Memory error computing surface for marker set

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-62-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.9 (2019-06-06)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/home/whunt003/Julio_Work_Files/Projects/Auer/H10_9/all_best_trace_0.05_0.05_used1.1_newlocalmax_interior_trimmed.cmm

Opened 1 marker sets containing 22937 markers  

> open "/home/whunt003/Julio_Work_Files/Projects/Auer/H10_9/Junha
results/H10_9_TaperActinModel_OriginalOrigin.cmm"

Opened 1 marker sets containing 4216 markers  

> hide #!2 models

> show #!2 models

> style selAtoms stick

Changed 27153 atom styles  

> style selAtoms sphere

Changed 27153 atom styles  

> style selAtoms ball

Changed 27153 atom styles  

> hide selAtoms surfaces

> show selAtoms surfaces

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 89, in handle_scheme  
shortcuts.keyboard_shortcuts(self.session).run_shortcut(value)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 286, in run  
commands.run(s, f)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 47, in show  
show_surfaces(session, objects, only, undo_state)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/std_commands/show.py", line 147, in show_surfaces  
surface(session, extra_atoms)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in surface  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 70, in apply_to_list  
raise r  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 31, in run  
r = self.function(*s)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in <lambda>  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 158, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 33, in ses_surface_geometry  
matrix = empty(shape, float32)  
MemoryError  
  
MemoryError  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 33, in ses_surface_geometry  
matrix = empty(shape, float32)  
  
See log for complete Python traceback.  
  

> interfaces selAtoms & ~solvent

1 buried areas: #1/M #2/M 3747357  
/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/networkx/drawing/nx_pylab.py:611: MatplotlibDeprecationWarning:
isinstance(..., numbers.Number)  
if cb.is_numlike(alpha):  

> view #2 clip false

> lighting soft

> lighting full

> set silhouettes true

> set silhouettes false

> set silhouettes true

> lighting simple

> set bgColor white

> set bgColor black

> set bgColor gray

> set bgColor black

> lighting shadows true

> lighting shadows false

> lighting shadows true

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands: surf hide; style
(protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh
def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20;
cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x
rect; cartoon style protein modeh tube rad 2 sides 24 thick 0.6; cartoon style
nucleic x round width 1.6 thick 1.6; nucleotides stubs  

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands: surf hide; style
(protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh
def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20;
cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x
rect; cartoon style protein modeh default arrows f x round width 1 thick 1;
cartoon style nucleic x round width 1.6 thick 1.6; nucleotides tube/slab shape
ellipsoid  

> style selAtoms ball

Changed 27153 atom styles  

> style selAtoms stick

Changed 27153 atom styles  

> style selAtoms stick

Changed 27153 atom styles  

> style selAtoms stick

Changed 27153 atom styles  

> hbonds selAtoms

0 hydrogen bonds found  

> ui mousemode rightMode "crop volume"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "move planes"

> ui mousemode rightMode windowing

> ui mousemode rightMode rotate

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode clip

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting simple

> ui mousemode rightMode "clip rotate"

> ui mousemode rightMode clip

> ui mousemode rightMode "clip rotate"

> ui mousemode rightMode clip

> ui mousemode rightMode zone

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 445, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 374, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 189, in mouse_down  
self._show_zone(res)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 43, in _show_zone  
nres = self._show_near_residues(residue, show_ligands=ribbon)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 97, in _show_near_residues  
cats = all_atoms.structure_categories  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
IndexError: Unknown structure category  
  
IndexError: Unknown structure category  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  

> ui mousemode rightMode clip

> ui mousemode rightMode "clip rotate"

> ui mousemode rightMode clip

> open "/home/whunt003/Julio_Work_Files/Projects/Auer/H10_9/Junha
results/H10_9_Subregion.mrc"

Opened H10_9_Subregion.mrc, grid size 100,200,100, pixel 9.47, shown at level
0.77, step 1, values float32  

> open /home/whunt003/Julio_Work_Files/Projects/Auer/H10_9/H10_9-taper.mrc

Opened H10_9-taper.mrc, grid size 347,629,292, pixel 9.47,9.47,9.47, shown at
level 0.673, step 2, values float32  

> volume selMaps projectionMode 3d

> volume #3 orthoplanes xyz positionPlanes 173,8,145

> volume #3 orthoplanes xyz positionPlanes 173,202,145

> volume #3 orthoplanes xyz positionPlanes 173,28,145

> volume #3 orthoplanes xyz positionPlanes 173,0,145

> ui mousemode rightMode clip

> ui mousemode rightMode "clip rotate"

> ui mousemode rightMode clip

> ui mousemode rightMode "clip rotate"

