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:
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    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
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    certifi: 2020.6.20
    chardet: 3.0.4
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    ChimeraX-BlastProtein: 1.0.1
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    ChimeraX-Contacts: 1.0
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    ChimeraX-DistUI: 1.0
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    ChimeraX-Graphics: 1.0
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    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
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    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
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    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
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    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
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    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
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    ChimeraX-RNALayout: 1.0
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    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
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    ChimeraX-Test: 1.0
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    ChimeraX-WebCam: 1.0
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    pyparsing: 2.4.7
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    PyQtWebEngine-commercial: 5.12.1
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    wheel: 0.34.2

[Tom Goddard]

A molecular surfaces was being computed for a molecule with atom coordinate bounds that were NaN. The molecule came from a morph of 3 structures. Likely one of the input structures had NaN coordinates. I don't think the morph command will produce NaN values from finite atom coordinates. A while ago a user reported an error with atom coordinate NaN values where it turned out the PDB file had "NaN" in the x,y,z fields and the ChimeraX read it without complaining as NaN. Maybe that happened here. Not enough info to know.