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#15007 assigned defect

Clipper: 'NoneType' object has no attribute 'dim'

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

Description

The following bug report has been submitted:
Platform:        Linux-6.2.0-36-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

> open /home/rk/Downloads/3aek_phases(2).mrc

Bad MRC grid size (1297373728,-284485120,1145110528)  

> open /home/rk/Downloads/3aek(2).pdb

3aek(2).pdb title:  
Structure of the light-independent protochlorophyllide reductase catalyzing A
key reduction for greening In the dark [more info...]  
  
Chain information for 3aek(2).pdb #1  
---  
Chain | Description | UniProt  
A C | light-independent protochlorophyllide reductase subunit N | BCHN_RHOCA
2-424  
B D | light-independent protochlorophyllide reductase subunit B | BCHB_RHOCA
1-525  
  
Non-standard residues in 3aek(2).pdb #1  
---  
PMR — protochlorophyllide  
SF4 — iron/sulfur cluster  
  

> open /home/rk/Downloads/3aek_phases(2).mrc

Bad MRC grid size (1297373728,-284485120,1145110528)  

> open /home/rk/Downloads/3aek_phases(2).mtz

Summary of feedback from opening /home/rk/Downloads/3aek_phases(2).mtz  
---  
warnings | WARNING: multiple experimental reflection datasets found:  
(dataset) HKL_base,  
(dataset) FP, SIGFP  
Automatically choosing "(dataset) FP, SIGFP".  
No free flags detected in this dataset! Automatically generated a new random
set with 1971 free from 100410 observed reflections. You should save your data
to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Discarding unrecognised/unsupported data array /cryst_1/data_1/FOM W  
Launching live xmap mgr took 1.137117862701416 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 54,46,46, pixel
0.567,0.564,0.543, shown at level 0.534, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 54,46,46, pixel
0.567,0.564,0.543, shown at level -0.141,0.141, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_9 as #1.1.1.4, grid size 54,46,46, pixel
0.567,0.564,0.543, shown at level 0.187, step 1, values float32  
Opened (STATIC) (dataset) FC, PHIC as #1.1.1.5, grid size 54,46,46, pixel
0.567,0.564,0.543, shown at level 0.598, step 1, values float32  
Opened (STATIC) (dataset) FC_ALL, PHIC_ALL as #1.1.1.6, grid size 54,46,46,
pixel 0.567,0.564,0.543, shown at level -0.615,0.615, step 1, values float32  
Opened (STATIC) (dataset) FWT, PHWT as #1.1.1.7, grid size 54,46,46, pixel
0.567,0.564,0.543, shown at level 0.545, step 1, values float32  
Opened (STATIC) (dataset) DELFWT, PHDELWT as #1.1.1.8, grid size 54,46,46,
pixel 0.567,0.564,0.543, shown at level -0.234,0.234, step 1, values float32  
Opened (STATIC) (dataset) FC_ALL_LS, PHIC_ALL_LS as #1.1.1.9, grid size
54,46,46, pixel 0.567,0.564,0.543, shown at level -0.632,0.632, step 1, values
float32  
3aek(2).pdb title:  
Structure of the light-independent protochlorophyllide reductase catalyzing A
key reduction for greening In the dark [more info...]  
  
Chain information for 3aek(2).pdb  
---  
Chain | Description | UniProt  
1.2/A 1.2/C | light-independent protochlorophyllide reductase subunit N |
BCHN_RHOCA 2-424  
1.2/B 1.2/D | light-independent protochlorophyllide reductase subunit B |
BCHB_RHOCA 1-525  
  
Non-standard residues in 3aek(2).pdb #1.2  
---  
PMR — protochlorophyllide  
SF4 — iron/sulfur cluster  
  
Opened crystallographic dataset from /home/rk/Downloads/3aek_phases(2).mtz  
Found experimental reflection data:  
(dataset) FP, SIGFP  
Rwork: 0.2334; Rfree: 0.2456  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_smooth_9  
(STATIC) (dataset) FC, PHIC  
(STATIC) (dataset) FC_ALL, PHIC_ALL  
(STATIC) (dataset) FWT, PHWT  
(STATIC) (dataset) DELFWT, PHDELWT  
(STATIC) (dataset) FC_ALL_LS, PHIC_ALL_LS  
Any unwanted maps may be safely closed via the Model panel.  

> hide #!1.1.1 models

> show #!1.1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1 models

> show #!1 models

> hide #!1.1.1.9 models

> hide #!1.1.1.8 models

> hide #!1.1.1.7 models

> hide #!1.1.1.6 models

> hide #!1.1.1.5 models

> hide #!1.1.1.4 models

> hide #!1.1.1.3 models

> ui tool show "Volume Viewer"

> close #1.1.1.4

Deleting (LIVE) 2mFo-DFc_smooth_9  

> close #1.1.1.6

> close #1.1.1.8

> close #1.1.1.9

> close #1.1.1.7

> close #1.1.1.5

> volume #1.1.1.2 style mesh

> dssp protein

> select ::name="PMR"

90 atoms, 98 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> select ~sel

13453 atoms, 13016 bonds, 8 pseudobonds, 2380 residues, 21 models selected  

> hide (#!1.2 & sel) target a

> cartoon hide (#!1.2 & sel)

> view sel

> volume #1.1.1.2 level 0.5345

> volume #1.1.1.3 level -0.1405 level 0.1484

> ui mousemode right zone

> set bgColor white

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

45 atoms, 49 bonds, 1 residue, 1 model selected  

> hide #!1.1.1.3 models

> ui mousemode right zone

[Repeated 2 time(s)]

> ui tool show "Volume Viewer"

> hide #!1.1.1.1 models

> volume #1.1.1.2 level 0.3089

> volume #1.1.1.2 style image

> volume #1.1.1.2 style surface

> close #1.1.1.3

Deleting (LIVE) mFo-DFc  

> close #1.1.1.1

> ui tool show "Surface Zone"

> surface zone #1.1.1.2 nearAtoms #1.2 distance 3.26

[Repeated 7 time(s)]

> surface zone #1.1.1.2 nearAtoms sel distance 3.26

[Repeated 4 time(s)]

> volume #1.1.1.2 style mesh

> hide #!1.1.1 models

> show #!1.1.1 models

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 776, in _box_changed_cb  
origin_grid, origin_xyz = _find_box_corner(center, self.cell, self.grid,
radius=radius)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight changed":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  

> hide #1.3 models

> show #1.3 models

> hide #!1 models

> show #!1 models

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 783, in _box_moved_cb  
bp.origin_grid, bp.origin_xyz = _find_box_corner(center, self.cell,  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
Error processing trigger "spotlight moved":  
AttributeError: 'NoneType' object has no attribute 'dim'  
  
File "/home/rk/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/xmapset.py", line 1102, in _find_box_corner  
radii_frac = Coord_frac(radius/cell.dim)  
  
See log for complete Python traceback.  
  

> ui tool show "Color Actions"

> color sel black target s

[Repeated 1 time(s)]




OpenGL version: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7E06
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 13th Gen Intel(R) Core(TM) i5-13600KF
Cache Size: 24576 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        22Gi       1.8Gi       1.7Gi       6.8Gi       6.4Gi
	Swap:          2.0Gi       1.6Gi       422Mi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3060] [10de:2487] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:397b]	
	Kernel driver in use: nouveau

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (1)

comment:1 by pett, 18 months ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Clipper: 'NoneType' object has no attribute 'dim'

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