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Opened 6 years ago
Closed 6 years ago
#2054 closed defect (can't reproduce)
Surface geometry calculation: cannot convert float NaN to integer
| Reported by: | 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. 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 , 6 years ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Surface geometry calculation: cannot convert float NaN to integer |
comment:2 by , 6 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Appears that some atom position was NaN causing an error in surface calculation code. The bad structure came from a morph of two structures the user loaded from files coral7.pdb and coral8.pdb. Match Maker was used to align those two structures and reported that the RMSD was 0, so it looks like they were identical. I tried morphing between identical structures, and surfacing no problem.
Would need the original structures to debug.