ISOLDE/Clipper: 'NXmapHandler' object has no attribute 'set_display_style'

[ne272@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-01-24)
Description
Trying to associate real-space map with current model

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
  
File
"/Users/ne272/Downloads/Setup/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
  
self.init_available_from_cache(logger)  
  
File
"/Users/ne272/Downloads/Setup/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 449, in
init_available_from_cache  
  
abc.load_from_cache()  
  
File
"/Users/ne272/Downloads/Setup/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/available.py", line 64, in load_from_cache  
  
b = _build_bundle(d)  
  
File
"/Users/ne272/Downloads/Setup/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/available.py", line 251, in _build_bundle  
  
keywords = _extract_extra_keywords(keywords)  
  
File
"/Users/ne272/Downloads/Setup/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/installed.py", line 270, in
_extract_extra_keywords  
  
all_kwds = [k.strip() for k in kwds.split(',')]  
  
AttributeError: 'list' object has no attribute 'split'  
  
  
  
  
UCSF ChimeraX version: 0.9 (2019-01-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/ne272/Documents/Papers/Kargas 2019/validation/StateVI/State-
VI-B3_Class10_model_final_real_space_refined_4-coot-0_real_space_refined-
coot-2_rpl24_Zincs_H38-coot-2FH.pdb"

Summary of feedback from opening /Users/ne272/Documents/Papers/Kargas
2019/validation/StateVI/State-
VI-B3_Class10_model_final_real_space_refined_4-coot-0_real_space_refined-
coot-2_rpl24_Zincs_H38-coot-2FH.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
  
  
Ignored bad PDB record found on line 410  
ALLOWED : 8.08 %  
  
Ignored bad PDB record found on line 411  
CIS-PROLINE : 0.829875518672  
  
Ignored bad PDB record found on line 412  
CIS-GENERAL : 0.0  
  
Ignored bad PDB record found on line 413  
FAVORED : 91.88 %  
  
17 messages similar to the above omitted  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
115281 messages similar to the above omitted  
  
Chain information for State-
VI-B3_Class10_model_final_real_space_refined_4-coot-0_real_space_refined-
coot-2_rpl24_Zincs_H38-coot-2FH.pdb #1  
---  
Chain | Description  
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  
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 | 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  
q | No description available  
t | No description available  
v | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> style selAtoms stick

Changed 215272 atom styles  

> lighting flat

> open "/Users/ne272/Documents/Papers/Kargas 2019/validation/StateVI/State-
VI.mrc"

Opened State-VI.mrc, grid size 360,360,360, pixel 1.07, shown at level 0.0891,
step 2, values float32  

> ui mousemode rightMode zoom

> color selAtoms byhetero

> color selAtoms bychain

> toolshed show "Side View"

> set bgColor white

> lighting shadows true intensity 0.5

> lighting soft

> lighting shadows true intensity 0.5

> lighting full

> lighting flat

> toolshed show ISOLDE

Expected a keyword  

Expected a keyword  

Chain information for State-
VI-B3_Class10_model_final_real_space_refined_4-coot-0_real_space_refined-
coot-2_rpl24_Zincs_H38-coot-2FH.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.3/B | No description available  
1.3/C | No description available  
1.3/D | No description available  
1.3/E | No description available  
1.3/F | No description available  
1.3/G | No description available  
1.3/H | No description available  
1.3/J | No description available  
1.3/K | No description available  
1.3/L | No description available  
1.3/M | No description available  
1.3/N | No description available  
1.3/O | No description available  
1.3/P | No description available  
1.3/Q | No description available  
1.3/R | No description available  
1.3/S | No description available  
1.3/T | No description available  
1.3/U | No description available  
1.3/V | No description available  
1.3/W | No description available  
1.3/X | No description available  
1.3/Y | No description available  
1.3/Z | No description available  
1.3/a | No description available  
1.3/b | No description available  
1.3/c | No description available  
1.3/d | No description available  
1.3/e | No description available  
1.3/f | No description available  
1.3/g | No description available  
1.3/h | No description available  
1.3/i | No description available  
1.3/j | No description available  
1.3/k | No description available  
1.3/l | No description available  
1.3/m | No description available  
1.3/n | No description available  
1.3/q | No description available  
1.3/t | No description available  
1.3/v | No description available  
1.3/x | No description available  
1.3/y | No description available  
1.3/z | No description available  
  
Done loading forcefield  
Traceback (most recent call last):  
File "/Users/ne272/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 1445, in
_add_real_space_map_from_gui  
self.add_real_space_map(existing_volume=v, to_model=self.selected_model)  
File "/Users/ne272/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 1337, in add_real_space_map  
nxmap = map_mgr.nxmapset.add_nxmap_handler_from_volume(existing_volume)  
File "/Users/ne272/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/nxmapset.py", line 59, in
add_nxmap_handler_from_volume  
color=color, style=style, contour=contour)  
File "/Users/ne272/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/nxmapset.py", line 95, in
set_nxmap_display_style  
nxmap_handler.set_display_style(style)  
AttributeError: 'NXmapHandler' object has no attribute 'set_display_style'  
  
AttributeError: 'NXmapHandler' object has no attribute 'set_display_style'  
  
File "/Users/ne272/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/nxmapset.py", line 95, in
set_nxmap_display_style  
nxmap_handler.set_display_style(style)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/ne272/Downloads/Setup/ChimeraX.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
"/Users/ne272/Downloads/Setup/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3413, in _update_drawings  
v.update_drawings()  
File
"/Users/ne272/Downloads/Setup/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 654, in update_drawings  
self._update_surfaces()  
File
"/Users/ne272/Downloads/Setup/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 669, in _update_surfaces  
s.update_surface(show_mesh, ro)  
TypeError: update_surface() takes 2 positional arguments but 3 were given  
  
Error processing trigger "graphics update": update_surface() takes 2
positional arguments but 3 were given:  
TypeError: update_surface() takes 2 positional arguments but 3 were given  
  
File
"/Users/ne272/Downloads/Setup/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 669, in _update_surfaces  
s.update_surface(show_mesh, ro)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.

[pett]

Reported by Norberto Urquijo

[Tristan Croll]

Duplicate of #2214.