Surface: cannot convert float NaN to integer

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-20.2.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/biaoyuan/Desktop/EscV manuscript/Final comparisons.cxs"

Log from Tue Mar 23 16:08:35 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/biaoyuan/Desktop/pdb/Comparison11_SctV.cxs

Log from Tue Mar 23 12:47:37 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/biaoyuan/Desktop/pdb/Comparison.cxs format session

Log from Tue Mar 23 12:36:41 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/biaoyuan/Desktop/EscV manuscript/EscV-C_salt_bridges1.cxs"

Log from Tue Mar 23 11:11:14 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/biaoyuan/Desktop/EscV
> manuscript/Dirk_job504-EscVC_final_model.cif"

Summary of feedback from opening /Users/biaoyuan/Desktop/EscV
manuscript/Dirk_job504-EscVC_final_model.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom H is not in the residue template for ASN /A:345  
Atom H is not in the residue template for ASN /B:345  
Atom H is not in the residue template for ASN /C:345  
Atom H is not in the residue template for ASN /D:345  
Atom H is not in the residue template for ASN /E:345  
4 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Dirk_job504-EscVC_final_model.cif #1  
---  
Chain | Description  
A C D E F G H I | No description available  
B | No description available  
  

> hide atoms

> show cartoons

> interfaces ~solvent

9 buried areas: D E 1123, A I 1122, G F 1121, H I 1120, B A 1118, H G 1117, E
F 1117, B C 1116, D C 1115  

> select /A

5319 atoms, 5361 bonds, 326 residues, 1 model selected  

> ui dockable false "Chain Contacts"

> delete atoms sel

> delete bonds sel

> color #2 A/B: 335-415 salmon

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1 a/b : 335-415 salmon

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1 A/B: 335-415 salmon

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1 /A,B: 354-415,464-483 salmon

> color #1 /A,B: 322-353 RED

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1 /A,B: 322-353 red

> color #1 /A,B: 416-463 rpink

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1 /A,B: 416-463 pink

> color #1 /A,B: 481-487 green

> color #1 /A,B: 481-487 light green

> color #1 /A,B: 481-487 dark green

> color #1 /A,B: 481-487 bright green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1 /A,B: 481-487 harlequin

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1 /A,B: 481-487 Harlequin

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1 /A,B: 481-487 green

> color #1 /A,B: 488-570 wheat

> color #1 /A,B: 488-570 orange

> color #1 /A,B: 571-675 magenta

> color #1 /A,B: 484-487 green

> color #1 /A,B: 354-415,464-483 salmon

> select /B:347

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 11 atom styles  

> show sel atoms

> color #1 /A,B: 484-487 lime

> color sel light gray

> select /A:532

24 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel gray

> select /A:532@CA

1 atom, 1 residue, 1 model selected  

> select /A:532@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select clear

> select /B:483

15 atoms, 14 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel white

> select /A:535

24 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel gray

> select /A:564

24 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel gray

> select /A:564@NH2

1 atom, 1 residue, 1 model selected  

> select /A:564@NH2

1 atom, 1 residue, 1 model selected  

> select clear

> select /B:485

19 atoms, 18 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select /B:484

20 atoms, 20 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select clear

> select clear

> select /B:486

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> show sel atoms

> style sel sphere

Changed 7 atom styles  

> hide sel atoms

> select /B:488

17 atoms, 16 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select /B:488

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /B:488

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /B:488

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /B:488

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select clear

> select /B:488

17 atoms, 16 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel white

> select /A:503

15 atoms, 14 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel gray

> select /A:501

21 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel gray

> select clear

> select /B:489

15 atoms, 14 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel white

> select clear

> lighting soft

> lighting full

> lighting simple

> save "/Users/biaoyuan/Desktop/EscV manuscript/EscV-C_salt_bridges.cxs"

> save SctV-c_model_side_salt_bridges.png width 2400 height 2400
> transparentBackground true

> hide cartoons

> save SctV-c_model_side_salt_bridges_sphere.png width 2400 height 2400
> transparentBackground true

> show cartoons

> interfaces ~solvent

5 buried areas: D E 1123, B A 1118, E F 1117, B C 1116, D C 1115  

> delete atoms sel

> delete bonds sel

> select /D

5319 atoms, 5361 bonds, 326 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /H

5319 atoms, 5361 bonds, 326 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> save SctV-c_model_side_salt_bridges_.png width 2400 height 2400
> transparentBackground true

