Opened 6 years ago

Closed 6 years ago

#2055 closed defect (duplicate)

Surface geometry calculation: cannot convert float NaN to integer

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

Description 

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-01)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-06-01)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/aiste/Downloads/coral7.pdb

Summary of feedback from opening /Users/aiste/Downloads/coral7.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Project description:  
  
Ignored bad PDB record found on line 2  
REMARK j: 75 T: 0.411E-02 Suc: 96 Eva: 796930 CPU: 0.116E+05 F: 2.4870 Pen:
1.4768  
  
Ignored bad PDB record found on line 3  
REMARK The best Chi^2 values: 1.01021  
  
Ignored bad PDB record found on line 4  
REMARK Cross: 0.00024 Center: 1.45307  
  
Ignored bad PDB record found on line 5  
REMARK Cont Penalt.: 0.00000  
  
9 messages similar to the above omitted  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
95 messages similar to the above omitted  
Ignored bad PDB record found on line 1449  
REMARK *******************************  
  
Ignored bad PDB record found on line 1450  
REMARK Evaluated from PDB file 2.pdb  
  
Ignored bad PDB record found on line 1451  
REMARK Old center positioned at 9.047 28.292 -40.031  
  
Ignored bad PDB record found on line 1452  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 1453  
REMARK New center positioned at 9.047 28.292 -40.031  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
194 messages similar to the above omitted  
Ignored bad PDB record found on line 1655  
REMARK *******************************  
  
Ignored bad PDB record found on line 1656  
REMARK Evaluated from PDB file 3.pdb  
  
Ignored bad PDB record found on line 1657  
REMARK Old center positioned at 24.230 40.969 -48.177  
  
Ignored bad PDB record found on line 1658  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 1659  
REMARK New center positioned at 24.230 40.969 -48.177  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
463 messages similar to the above omitted  
Ignored bad PDB record found on line 2130  
REMARK *******************************  
  
Ignored bad PDB record found on line 2131  
REMARK Evaluated from PDB file 4.pdb  
  
Ignored bad PDB record found on line 2132  
REMARK Old center positioned at -26.383 41.634 -20.071  
  
Ignored bad PDB record found on line 2133  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 2134  
REMARK New center positioned at -26.383 41.634 -20.071  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1332 messages similar to the above omitted  
Ignored bad PDB record found on line 5688  
REMARK *******************************  
  
Ignored bad PDB record found on line 5689  
REMARK Evaluated from PDB file 5.pdb  
  
Ignored bad PDB record found on line 5690  
REMARK Old center positioned at -28.198 23.077 8.429  
  
Ignored bad PDB record found on line 5691  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 5692  
REMARK New center positioned at -28.198 23.077 8.429  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1060 messages similar to the above omitted  
Ignored bad PDB record found on line 6760  
REMARK *******************************  
  
Ignored bad PDB record found on line 6761  
REMARK Evaluated from PDB file 6.pdb  
  
Ignored bad PDB record found on line 6762  
REMARK Old center positioned at -13.895 72.598 -36.399  
  
Ignored bad PDB record found on line 6763  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 6764  
REMARK New center positioned at -13.895 72.598 -36.399  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
237 messages similar to the above omitted  
Ignored bad PDB record found on line 7009  
REMARK *******************************  
  
Ignored bad PDB record found on line 7010  
REMARK Evaluated from PDB file domain_3PSJ.pdb  
  
Ignored bad PDB record found on line 7011  
REMARK Old center positioned at 49.673 35.982 45.003  
  
Ignored bad PDB record found on line 7012  
REMARK Rotated by Euler angles 352.707 67.593 46.057  
  
Ignored bad PDB record found on line 7013  
REMARK New center positioned at 6.140 67.499 -52.089  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1589 messages similar to the above omitted  
  
Chain information for coral7.pdb #1  
---  
Chain | Description  
| 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  
  

> open /Users/aiste/Downloads/coral8.pdb

Summary of feedback from opening /Users/aiste/Downloads/coral8.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Project description:  
  
Ignored bad PDB record found on line 2  
REMARK j: 75 T: 0.411E-02 Suc: 97 Eva: 797197 CPU: 0.116E+05 F: 2.4586 Pen:
1.4571  
  
Ignored bad PDB record found on line 3  
REMARK The best Chi^2 values: 1.00155  
  
Ignored bad PDB record found on line 4  
REMARK Cross: 0.00029 Center: 1.42812  
  
Ignored bad PDB record found on line 5  
REMARK Cont Penalt.: 0.00000  
  
9 messages similar to the above omitted  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
95 messages similar to the above omitted  
Ignored bad PDB record found on line 1449  
REMARK *******************************  
  
Ignored bad PDB record found on line 1450  
REMARK Evaluated from PDB file 2.pdb  
  
Ignored bad PDB record found on line 1451  
REMARK Old center positioned at 9.047 28.292 -40.031  
  
