Opened 14 months ago

Closed 14 months ago

#15837 closed defect (duplicate)

'MarkedHistogram' object has no attribute '_min_val'

Reported by: pngoi@… Owned by: pett
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
using render attribute to color structure by sequence conservation

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/peterngoi/Desktop/Lab/CycF/Figures/SCF-cycF.cxs format session

Log from Wed Aug 28 14:18:00 2024UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> fetch 1ldk

Unknown command: fetch 1ldk  

> open /Users/peterngoi/Downloads/1ldk.pdb

1ldk.pdb title:  
Structure of the CUL1-RBX1-SKP1-F BOXSKP2 SCF ubiquitin ligase complex [more
info...]  
  
Chain information for 1ldk.pdb #1  
---  
Chain | Description | UniProt  
A | CUL1 | CUL1_HUMAN  
B | CUL1 | CUL1_HUMAN  
C | RBX1 | RBX1_HUMAN  
D | cyclin A/CDK2-associated protein P19 | SKP1_HUMAN  
E | SKP2-FBOX | SKP2_HUMAN  
  
Non-standard residues in 1ldk.pdb #1  
---  
ZN — zinc ion  
  

> show cartoons

> hide atoms

> sequence chain #1/E

Alignment identifier is 1/E  

> select /E:3109

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select /E

331 atoms, 340 bonds, 41 residues, 1 model selected  

> open
> /Users/peterngoi/Desktop/Lab/CycF/Figures/S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb

Chain information for
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select add #1

7922 atoms, 8059 bonds, 17 pseudobonds, 974 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select add #2

4984 atoms, 5073 bonds, 3 pseudobonds, 672 residues, 2 models selected  
Alignment identifier is 2/A  
Alignment identifier is 2/B  
Alignment identifier is 2/C  

> sequence chain #1/D

Alignment identifier is 1/D  

> select #1/D:2002

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/D

926 atoms, 940 bonds, 1 pseudobond, 118 residues, 2 models selected  

> select #2/B:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #2/B

967 atoms, 975 bonds, 3 pseudobonds, 140 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!2 & sel to #1 & sel

No 'to' model specified  

> matchmaker #!2 & sel to #1 & sel

No 'to' model specified  

> select #1/D:2002-2140

926 atoms, 940 bonds, 1 pseudobond, 118 residues, 2 models selected  
Drag select of 134 residues, 1 pseudobonds  

> ui tool show Matchmaker

> matchmaker #!2 & sel to #1 & sel

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1ldk.pdb, chain D (#1) with
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb,
chain B (#2), sequence alignment score = 316.3  
RMSD between 58 pruned atom pairs is 1.157 angstroms; (across all 87 pairs:
2.555)  
  

> select clear

> open
> /Users/peterngoi/Desktop/Lab/CycF/Scripting/CCNF_conservation/CCNF_conservation.aln

Summary of feedback from opening
/Users/peterngoi/Desktop/Lab/CycF/Scripting/CCNF_conservation/CCNF_conservation.aln  
---  
notes | Alignment identifier is CCNF_conservation.aln  
Showing conservation header ("seq_conservation" residue attribute) for
alignment CCNF_conservation.aln  
  
Opened 5 sequences from CCNF_conservation.aln  

> select

12906 atoms, 13132 bonds, 20 pseudobonds, 1646 residues, 5 models selected  

> select #2/A

3912 atoms, 3992 bonds, 519 residues, 1 model selected  

> ui tool show "Color Actions"

> ui tool show "Surface Color"

> sequence associate #2/A CCNF_conservation.aln

Associated
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
chain A to CycF_hs/1-677 with 321 mismatches and/or gaps  

> open /Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF-conservation.aln

Summary of feedback from opening
/Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF-conservation.aln  
---  
notes | Alignment identifier is CCNF-conservation.aln  
Associated
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
chain A to NP_001752.2/1-786 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment CCNF-conservation.aln  
  
Opened 6 sequences from CCNF-conservation.aln  

> sequence associate #2/A CCNF-conservation.aln

Disassociated
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
chain A from NP_001752.2/1-786  
Associated
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
chain A to NP_001752.2/1-786 with 0 mismatches  

> sequence associate #2/A CCNF-conservation.aln

Disassociated
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
chain A from NP_001752.2/1-786  
Associated
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
chain A to NP_001752.2/1-786 with 0 mismatches  

