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#3712 closed defect (can't reproduce)

Clipper map roaming overflow in computing bounds

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

Description (last modified by Eric Pettersen)

The following bug report has been submitted:
Platform:        Linux-4.15.0-96-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /misc/biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/J384/cryosparc_P1_J384_011_volume_map_filtered.mrc
> format mrc

Opened cryosparc_P1_J384_011_volume_map_filtered.mrc, grid size 384,384,384,
pixel 1.06, shown at level 7.68e-05, step 2, values float32  

> open
> /misc/biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/Autosharpen_39/J384_sharpened_res_5.ccp4

Opened J384_sharpened_res_5.ccp4, grid size 384,384,384, pixel 1.06, shown at
level 1.33, step 2, values float32  

> open
> /misc/biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_001.pdb

Chain information for refine_59_minimized_isolde_001.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
R | No description available  
  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for refine_59_minimized_isolde_001.pdb  
---  
Chain | Description  
3.2/A | No description available  
3.2/B | No description available  
3.2/C | No description available  
3.2/D | No description available  
3.2/E | No description available  
3.2/F | No description available  
3.2/G | No description available  
3.2/H | No description available  
3.2/I | No description available  
3.2/J | No description available  
3.2/R | No description available  
  
Done loading forcefield  

> volume #3.1.1.2 color #1d1c8d

> select #3/a

4353 atoms, 4394 bonds, 1 model selected  
Alignment identifier is 3.2.A  

> select #3/b

3528 atoms, 3551 bonds, 2 pseudobonds, 2 models selected  
Alignment identifier is 3.2.B  

> select #3/c

4305 atoms, 4349 bonds, 6 pseudobonds, 2 models selected  
Alignment identifier is 3.2.C  

> select #3/d

3142 atoms, 3171 bonds, 2 pseudobonds, 2 models selected  
Alignment identifier is 3.2.D  

> select #3/e

4348 atoms, 4391 bonds, 4 pseudobonds, 2 models selected  
Alignment identifier is 3.2.E  

> select #3/f

4247 atoms, 4284 bonds, 1 model selected  
Alignment identifier is 3.2.F  

> select #3/g

3917 atoms, 3957 bonds, 1 model selected  
Alignment identifier is 3.2.G  

> select #3/h

4455 atoms, 4488 bonds, 2 pseudobonds, 2 models selected  
Alignment identifier is 3.2.H  

> save
> /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb
> #3.2

> volume #3.1.1.1 level 0.6141

> select clear

> volume #3.1.1.1 level 0.9801

> volume #3.1.1.1 level 0.1311

> select clear

> volume #3.1.1.1 level 0.5117

> select clear

> select clear

> select clear

> select clear

> select clear

> volume #3.1.1.1 level 0.3799

> volume #3.1.1.1 level 0.863

> select clear

> save
> /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb
> #3.2

> select #3/i

2770 atoms, 2793 bonds, 2 pseudobonds, 2 models selected  
Alignment identifier is 3.2.I  

> select clear

> select clear

> select clear

> save
> /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb
> #3.2

> select #3/a

4353 atoms, 4394 bonds, 1 model selected  

> select #3/b

3528 atoms, 3551 bonds, 2 pseudobonds, 2 models selected  

> save
> /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb
> #3.2

> select #3/b

3528 atoms, 3551 bonds, 2 pseudobonds, 2 models selected  
reverting to start  

> save
> /misc/biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/isolde.cxs
> includeMaps true

Taking snapshot of stepper: refine_59_minimized_isolde_001.pdb  

> select #3/j

14778 atoms, 14921 bonds, 6 pseudobonds, 2 models selected  
Alignment identifier is 3.2.J  

> select clear

> open
> /misc/biophysik/lad58072/exosome_project/EM/CtExo10_homology_models/CtExo10_hs_6d6q_model_reviewed-
> coot-1.pdb

Chain information for CtExo10_hs_6d6q_model_reviewed-coot-1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
  

> mmaker #1/j:1-245 to #3.2/j:1-245

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 refine_59_minimized_isolde_001.pdb, chain J (#3.2) with
CtExo10_hs_6d6q_model_reviewed-coot-1.pdb, chain J (#1), sequence alignment
score = 993.6  
RMSD between 84 pruned atom pairs is 1.208 angstroms; (across all 219 pairs:
7.039)  
  

> select #1

48833 atoms, 49281 bonds, 30 pseudobonds, 2 models selected  

> hide sel atoms

> show sel cartoons

> select #1/j

14327 atoms, 14466 bonds, 6 pseudobonds, 2 models selected  
Alignment identifier is 1.J  

