A lot of array size mismatches after deletions

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.4.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.91 (2019-12-17)
Description
Wanted to delete a few residues. This error kept on popping. Couldn't close it

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-12-17)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /nfs4/suffolk/WorkComplexID/ym337/Para_SC_Biochem_16Inga19/PostProcess/job775/ISOLDE/working_22_3.cif

Summary of feedback from opening
/nfs4/suffolk/WorkComplexID/ym337/Para_SC_Biochem_16Inga19/PostProcess/job775/ISOLDE/working_22_3.cif  
---  
warnings | Unknown polymer entity '1' near line 202  
Unknown polymer entity '2' near line 2139  
Unknown polymer entity '3' near line 4679  
Unknown polymer entity '4' near line 7830  
Unknown polymer entity '5' near line 14322  
7 messages similar to the above omitted  
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "MET" near line 57520  
Unknown polymer entity '13' near line 57536  
Unknown polymer entity '14' near line 65475  
Unknown polymer entity '15' near line 72632  
Unknown polymer entity '16' near line 77600  
Unknown polymer entity '17' near line 79192  
2 messages similar to the above omitted  
Atom H1 is not in the residue template for MET #1 in chain A  
Atom H1 is not in the residue template for LEU #14 in chain B  
Atom H1 is not in the residue template for ALA #4 in chain C  
Atom H1 is not in the residue template for ASP #2 in chain D  
Atom H1 is not in the residue template for MET #1 in chain E  
Atom H3 is not in the residue template for GLN #9 in chain E  
Atom H1 is not in the residue template for LEU #2 in chain F  
Atom HN is not in the residue template for FMN #501 in chain F  
Atom H1 is not in the residue template for ALA #2 in chain G  
Atom H1 is not in the residue template for ALA #2 in chain H  
Atom H1 is not in the residue template for ALA #2 in chain I  
Atom H1 is not in the residue template for MET #1 in chain J  
Atom H1 is not in the residue template for MET #1 in chain K  
Atom HC is not in the residue template for MET #1 in chain L  
Atom H1 is not in the residue template for MET #1 in chain M  
Atom H1 is not in the residue template for LEU #4 in chain N  
Atom H1 is not in the residue template for ALA #3 in chain P  
Atom H1 is not in the residue template for MET #1 in chain Q  
Atom H1 is not in the residue template for THR #2 in chain Z  
1 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for working_22_3.cif #1  
---  
Chain | Description  
A | ?  
B | ?  
C | ?  
D | ?  
E | ?  
F | ?  
G | ?  
H | ?  
I | ?  
J | ?  
K | ?  
L | ?  
M | ?  
N | ?  
P | ?  
Q | ?  
R | ?  
Z | ?  
q | ?  
  

> open
> /nfs4/suffolk/WorkComplexID/ym337/Para_SC_Biochem_16Inga19/PostProcess/job775/375Box_40Bfactor_Nmodule_job775_postprocess.mrc
> /nfs4/suffolk/WorkComplexID/ym337/Para_SC_Biochem_16Inga19/PostProcess/job775/375Box_DefaultBfactor_Nmodule_job775_postprocess.mrc

Opened 375Box_40Bfactor_Nmodule_job775_postprocess.mrc, grid size 375,375,375,
pixel 1.05, shown at level 0.0103, step 2, values float32  

> set bgColor white

> clipper associate #2 toModel #1

Chain information for working_22_3.cif  
---  
Chain | Description  
1.3/A | ?  
1.3/B | ?  
1.3/C | ?  
1.3/D | ?  
1.3/E | ?  
1.3/F | ?  
1.3/G | ?  
1.3/H | ?  
1.3/I | ?  
1.3/J | ?  
1.3/K | ?  
1.3/L | ?  
1.3/M | ?  
1.3/N | ?  
1.3/P | ?  
1.3/Q | ?  
1.3/R | ?  
1.3/Z | ?  
1.3/q | ?  
  

> close #2

> isolde start

> set selectionWidth 4

Done loading forcefield  

> sequence chain /E

Alignment identifier is 1.3.E  
Loading residue template for FMN from internal database  
Bad residue number: match  
Doing nothing  

> delete sel

> isolde ignore ~sel

Changes to the set of ignored residues will notbe applied until you stop the
current simulation.  