Ignored bad PDB record found on line 1452  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 1453  
REMARK New center positioned at 9.047 28.292 -40.031  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
194 messages similar to the above omitted  
Ignored bad PDB record found on line 1655  
REMARK *******************************  
  
Ignored bad PDB record found on line 1656  
REMARK Evaluated from PDB file 3.pdb  
  
Ignored bad PDB record found on line 1657  
REMARK Old center positioned at 24.230 40.969 -48.177  
  
Ignored bad PDB record found on line 1658  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 1659  
REMARK New center positioned at 24.230 40.969 -48.177  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
463 messages similar to the above omitted  
Ignored bad PDB record found on line 2130  
REMARK *******************************  
  
Ignored bad PDB record found on line 2131  
REMARK Evaluated from PDB file 4.pdb  
  
Ignored bad PDB record found on line 2132  
REMARK Old center positioned at -26.383 41.634 -20.071  
  
Ignored bad PDB record found on line 2133  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 2134  
REMARK New center positioned at -26.383 41.634 -20.071  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1332 messages similar to the above omitted  
Ignored bad PDB record found on line 5688  
REMARK *******************************  
  
Ignored bad PDB record found on line 5689  
REMARK Evaluated from PDB file 5.pdb  
  
Ignored bad PDB record found on line 5690  
REMARK Old center positioned at -28.198 23.077 8.429  
  
Ignored bad PDB record found on line 5691  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 5692  
REMARK New center positioned at -28.198 23.077 8.429  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1060 messages similar to the above omitted  
Ignored bad PDB record found on line 6760  
REMARK *******************************  
  
Ignored bad PDB record found on line 6761  
REMARK Evaluated from PDB file 6.pdb  
  
Ignored bad PDB record found on line 6762  
REMARK Old center positioned at -13.895 72.598 -36.399  
  
Ignored bad PDB record found on line 6763  
REMARK Rotated by Euler angles 0.000 0.000 0.000  
  
Ignored bad PDB record found on line 6764  
REMARK New center positioned at -13.895 72.598 -36.399  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
237 messages similar to the above omitted  
Ignored bad PDB record found on line 7009  
REMARK *******************************  
  
Ignored bad PDB record found on line 7010  
REMARK Evaluated from PDB file domain_3PSJ.pdb  
  
Ignored bad PDB record found on line 7011  
REMARK Old center positioned at 49.673 35.982 45.003  
  
Ignored bad PDB record found on line 7012  
REMARK Rotated by Euler angles 327.825 66.437 65.120  
  
Ignored bad PDB record found on line 7013  
REMARK New center positioned at 11.599 67.625 -46.981  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1589 messages similar to the above omitted  
  
Chain information for coral8.pdb #2  
---  
Chain | Description  
| 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  
  

> set bgColor white

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> select #1:1239@CA

2 atoms selected  

> delete sel

> delete sel

> select clear

> delete sel

> delete sel

> select clear

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> matchmaker #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 coral7.pdb, chain D (#1) with coral8.pdb, chain D (#2), sequence
alignment score = 2262.1  
RMSD between 436 pruned atom pairs is 0.000 angstroms; (across all 436 pairs:
0.000)  
  

> morph #2,1

Computed 21 frame morph #3  

> coordset #3 1,21

> preset "overall look" publication

Preset expands to these ChimeraX commands: set bg white; set silhouettes t  

> toolshed show "Basic Actions"

> show #3/A target s

> show #3/B target s

> show #3/C target s

> show #3/E target s

> show #3/E target s

> show #3/F target s

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 556, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 160, in handle_scheme  
method(query)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 170, in _cb_show_hide  
run(self.session, cmd)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 47, in show  
show_surfaces(session, objects, only, undo_state)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 147, in show_surfaces  
surface(session, extra_atoms)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in surface  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 47, in apply_to_list  
return [func(*a) for a in args]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 47, in <listcomp>  
return [func(*a) for a in args]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in <lambda>  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 158, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in ses_surface_geometry  
for a in (2,1,0)]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in <listcomp>  
for a in (2,1,0)]  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in  
for a in (2,1,0)]  
  
See log for complete Python traceback.  
  

> show #3/F target s

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 556, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 160, in handle_scheme  
method(query)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 170, in _cb_show_hide  
run(self.session, cmd)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 47, in show  
show_surfaces(session, objects, only, undo_state)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 147, in show_surfaces  
surface(session, extra_atoms)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in surface  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 47, in apply_to_list  
return [func(*a) for a in args]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 47, in <listcomp>  
return [func(*a) for a in args]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in <lambda>  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 158, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in ses_surface_geometry  
for a in (2,1,0)]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in <listcomp>  
for a in (2,1,0)]  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in  
for a in (2,1,0)]  
  
See log for complete Python traceback.  
  