> style sel stick

Changed 33 atom styles  

> select #1

48833 atoms, 49281 bonds, 30 pseudobonds, 2 models selected  

> rainbow sel

> hide #!1 models

> select clear

> select clear

> select clear

> select clear

> select clear

> save
> /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb
> #3.2

> save
> /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb
> #3.2

> save
> /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb
> #3.2

> volume #3.1.1.1 level 1.298

> volume #3.1.1.1 level 1.019

> select clear

> select clear

> volume #3.1.1.1 level 0.8163

> save
> /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb
> #3.2

No rotamer preview selected! Ignoring command.  

No rotamer preview selected! Ignoring command.  

> save
> /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb
> #3.2

> volume #3.1.1.1 level 1.457

> volume #3.1.1.1 level 0.8746

> volume #3.1.1.1 level 1.355

> volume #3.1.1.1 level 0.86

> volume #3.1.1.1 level 1.297

> volume #3.1.1.1 level 0.758

> volume #3.1.1.1 level 1.224

> volume #3.1.1.1 level 0.5686

> volume #3.1.1.1 level 0.9329

> volume #3.1.1.1 level 0.6123

> volume #3.1.1.1 level 0.2043

> volume #3.1.1.1 level 0.5395

> volume #3.1.1.1 level 0.86

> volume #3.1.1.1 level 0.5249

> volume #3.1.1.1 level 1.02

> select clear

> select clear

> select clear

> select clear

> volume #3.1.1.1 level 0.6998

> volume #3.1.1.1 level 1.224

> select clear

> select clear

> volume #3.1.1.1 level 1.035

> select clear

> volume #3.1.1.1 level 0.5832

> volume #3.1.1.1 level 0.7289

> select clear

> select clear

> volume #3.1.1.1 level 1.239

> volume #3.1.1.1 level 0.6123

> volume #3.1.1.1 level 2.026

> volume #3.1.1.1 level 1.21

/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/geometry/bounds.py:51: RuntimeWarning: overflow encountered
in subtract  
size = self.xyz_max - self.xyz_min  
/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/geometry/bounds.py:53: RuntimeWarning: overflow encountered
in multiply  
r = 0.5*sqrt((size*size).sum())  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
[many repetitions of this error deleted]  

See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb  
self.set_surface_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask  
indices = numpy.where(self.mgr.get_vertex_mask(v))[0]  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask  
self._update_mask()  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask  
step=self.grid_step, pad=self.pad)  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask  
self.replace_data(self._generate_data_array(coords, step, radius, pad=pad))  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
ValueError: negative dimensions are not allowed  
  
Error processing trigger "atom coords updated":  
ValueError: negative dimensions are not allowed  
  
File "/home/lad58072/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 236, in
_generate_data_array  
data = numpy.zeros(dim, numpy.uint8)  
  
See log for complete Python traceback.  
  
/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py:763: RuntimeWarning: invalid value
encountered in greater  
tethered = norm(offsets, axis=1) > min_tether_offset  




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 28 Intel(R) Core(TM) i9-9940X CPU @ 3.30GHz
Cache Size: 19712 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G         11G        104G        427M        9.7G        112G
	Swap:           93G          0B         93G

Graphics:
	19:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1e04] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:37c4]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (3)

comment:1 by Eric Pettersen, 5 years ago

Component:	Unassigned → Volume Data
Description:	modified (diff)
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → volume command: overflow encountered in subtract

comment:2 by Tom Goddard, 5 years ago

Cc:	Tom Goddard added
Owner:	changed from Tom Goddard to Tristan Croll
Summary:	volume command: overflow encountered in subtract → Clipper map roaming overflow in computing bounds

There is a numeric overflow warning in Bounds.size() subtracting b.xyz_max - b.xyz_min that indicates the xyz_min. xyz_max bounds are huge or NaN. Then there is a Clipper error trying to compute a mask for showing a map. It is not clear if the incorrect bounds are caused by the Clipper masked map but the command that preceded the warnings and errors was changing the volume threshold on map #3.1.1.1. The user was changing the level of that map a lot. The Clipper map/mask_handler.py is using atom coordinates to determine bounds. It seems likely that infinite atom coordinates caused this problem. Since MD is prone to exploding and giving such coordinates some additional check may be needed to avoid continuous stream of errors that happened in this bug report.

comment:3 by Tristan Croll, 3 years ago

Resolution:	→ can't reproduce
Status:	assigned → closed

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