> ui mousemode rightMode clip

> lighting full

> lighting shadows false

> lighting simple

> set silhouettes false

> set silhouettes true

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!1 models

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 454, in run_provider  
return api._api_caller.run_provider(api, session, self, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1455, in run_provider  
return cls._get_func(api, "run_provider")(session, bi, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/preset_mgr/__init__.py", line 45, in run_provider  
run_preset(session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/preset_mgr/builtin.py", line 47, in run_preset  
mgr.execute(cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/preset_mgr/manager.py", line 69, in execute  
run(self.session, preset, log=False)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in surface  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 70, in apply_to_list  
raise r  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 31, in run  
r = self.function(*s)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in <lambda>  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 158, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 33, in ses_surface_geometry  
matrix = empty(shape, float32)  
MemoryError  
  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 454, in run_provider  
return api._api_caller.run_provider(api, session, self, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1455, in run_provider  
return cls._get_func(api, "run_provider")(session, bi, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/preset_mgr/__init__.py", line 45, in run_provider  
run_preset(session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/preset_mgr/builtin.py", line 47, in run_preset  
mgr.execute(cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/preset_mgr/manager.py", line 69, in execute  
run(self.session, preset, log=False)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in surface  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 70, in apply_to_list  
raise r  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/threadq.py", line 31, in run  
r = self.function(*s)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/surface/surfacecmds.py", line 147, in <lambda>  
threadq.apply_to_list(lambda s: s.calculate_surface_geometry(), args, nthread)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 158, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/surface/gridsurf.py", line 33, in ses_surface_geometry  
matrix = empty(shape, float32)  
MemoryError  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 990, in <lambda>  
run(ses, "preset %s%s" % (cat, quote_if_necessary(name.lower()))))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/preset_mgr/cmd.py", line 49, in preset_cmd  
session.presets.preset_function(cat, matches[0])()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/preset_mgr/manager.py", line 53, in cb  
bi.run_provider(self.session, name, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 459, in run_provider  
"run_provider() failed in bundle %s:\n%s" % (self.name, str(e)))  
chimerax.core.toolshed.ToolshedError: run_provider() failed in bundle
ChimeraX-Preset-Mgr:  
  
  
chimerax.core.toolshed.ToolshedError: run_provider() failed in bundle
ChimeraX-Preset-Mgr:  
  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 459, in run_provider  
"run_provider() failed in bundle %s:\n%s" % (self.name, str(e)))  
  
See log for complete Python traceback.  
  

> set silhouettes false

> set silhouettes true

> view orient cofr false

> view orient cofr false

> view cofr false

> view orient cofr false

> vop gaussian #3 sdev 28.4

> toolshed show Registration

> toolshed show "Cage Builder"

> toolshed show Distances

> help help:user

> ui mousemode rightMode translate

> ui mousemode rightMode zoom

> lighting simple

> lighting soft

> lighting full

> lighting flat

> ui mousemode rightMode clip

> view orient cofr false

> ui mousemode rightMode pivot

> ui mousemode rightMode clip

> ui mousemode rightMode zone

> zone clear

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 446, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 374, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 197, in mouse_drag  
self._scale_range(scale)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 183, in _scale_range  
self._show_zone(r, ribbon=ribbon, log_command = 'include distances')  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 43, in _show_zone  
nres = self._show_near_residues(residue, show_ligands=ribbon)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 97, in _show_near_residues  
cats = all_atoms.structure_categories  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
IndexError: Unknown structure category  
  
IndexError: Unknown structure category  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 446, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 374, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 197, in mouse_drag  
self._scale_range(scale)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 183, in _scale_range  
self._show_zone(r, ribbon=ribbon, log_command = 'include distances')  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 43, in _show_zone  
nres = self._show_near_residues(residue, show_ligands=ribbon)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 97, in _show_near_residues  
cats = all_atoms.structure_categories  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
IndexError: Unknown structure category  
  
IndexError: Unknown structure category  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 446, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 374, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 197, in mouse_drag  
self._scale_range(scale)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 183, in _scale_range  
self._show_zone(r, ribbon=ribbon, log_command = 'include distances')  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 43, in _show_zone  
nres = self._show_near_residues(residue, show_ligands=ribbon)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 97, in _show_near_residues  
cats = all_atoms.structure_categories  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
IndexError: Unknown structure category  
  
IndexError: Unknown structure category  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 446, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 374, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 197, in mouse_drag  
self._scale_range(scale)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 183, in _scale_range  
self._show_zone(r, ribbon=ribbon, log_command = 'include distances')  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 43, in _show_zone  
nres = self._show_near_residues(residue, show_ligands=ribbon)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 97, in _show_near_residues  
cats = all_atoms.structure_categories  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
IndexError: Unknown structure category  
  
IndexError: Unknown structure category  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 446, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 374, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 197, in mouse_drag  
self._scale_range(scale)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 183, in _scale_range  
self._show_zone(r, ribbon=ribbon, log_command = 'include distances')  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 43, in _show_zone  
nres = self._show_near_residues(residue, show_ligands=ribbon)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 97, in _show_near_residues  
cats = all_atoms.structure_categories  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
IndexError: Unknown structure category  
  
IndexError: Unknown structure category  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 430.26
OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

Tried to surface markers with huge bounds. User does not realize a molecular surface is not appropriate. Improved error message to indicate what is going on.

I reported the second error about zone mouse mode raising an error as a separate bug #2648