> show #3/G target s

> show #3/F target s

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 556, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 160, in handle_scheme  
method(query)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 170, in _cb_show_hide  
run(self.session, cmd)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 47, in show  
show_surfaces(session, objects, only, undo_state)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 147, in show_surfaces  
surface(session, extra_atoms)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in surface  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 47, in apply_to_list  
return [func(*a) for a in args]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 47, in <listcomp>  
return [func(*a) for a in args]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in <lambda>  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 158, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in ses_surface_geometry  
for a in (2,1,0)]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in <listcomp>  
for a in (2,1,0)]  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in  
for a in (2,1,0)]  
  
See log for complete Python traceback.  
  

> hide #3/G target abp

> hide #3/F target abp

> hide #3/E target abp

> hide #3/D target abp

> hide #3/D target abp

> show #3/D target abp

> show #3/D target s

> hide #3/G target abp

> hide #3/F target abp

> hide #3/E target abp

> hide #3/D target abp

> hide #3/C target abp

> hide #3/B target abp

> hide #3/A target abp

> show #3 target s

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 556, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 160, in handle_scheme  
method(query)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 170, in _cb_show_hide  
run(self.session, cmd)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 47, in show  
show_surfaces(session, objects, only, undo_state)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 147, in show_surfaces  
surface(session, extra_atoms)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in surface  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 70, in apply_to_list  
raise r  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 31, in run  
r = self.function(*s)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in <lambda>  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 158, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in ses_surface_geometry  
for a in (2,1,0)]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in <listcomp>  
for a in (2,1,0)]  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in  
for a in (2,1,0)]  
  
See log for complete Python traceback.  
  

> hide #!3.1 models

> hide #3 target abp

> show #3 target abp

> show #3/A target c

> hide #3/A target abp

> hide #3 target abp

> show #3 target abp

> show #3 target c

> hide #!3.6 models

> hide #!1.1 models

> hide #!3 models

> show #!3 models

> hide #!2.1 models

> show #3/G target s

> hide #3/G target abp

> show #3 target s

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 556, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 160, in handle_scheme  
method(query)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 170, in _cb_show_hide  
run(self.session, cmd)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 47, in show  
show_surfaces(session, objects, only, undo_state)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 147, in show_surfaces  
surface(session, extra_atoms)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in surface  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 70, in apply_to_list  
raise r  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 31, in run  
r = self.function(*s)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in <lambda>  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 158, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in ses_surface_geometry  
for a in (2,1,0)]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in <listcomp>  
for a in (2,1,0)]  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in  
for a in (2,1,0)]  
  
See log for complete Python traceback.  
  

> show #3 target s

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 556, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 160, in handle_scheme  
method(query)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 170, in _cb_show_hide  
run(self.session, cmd)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 47, in show  
show_surfaces(session, objects, only, undo_state)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 147, in show_surfaces  
surface(session, extra_atoms)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in surface  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 70, in apply_to_list  
raise r  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 31, in run  
r = self.function(*s)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in <lambda>  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 158, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in ses_surface_geometry  
for a in (2,1,0)]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in <listcomp>  
for a in (2,1,0)]  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in  
for a in (2,1,0)]  
  
See log for complete Python traceback.  
  

> lighting soft

> hide #3/A target c

> hide #3/A target abp

> hide #3/B target abp

> hide #3/C target abp

> hide #3/D target abp

> hide #3/E target abp

> hide #3/F target abp

> hide #3/G target abp

> delete sel

> select #3/F:1240

8 atoms, 7 bonds selected  

> select #3/F:1238

11 atoms, 10 bonds selected  

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> delete sel

> hide #3/G target c

> delete sel

> select clear

> hide #3/F target c

> delete sel

> show #3 target abp

> hide #3 target abp

> show #1 target abp

> hide #1 target abp

> show #1 target abp

> show #2 target abp

> hide #2 target abp

> show #3 target abp

> hide #3 target abp

> show #3 target s

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 556, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 160, in handle_scheme  
method(query)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/basic_actions/tool.py", line 170, in _cb_show_hide  
run(self.session, cmd)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 47, in show  
show_surfaces(session, objects, only, undo_state)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 147, in show_surfaces  
surface(session, extra_atoms)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in surface  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 70, in apply_to_list  
raise r  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 31, in run  
r = self.function(*s)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in <lambda>  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 158, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in ses_surface_geometry  
for a in (2,1,0)]  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in <listcomp>  
for a in (2,1,0)]  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File
"/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 30, in  
for a in (2,1,0)]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon HD - FirePro D700 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by pett, 6 years ago

Component: Unassigned → Surface
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Surface geometry calculation: cannot convert float NaN to integer

comment:2 by pett, 6 years ago

Resolution: → duplicate
Status: assigned → closed

Functional duplicate of #2054

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