> select add #2

4984 atoms, 5073 bonds, 3 pseudobonds, 672 residues, 2 models selected  

> select subtract #2

Nothing selected  

> open
> /Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF_conservation_score

'/Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF_conservation_score'
has no suffix  

> open
> /Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF_conservation_score.txt

Unrecognized file suffix '.txt'  

> open /Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF_conservation-
> score

'/Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF_conservation-score'
has no suffix  

> label #1-2 residues attribute seq_conservation

> undo

[Repeated 2 time(s)]

> hide #2.2 models

> close #2.2

> select #2/A

3912 atoms, 3992 bonds, 519 residues, 1 model selected  

> color sel byhetero

> ui tool show "Surface Color"

> ui tool show "Color Actions"

> toolshed show

> sequence associate #2/A CCNF-conservation.aln

Disassociated
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
chain A from NP_001752.2/1-786  
Associated
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
chain A to NP_001752.2/1-786 with 0 mismatches  

> ui tool show "Color Actions"

> ui tool show "Scale Bar"

> ui tool show "Selection Inspector"

> save /Users/peterngoi/Desktop/Lab/CycF/Figures/SCF-cycF.cxs

——— End of log from Wed Aug 28 14:18:00 2024 ———

opened ChimeraX session  

> ui tool show "Render/Select by Attribute"

> sequence align CCNF-conservation.aln program clustalOmega replace true

Webservices job id: SP8EWY1NXO2CNTH7  

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_conservation #!2 target abcs palette
> -1.976,blue:49.012,white:100,red

4984 atoms, 672 residues, atom seq_conservation range -1.98 to 100  

> color byattribute r:seq_conservation #!2 target abcs palette
> -1.976,blue:2.18314,red:49.012,white

4984 atoms, 672 residues, atom seq_conservation range -1.98 to 100  

> color byattribute r:seq_conservation #!2 target abcs palette
> -1.976,blue:-0.127492,white:2.18314,red

4984 atoms, 672 residues, atom seq_conservation range -1.98 to 100  

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_conservation #!2 target abcs palette
> -1.976,blue:-0.743662,white:3.41548,red

4984 atoms, 672 residues, atom seq_conservation range -1.98 to 100  

> select add #2

4984 atoms, 5073 bonds, 3 pseudobonds, 672 residues, 2 models selected  

> select subtract #2

Nothing selected  

> undo

> select #2/B

967 atoms, 975 bonds, 3 pseudobonds, 140 residues, 2 models selected  

> ui tool show "Selection Inspector"

> color sel #85cc9b atoms

> ui tool show "Selection Inspector"

> color sel #85cc9b target r

> select #2/A

3912 atoms, 3992 bonds, 519 residues, 1 model selected  

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_conservation #!2 target abcs palette
> -1.976,blue:-0.743662,white:1.25889,red

4984 atoms, 672 residues, atom seq_conservation range -1.98 to 100  

> color byattribute r:seq_conservation #!2 target abcs palette
> -1.976,blue:-0.127492,white:1.25889,red

4984 atoms, 672 residues, atom seq_conservation range -1.98 to 100  

> color byattribute r:seq_conservation #!2 target abcs palette
> -1.976,blue:-0.743662,white:1.25889,red

4984 atoms, 672 residues, atom seq_conservation range -1.98 to 100  

> color byattribute r:seq_conservation #!2 target abcs palette
> -1.976,blue:-0.743662,white:1.25889,red

4984 atoms, 672 residues, atom seq_conservation range -1.98 to 100  

> select add #2

4984 atoms, 5073 bonds, 3 pseudobonds, 672 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select #2/B

967 atoms, 975 bonds, 3 pseudobonds, 140 residues, 2 models selected  

> ui tool show "Selection Inspector"

> color sel #85cc9b atoms

> color sel #85cc9b target r

> select add #2

4984 atoms, 5073 bonds, 3 pseudobonds, 672 residues, 2 models selected  

> select subtract #2

Nothing selected  

> hide #1.3 models

> select #2/A

3912 atoms, 3992 bonds, 519 residues, 1 model selected  
Alignment identifier is 2/A  

> select #2/A:385

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #2/A:385

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #2/A:387

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #2/A:387-388

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select #2/A:387

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #2/A:387

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/C

105 atoms, 106 bonds, 13 residues, 1 model selected  

> ui tool show "Selection Inspector"

