Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#7085 closed defect (fixed)

NaN in surface calculation

Reported by: ryan.kissinger1@… 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:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Trying to morph has become a nightmare for me 

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "R:\Bethesda Work\LISB\Margulies, David\cwt40_md_fr_6_P1.pdb" format
> pdb

Chain information for cwt40_md_fr_6_P1.pdb #1  
---  
Chain | Description  
P | No description available  
  

> surface

> cartoon hide

> open "R:/Bethesda Work/LISB/Margulies, David/ref32_b446mer-LD-splice-
> jjfix3.pdb"

Chain information for ref32_b446mer-LD-splice-jjfix3.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
P | No description available  
Q | No description available  
  

> cartoon hide

> hide target a

> surface

> ui tool show Matchmaker

> 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 cwt40_md_fr_6_P1.pdb, chain P (#1) with ref32_b446mer-LD-splice-
jjfix3.pdb, chain A (#2), sequence alignment score = 1050.2  
RMSD between 106 pruned atom pairs is 1.176 angstroms; (across all 272 pairs:
4.189)  
  

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select #2.2

826 atoms, 100 residues, 1 model selected  

> surface hidePatches (#!2 & sel)

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2.3

51 atoms, 6 residues, 1 model selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2.4

13 atoms, 2 residues, 1 model selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> morph #1,2 frames 60

Computed 61 frame morph #3  

> coordset #3 1,61

> surface #3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 175, in _atoms_changed  
self._recompute_shape()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 208, in _recompute_shape  
self.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
Error processing trigger "changes":  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 512.78
OpenGL renderer: Quadro RTX 5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 5820 Tower X-Series
OS: Microsoft Windows 10 Enterprise (Build 19043)
Memory: 137,133,125,632
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
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    line-profiler: 2.1.2
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    MolecularDynamicsViewer: 1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
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    parso: 0.7.1
    pickleshare: 0.7.5
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    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
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    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
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    traitlets: 5.0.5
    urllib3: 1.25.11
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    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (5)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Surface
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → NaN in surface calculation

comment:2 by Tom Goddard, 3 years ago

Hi Ryan,

Looks like you morphed 2 structures then showed a surface and it gave a bunch of NaN (not-a-number) errors. This happened because some atoms in the morph had NaN values. I never saw the ChimeraX morph code produce NaN atom coordinates. You could try it with ChimeraX 1.4 (you are using version 1.2.5). Or if you sent me the two PDB files I could see if I get the error, that would allow me to fix it. If you send the PDB files and they need to be kept private then send them directly to me (goddard@…) instead of replying directly to this bug report email.

Tom

comment:3 by Tom Goddard, 3 years ago

Thanks for sending me your PDB files. I get the same error in ChimeraX 1.4 and I am looking into what is going wrong in the morph code to produce the NaN atom coordinates.

comment:4 by Tom Goddard, 3 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in tomorrow's ChimeraX daily build.

The morph code incorrectly calculated dihedral angle residue interpolation using the unpaired atoms and that used uninitialized atom coordinate value leading to NaN atom coordinates in the result. I fixed the code to make sure the dihedral angle interpolating only uses the paired atoms.

in reply to:  5 ; comment:5 by ryan.kissinger1@…, 3 years ago 

Thank you so much Tom! I will download the daily build and see what happens!

On Mon, Jun 13, 2022 at 6:06 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:
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