Currently ignoring 5459 residues in model 1.3  

> select clear

> isolde ignore ~sel

Currently ignoring 5468 residues in model 1.3  

> isolde ignore ~sel

Currently ignoring 5477 residues in model 1.3  

> isolde ignore ~sel

Currently ignoring 5477 residues in model 1.3  

> isolde ignore ~sel

Currently ignoring 5477 residues in model 1.3  

> isolde ~ignore

> isolde ignore ~sel

Currently ignoring 5445 residues in model 1.3  

> select up

982 atoms, 991 bonds, 1 model selected  

> isolde ~ignore

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  

> save working_22_3.cif #1.3

Not saving entity_poly_seq for non-authoritative sequences  

> select clear

> save working_22_3.cif #1.3

Not saving entity_poly_seq for non-authoritative sequences  

> save working_22_4.cif #1.3

Not saving entity_poly_seq for non-authoritative sequences  

> save working_22_4.cif #1.3

Not saving entity_poly_seq for non-authoritative sequences  

> toolshed show Shell

/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select clear

> select clear

Traceback (most recent call last):  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 1878, in _apply_register_shift  
rs = self._register_shifter = Protein_Register_Shifter(self.session, self,
sel)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/manipulations/register_shift.py", line 129, in
__init__  
nspl = self.n_spline = interpolate.splprep(ncoords.transpose(), u=u_vals)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/scipy/interpolate/fitpack.py", line 157, in splprep  
quiet)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/scipy/interpolate/_fitpack_impl.py", line 263, in splprep  
raise TypeError('m > k must hold')  
TypeError: m > k must hold  
  
TypeError: m > k must hold  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/scipy/interpolate/_fitpack_impl.py", line 263, in splprep  
raise TypeError('m > k must hold')  
  
See log for complete Python traceback.  
  

> save working_22_4.cif #1.3

Not saving entity_poly_seq for non-authoritative sequences  

> select clear

> select clear

> select clear

> select clear

> delete sel

Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2661, in
_update_graphics_if_needed  
s[i]._update_graphics_if_needed()  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 316, in
_update_graphics_if_needed  
self._update_ribbon_tethers()  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1671, in _update_ribbon_tethers  
tp.positions = _tether_placements(xyz1, xyz2, radii, shape)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 3171, in _tether_placements  
return _bond_cylinder_placements(xyz0, xyz1, radius)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 3096, in
_bond_cylinder_placements  
cylinder_rotations(axyz0, axyz1, radii, p)  
ValueError: Cylinder end-point and radii arrays must have same size, got 491
490 490  
  
Error processing trigger "graphics update":  
ValueError: Cylinder end-point and radii arrays must have same size, got 491
490 490  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 3096, in
_bond_cylinder_placements  
cylinder_rotations(axyz0, axyz1, radii, p)  
  
See log for complete Python traceback.  
  

> select /E:237-239

30 atoms, 23 bonds, 1 pseudobond, 2 models selected  

> delete sel

> select clear

> select clear

> select clear

Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 60, in mouse_up  
self.mouse_select(event, mode, self.session, self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 92, in mouse_select  
select_pick(session, pick, mode)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 136, in select_pick  
pick.select(mode)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 3045, in select  
a = self.residue.atoms  
File "cymol.pyx", line 889, in chimerax.atomic.cymol.CyResidue.atoms.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 889, in chimerax.atomic.cymol.CyResidue.atoms.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 134, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 495, in pause  
pu.show_text(p.description(), (x+10,y))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 3041, in description  
return str(self.residue)  
File "cymol.pyx", line 878, in chimerax.atomic.cymol.CyResidue.__str__  
File "cymol.pyx", line 1486, in chimerax.atomic.cymol.CyResidue.string  
File "cymol.pyx", line 1042, in
chimerax.atomic.cymol.CyResidue.insertion_code.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1042, in
chimerax.atomic.cymol.CyResidue.insertion_code.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2159, in planes_pick  
bonds = self.visible_bonds.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2538 but corresponding boolean dimension is 2563  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2538 but corresponding boolean dimension is 2563  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in <listcomp>  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "cymol.pyx", line 858, in
chimerax.atomic.cymol.CyResidue._c_pointer.__get__  
File "cymol.pyx", line 854, in
chimerax.atomic.cymol.CyResidue.cpp_pointer.__get__  
RuntimeError: Residue already deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
[Previous line repeated 1 more time]  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2222, in planes_pick  
rc = Residues(res)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 1054, in __init__  
Collection.__init__(self, residue_pointers, molobject.Residue, Residues)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type "<class 'list'>"  
  