> color sel #aa63fe target r

> select clear

> select #2/A:387

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #2/A:387

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide #!1 models

> select clear

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 332, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 464, in _dispatch  
self.render(apply=apply)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 355, in render  
markers.coord_type = "absolute"  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 953, in coord_type  
self._convert_coords()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 1112, in _convert_coords  
m.xy = conv_func(m.xy)  
^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 718, in _rel2abs  
abs_x = self._min_val * (1-x) + x * self._max_val  
^^^^^^^^^^^^^  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 718, in _rel2abs  
abs_x = self._min_val * (1-x) + x * self._max_val  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_conservation #!2 target abcs palette
> 0,blue:0.5,white:1,red noValueColor gold

4984 atoms, 672 residues, atom seq_conservation range 100 to 100  

> undo

> select #2/A

3912 atoms, 3992 bonds, 519 residues, 1 model selected  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 332, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 464, in _dispatch  
self.render(apply=apply)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 355, in render  
markers.coord_type = "absolute"  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 953, in coord_type  
self._convert_coords()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 1112, in _convert_coords  
m.xy = conv_func(m.xy)  
^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 718, in _rel2abs  
abs_x = self._min_val * (1-x) + x * self._max_val  
^^^^^^^^^^^^^  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 718, in _rel2abs  
abs_x = self._min_val * (1-x) + x * self._max_val  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select add #2

4984 atoms, 5073 bonds, 3 pseudobonds, 672 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select add #2

4984 atoms, 5073 bonds, 3 pseudobonds, 672 residues, 2 models selected  

> ui tool show "Render/Select by Attribute"

> save /Users/peterngoi/Desktop/Lab/CycF/Figures/SCF-cycf-conservation.cxs

> close #1-2

> open
> /Users/peterngoi/Desktop/Lab/CycF/Figures/S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb

Chain information for
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open
> /Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF_refseq_protein.fasta

Sequence 'NP_031660.3 cyclin-F isoform 4 [Mus musculus]' differs in length
from preceding sequences, and it is therefore impossible to open these
sequences as an alignment. If you want to open the sequences individually,
specify 'false' as the value of the 'alignment' keyword in the 'open' command.  

> open
> /Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF_refseq_protein.fasta

Sequence 'NP_031660.3 cyclin-F isoform 4 [Mus musculus]' differs in length
from preceding sequences, and it is therefore impossible to open these
sequences as an alignment. If you want to open the sequences individually,
specify 'false' as the value of the 'alignment' keyword in the 'open' command.  

> open /Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF-conservation.aln

Summary of feedback from opening
/Users/peterngoi/Desktop/Lab/CycF/Modeling/Cyclin/CCNF-conservation.aln  
---  
notes | Alignment identifier is CCNF-conservation.aln  
Associated
S1F3-E2F1-pep_cf3_in_J501_real_space_refined_030-coot-4_real_space_refined_047-1_real_space_refined_052-1_real_space_refined_055.pdb
chain A to NP_001752.2/1-786 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment CCNF-conservation.aln  
  
Opened 6 sequences from CCNF-conservation.aln  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
Alignment identifier is 1/C  

> select /A:35-87

417 atoms, 430 bonds, 53 residues, 1 model selected  

> select /A:35-454

3213 atoms, 3279 bonds, 420 residues, 1 model selected  

> select add #1

4984 atoms, 5073 bonds, 3 pseudobonds, 672 residues, 2 models selected  

> select /A

3912 atoms, 3992 bonds, 519 residues, 1 model selected  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 332, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 464, in _dispatch  
self.render(apply=apply)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 355, in render  
markers.coord_type = "absolute"  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 953, in coord_type  
self._convert_coords()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 1112, in _convert_coords  
m.xy = conv_func(m.xy)  
^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 718, in _rel2abs  
abs_x = self._min_val * (1-x) + x * self._max_val  
^^^^^^^^^^^^^  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 718, in _rel2abs  
abs_x = self._min_val * (1-x) + x * self._max_val  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,4
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
      OS Loader Version: 580~2215

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 2 days, 3 hours, 47 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.2.2
    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-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by pett, 14 months ago

Component: Unassigned → General Controls
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → 'MarkedHistogram' object has no attribute '_min_val'

comment:2 by pett, 14 months ago

Resolution: → duplicate
Status: accepted → closed

Hi Peter,

Thanks for reporting this problem. It has been fixed in the daily build, so if you use that then you won't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

Note: See TracTickets for help on using tickets.