> save SctV-c_model_side_salt_bridges_spheres.png width 2400 height 2400
> transparentBackground true

> show cartoons

> hide cartoons

> save SctV-c_model_side_salt_bridges_spheres.png width 2400 height 2400
> transparentBackground true

> show cartoons

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> select /B:483@CB

1 atom, 1 residue, 1 model selected  

> select /B:483@CA

1 atom, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> hide sel atoms

> show sel atoms

> show sel atoms

> show sel atoms

> select /B:483@CA

1 atom, 1 residue, 1 model selected  

> select /B:483@CA

1 atom, 1 residue, 1 model selected  

> select /B:483@CD

1 atom, 1 residue, 1 model selected  

> select /B:483@CA

1 atom, 1 residue, 1 model selected  

> select /B:482

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select /B:483@CA

1 atom, 1 residue, 1 model selected  

> select /B:483@CG

1 atom, 1 residue, 1 model selected  

> select /B:483@OE1

1 atom, 1 residue, 1 model selected  

> select /B:483@CA

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> hide sel cartoons

> hide sel cartoons

> hide sel cartoons

> select clear

> show cartoons

> show cartoons

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> hide cartoons

> select /B:483@C

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> select /B:483@CA

1 atom, 1 residue, 1 model selected  

> select clear

> show cartoons

> hide cartoons

> show cartoons

> hide cartoons

Drag select of 166 atoms  

> style sel stick

Changed 166 atom styles  

> color sel byhetero

> hide HC

> hbonds true

Expected a keyword  

> hbonds

1100 hydrogen bonds found  

> show sel cartoons

> show sel cartoons

> select clear

> select #1

21290 atoms, 21458 bonds, 1100 pseudobonds, 1305 residues, 2 models selected  

> show sel cartoons

> hbonds sel

1100 hydrogen bonds found  

> ~hbonds

> save "/Users/biaoyuan/Desktop/EscV manuscript/EscV-C_salt_bridges1.cxs"

opened ChimeraX session  

> select /B

5333 atoms, 5375 bonds, 327 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide atoms

> color #1 /A,B: 488-570 orange

> open /Users/biaoyuan/Desktop/pdb/MxiA.pdb

MxiA.pdb title:  
Structure of the shigella flexneri mxia protein [more info...]  
  
Chain information for MxiA.pdb #2  
---  
Chain | Description  
A B C | protein VIRH  
  
Non-standard residues in MxiA.pdb #2  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
  
Drag select of 629 residues  
Drag select of 675 residues  

> select clear

Drag select of 652 residues  

> delete atoms sel

> delete bonds sel

> save /Users/biaoyuan/Desktop/pdb/Comparison.cxs

opened ChimeraX session  

> select #2

7414 atoms, 7486 bonds, 24 pseudobonds, 915 residues, 2 models selected  

> ~select #2

Nothing selected  

> select #2/B

2522 atoms, 2544 bonds, 8 pseudobonds, 314 residues, 2 models selected  
No model chosen to save relative to  

> save /Users/biaoyuan/Desktop/pdb/MxiA_monamer.pdb models #1 selectedOnly
> true relModel #1

> open 6wa6

6wa6 title:  
Structure of the Chlamydia pneumoniae CdsV protein [more info...]  
  
Chain information for 6wa6 #3  
---  
Chain | Description  
A B C D E F G H I | Low calcium response locus protein D  
  
Non-standard residues in 6wa6 #3  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  

> select #3/A

2852 atoms, 2892 bonds, 369 residues, 1 model selected  

> save /Users/biaoyuan/Desktop/pdb/CdsV_monamer.pdb models #3 selectedOnly
> true relModel #1

> close #3

> close #2

> open /Users/biaoyuan/Desktop/pdb/MxiA_monamer.pdb

> open /Users/biaoyuan/Desktop/pdb/CdsV_monamer.pdb

Summary of feedback from opening /Users/biaoyuan/Desktop/pdb/CdsV_monamer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 19 19 GLY B
377 HIS B 386 1 10  
Start residue of secondary structure not found: HELIX 20 20 ASP B 397 ILE B
410 1 14  
Start residue of secondary structure not found: HELIX 21 21 VAL B 455 SER B
460 1 6  
Start residue of secondary structure not found: HELIX 22 22 ALA B 484 ALA B
491 1 8  
Start residue of secondary structure not found: HELIX 23 23 THR B 497 LYS B
512 1 16  
224 messages similar to the above omitted  
  
Chain information for CdsV_monamer.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open /Users/biaoyuan/Desktop/pdb/MxiA_monamer.pdb

> open /Users/biaoyuan/Desktop/pdb/MxiA.pdb

MxiA.pdb title:  
Structure of the shigella flexneri mxia protein [more info...]  
  
