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#3712 closed defect

volume command: overflow encountered in subtract — at Version 1

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
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 (1)

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

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