  
B8H —
[(2~{R},3~{S},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
B8K — 7-acetyl, guanosine-5'-monophosphate  
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid  
B8Q — 3-methyl, cytidine-5'-monophosphate  
B8T — 4-methyl, cytidine-5'-monophosphate  
B8W — 6-methyl, guanosine-5'-monophosphate  
B9B — 6-propyl, guanosine-5'-monophosphate  
B9H — 2'-methyl, 3-propyl, cytidine-5'-monophosphate  
BGH —
[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-ethanoyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-4-methoxy-3-oxidanyl-
oxolan-2-yl]methyl dihydrogen phosphate  
E3C — 3-ethyl, cytidine-5'-monophosphate  
E6G — 6-ethyl, guanosine-5'-monophosphate  
E7G — 7-ethyl, guanosine-5'-monophosphate  
HMT —
(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine
(Homoharringtonine, Cephalotaxine, [3(R)]-4-methyl
2-hydroxy-2-(4-hydroxy-4-methylpentyl)butanedioate)  
HYG — hygromycin B (hygromix, antihelmycin, hydromycin B, destomysin,
antibiotic A-396-II)  
I4U — 4-isopropyl, uridine-5'-monophosphate  
M7A — 7-methyl, adenosine-5'-monophosphate  
MG — magnesium ion  
MHG — 2-methyl, 7-(3-methyl-pentane), guanosine-5'-monophosphate  
P4U — 4-propyl, uridine-5'-monophosphate  
P7G — 7-propyl, guanosine-5'-monophosphate  
ZN — zinc ion  
  
  

> lighting soft

> lighting full

> lighting soft

> set bgColor white

> view cofr false

> set silhouettes true

> set silhouettes false

> set silhouettes true

> lighting flat

> lighting flat

> lighting flat

> lighting soft

> close

> pwd

Current working directory is: /Users/lijuanyin/Desktop  

> open ~/Users/lijuanyin/project/jen/jd_process/relion_locres_filtered.mrc

File not found:
/Users/lijuanyin/Users/lijuanyin/project/jen/jd_process/relion_locres_filtered.mrc  

> open /Users/lijuanyin/project/jen/jd_process/relion_locres_filtered.mrc

Opened relion_locres_filtered.mrc, grid size 400,400,400, pixel 1.08, shown at
level 0.101, step 2, values float32  

> close

> open /Users/lijuanyin/project/jen/jd_process/relion_locres_filtered.mrc step
1 level 0.05

Opened relion_locres_filtered.mrc, grid size 400,400,400, pixel 1.08, shown at
level 0.101, step 2, values float32  
Fetching url http://files.rcsb.org/download/step.cif failed: HTTP Error 404:
Not Found  

Expected a density maps specifier or a keyword  

> volume #1 step 1 level 0.05

Missing or invalid "surfaces" argument: empty atom specifier  

> surface dust #1

> surface dust #1 size 10

> open /Users/lijuanyin/project/jen/yeast_los2_20181212.pdb

Summary of feedback from opening
/Users/lijuanyin/project/jen/yeast_los2_20181212.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.018 3.236 210963  
  
Ignored bad PDB record found on line 23  
ANGLE : 1.337 105.456 309686  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.072 2.984 38796  
  
16 messages similar to the above omitted  
  
Chain information for yeast_los2_20181212.pdb #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | 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  
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  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b f | No description available  
c | No description available  
d | No description available  
e | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
  

> cartoon #2

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> show selAtoms ribbons

> hide selAtoms ribbons

> show selAtoms surfaces

> hide selAtoms surfaces

> close

> open /Users/lijuanyin/project/jen/figure/relion_locres_filtered.mrc

Opened relion_locres_filtered.mrc, grid size 400,400,400, pixel 1.08, shown at
level 0.101, step 2, values float32  

> open /Users/lijuanyin/project/jen/figure/yeast_los2_20181212_L.pdb

Summary of feedback from opening
/Users/lijuanyin/project/jen/figure/yeast_los2_20181212_L.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 3 3 THRSA 10
ASNSA 21 1 12  
Start residue of secondary structure not found: HELIX 4 4 GLNSA 30 PHESA 38 1
9  
Start residue of secondary structure not found: HELIX 5 5 ASNSA 49 ILESA 67 1
19  
Start residue of secondary structure not found: HELIX 6 6 ARGSA 79 THRSA 93 1
15  
Start residue of secondary structure not found: HELIX 7 7 ASPSA 125 ALASA 130
1 6  
288 messages similar to the above omitted  
  
Chain information for yeast_los2_20181212_L.pdb #2  
---  
Chain | Description  
1 | No description available  
3 E | No description available  
4 | No description available  
5 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | 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  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | 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  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
  

> open /Users/lijuanyin/project/jen/figure/yeast_los2_20181212_S.pdb

Summary of feedback from opening
/Users/lijuanyin/project/jen/figure/yeast_los2_20181212_S.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 SERC5 8
GLNC5 44 1 37  
Start residue of secondary structure not found: HELIX 2 2 ASNC5 50 GLNC5 80 1
31  
Start residue of secondary structure not found: HELIX 149 149 ILELA 5 GLYLA 11
1 7  
Start residue of secondary structure not found: HELIX 150 150 ASPLA 33 HISLA
38 1 6  
Start residue of secondary structure not found: HELIX 151 151 PROLA 103 PROLA
108 1 6  
368 messages similar to the above omitted  
  
Chain information for yeast_los2_20181212_S.pdb #3  
---  
Chain | Description  
2 | No description available  
A F | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
G | No description available  
H J | No description available  
I | No description available  
K | 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  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | 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  
  

> volume #1 step 1 level 0.05

> surface dust #1 size 10

Unknown command: bg white  

> lighting soft

> set bgColor white

> alias cylinders cartoon style protein modeh tube rad 2 sides 24

> hide #!1 models

Expected an atom specifier or a keyword  

> cartoon #3 #2

> alias cylinders cartoon style protein modeh tube rad 2 sides 24

> hide selAtoms surfaces

> select #2

122774 atoms, 132330 bonds selected  

> select #3

73713 atoms, 78626 bonds selected  

> hide selAtoms surfaces

> style selAtoms stick

Changed 73713 atom styles  

> show selAtoms ribbons

> select #2

122774 atoms, 132330 bonds selected  

> hide selAtoms ribbons

> hide selAtoms surfaces

> hide selAtoms

> select #3

73713 atoms, 78626 bonds selected  

> hide selAtoms

> ~select #3

Nothing selected  

> cartoon #3 #2

> hide #2 #3 /a

> cartoon style protein modeHelix tube radius 2 sides 24

> nucleotides #2 #3 slab

> nucleotides #2 #3/2 slab

> nucleotides #2 #3/2 ladder

> nucleotides #3/2 ladder

> nucleotides #3/2 ladder hideAtoms false

> nucleotides #2 #3/2 slab

Traceback (most recent call last):  
File "/Applications/ChimeraX
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 217, in interceptRequest  
self._callback(info)  
File "/Applications/ChimeraX
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/help_viewer/tool.py", line 95, in link_clicked  
new_path = _generate_index(path)  
TypeError: _generate_index() missing 1 required positional argument: 'logger'  
  
TypeError: _generate_index() missing 1 required positional argument: 'logger'  
  
File "/Applications/ChimeraX
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/help_viewer/tool.py", line 95, in link_clicked  
new_path = _generate_index(path)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-1.66.31
OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Greg Couch]

Reproduced by clicking on documentation link for a command and then click on the document index icon link in the upper right hand corner. Fixed by adding missing argument.