Chain information for MxiA.pdb #3  
---  
Chain | Description  
A B C | protein VIRH  
  
Non-standard residues in MxiA.pdb #3  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
  

> select #3/A

2438 atoms, 2461 bonds, 8 pseudobonds, 301 residues, 2 models selected  

> save /Users/biaoyuan/Desktop/pdb/MxiA_monamer.pdb models #3 selectedOnly
> true relModel #1

> open /Users/biaoyuan/Desktop/pdb/MxiA_monamer.pdb

Summary of feedback from opening /Users/biaoyuan/Desktop/pdb/MxiA_monamer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 13 13 ASP B
376 TYR B 392 1 17  
Start residue of secondary structure not found: HELIX 14 14 SER B 463 THR B
465 1 3  
Start residue of secondary structure not found: HELIX 15 15 ALA B 478 ASN B
492 1 15  
Start residue of secondary structure not found: HELIX 16 16 ASN B 493 ILE B
497 1 5  
Start residue of secondary structure not found: HELIX 17 17 GLY B 499 ASN B
512 1 14  
45 messages similar to the above omitted  
  
MxiA_monamer.pdb title:  
Structure of the shigella flexneri mxia protein [more info...]  
  
Chain information for MxiA_monamer.pdb #4  
---  
Chain | Description  
A | protein VIRH  
  
Non-standard residues in MxiA_monamer.pdb #4  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
  

> hide #!3 models

> close #3

> ui tool show Matchmaker

> matchmaker #2#!4 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 Dirk_job504-EscVC_final_model.cif, chain A (#1) with
CdsV_monamer.pdb, chain A (#2), sequence alignment score = 615.9  
RMSD between 207 pruned atom pairs is 1.086 angstroms; (across all 319 pairs:
4.565)  
  
Matchmaker Dirk_job504-EscVC_final_model.cif, chain A (#1) with
MxiA_monamer.pdb, chain A (#4), sequence alignment score = 670.3  
RMSD between 168 pruned atom pairs is 1.022 angstroms; (across all 289 pairs:
3.797)  
  

> hide atoms

> save /Users/biaoyuan/Desktop/pdb/Comparison11_SctV.cxs

opened ChimeraX session  

> close #4

> open 3myd

3myd title:  
Structure of the Cytoplasmic domain of FlhA from Helicobacter pylori [more
info...]  
  
Chain information for 3myd #3  
---  
Chain | Description  
A | Flagellar biosynthesis protein flhA  
  

> ui tool show Matchmaker

> matchmaker #2-3 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 Dirk_job504-EscVC_final_model.cif, chain A (#1) with
CdsV_monamer.pdb, chain A (#2), sequence alignment score = 615.9  
RMSD between 207 pruned atom pairs is 1.086 angstroms; (across all 319 pairs:
4.565)  
  
Matchmaker Dirk_job504-EscVC_final_model.cif, chain A (#1) with 3myd, chain A
(#3), sequence alignment score = 465.9  
RMSD between 104 pruned atom pairs is 0.964 angstroms; (across all 320 pairs:
5.054)  
  

> save "/Users/biaoyuan/Desktop/EscV manuscript/Final comparisons.cxs"

opened ChimeraX session  

> morph #2,3,1

Computed 41 frame morph #4  

> coordset #4 1,41

> surface #4

Traceback (most recent call last):  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 232, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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.  
  
Traceback (most recent call last):  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 232, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  

[_many_ of these deleted]

File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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.  
  
Traceback (most recent call last):  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 232, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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.  
  
Traceback (most recent call last):  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 232, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File
"/Users/biaoyuan/Desktop/ChimeraX-1.1.1.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 INTEL-16.1.7
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro12,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2,7 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 425.0.0.0.0
      SMC Version (system): 2.28f7

Software:

    System Software Overview:

      System Version: macOS 11.1 (20C69)
      Kernel Version: Darwin 20.2.0
      Time since boot: 28 days 9:27

Graphics/Displays:

    Intel Iris Graphics 6100:

      Chipset Model: Intel Iris Graphics 6100
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x162b
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        U28E590:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: HTPM110173  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: Thunderbolt/DisplayPort

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
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    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
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    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
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    tinyarray: 1.2.2
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    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2