ValueError: Collection items of unrecognized type ""  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in <listcomp>  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "cymol.pyx", line 858, in
chimerax.atomic.cymol.CyResidue._c_pointer.__get__  
File "cymol.pyx", line 854, in
chimerax.atomic.cymol.CyResidue.cpp_pointer.__get__  
RuntimeError: Residue already deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
[Previous line repeated 1 more time]  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2222, in planes_pick  
rc = Residues(res)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 1054, in __init__  
Collection.__init__(self, residue_pointers, molobject.Residue, Residues)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type "<class 'list'>"  
  
ValueError: Collection items of unrecognized type ""  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in <listcomp>  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "cymol.pyx", line 858, in
chimerax.atomic.cymol.CyResidue._c_pointer.__get__  
File "cymol.pyx", line 854, in
chimerax.atomic.cymol.CyResidue.cpp_pointer.__get__  
RuntimeError: Residue already deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
[Previous line repeated 1 more time]  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2222, in planes_pick  
rc = Residues(res)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 1054, in __init__  
Collection.__init__(self, residue_pointers, molobject.Residue, Residues)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type "<class 'list'>"  
  
ValueError: Collection items of unrecognized type ""  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in <listcomp>  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "cymol.pyx", line 858, in
chimerax.atomic.cymol.CyResidue._c_pointer.__get__  
File "cymol.pyx", line 854, in
chimerax.atomic.cymol.CyResidue.cpp_pointer.__get__  
RuntimeError: Residue already deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
[Previous line repeated 1 more time]  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2222, in planes_pick  
rc = Residues(res)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 1054, in __init__  
Collection.__init__(self, residue_pointers, molobject.Residue, Residues)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type "<class 'list'>"  
  
ValueError: Collection items of unrecognized type ""  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in <listcomp>  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "cymol.pyx", line 858, in
chimerax.atomic.cymol.CyResidue._c_pointer.__get__  
File "cymol.pyx", line 854, in
chimerax.atomic.cymol.CyResidue.cpp_pointer.__get__  
RuntimeError: Residue already deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
[Previous line repeated 1 more time]  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2222, in planes_pick  
rc = Residues(res)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 1054, in __init__  
Collection.__init__(self, residue_pointers, molobject.Residue, Residues)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type "<class 'list'>"  
  
ValueError: Collection items of unrecognized type ""  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in <listcomp>  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "cymol.pyx", line 858, in
chimerax.atomic.cymol.CyResidue._c_pointer.__get__  
File "cymol.pyx", line 854, in
chimerax.atomic.cymol.CyResidue.cpp_pointer.__get__  
RuntimeError: Residue already deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
[Previous line repeated 1 more time]  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2222, in planes_pick  
rc = Residues(res)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 1054, in __init__  
Collection.__init__(self, residue_pointers, molobject.Residue, Residues)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type "<class 'list'>"  
  
ValueError: Collection items of unrecognized type ""  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 57, in mouse_up  
self.mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File "/home/ym337/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/mousemodes.py", line 100, in mouse_drag_select  
pick = view.rectangle_intercept(sx, sy, x, y, exclude=self._pick_exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 809, in rectangle_intercept  
picks = self.drawing.planes_pick(planes, exclude=exclude)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1107, in planes_pick  
picks.extend(d.planes_pick(pplanes, exclude))  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2078, in planes_pick  
atoms = self.visible_atoms.filter(pmask)  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2514 but corresponding boolean dimension is 2539  
  
File "/usr/mbu/software/chimerax/chimerax-2019.12.17/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 237, in filter  
return self._objects_class(self._pointers[mask_or_indices])  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.87.01
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Conrad Huang]

The ribbon code has been rearranged, so the code throwing the error may not exist anymore.

[Tom Goddard]

This does not look like a ribbon error. It was caused by deleting atoms (with "delete sel") then drag select. The Structure somehow did not update the array of positions for the shown atoms used by the graphics so the array of positions was longer than the array of atoms. The drag select made a mask saying which atom positions were in the drag rectangle and that mask was longer than the length of the array of atoms giving the error. This mismatch does not appear possible with the current code. Bug was from 6 months ago.