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Opened 9 months ago
Closed 9 months ago
#16888 closed defect (duplicate)
Render By Attribute: switching attributes does not preserve marker radius
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
warning | QCoreApplication::postEvent: Unexpected null receiver
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1pho format mmcif fromDatabase pdb
1pho title:
Crystal structures explain functional properties of two E. Coli porins [more
info...]
Chain information for 1pho #1
---
Chain | Description | UniProt
A | PHOSPHOPORIN | PHOE_ECOLI 1-340
1pho mmCIF Assemblies
---
1| author_and_software_defined_assembly
> sym #1 assembly 1
Made 3 copies for 1pho assembly 1
> ui tool show "Render/Select by Attribute"
> cartoon byattribute a:bfactor #1#2.1-3 3.77:0.25 72.57:2
1320 residues, residue bfactor range 9.69 to 60.5
Cell requested for row 1 is out of bounds for table with 5 rows! Resizing
table model.
> close #2
> select add #1
2602 atoms, 2654 bonds, 330 residues, 1 model selected
> close
> open /Users/martinaaudagnotto/Desktop/flub/1.prediction/*.pdb format pdb
Chain information for
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1
---
Chain | Description
A B C | No description available
Chain information for
bfd_uniref_hits_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
#2
---
Chain | Description
A B C | No description available
Chain information for
bfd_uniref_hits_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb
#3
---
Chain | Description
A B C | No description available
Chain information for
bfd_uniref_hits_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb
#4
---
Chain | Description
A B C | No description available
Chain information for
bfd_uniref_hits_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb
#5
---
Chain | Description
A B C | No description available
Computing secondary structure
[Repeated 4 time(s)]
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> lighting flat
> open
> /Users/martinaaudagnotto/Desktop/FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb
#6
---
Chain | Description
E G K | No description available
F I N | No description available
H J O | No description available
L M P | No description available
V W X | No description available
> mmaker #6 to #1 show true
Computing secondary structure
[Repeated 1 time(s)] 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
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1) with FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb,
chain E (#6), sequence alignment score = 1739
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1/A, FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb #6/E
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 330 pruned atom pairs is 0.661 angstroms; (across all 349 pairs:
1.379)
> select add #6
19719 atoms, 20163 bonds, 2592 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> split #6
Split FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb (#6) into 15
models
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb E
#6.1
---
Chain | Description
E | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb F
#6.2
---
Chain | Description
F | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb G
#6.3
---
Chain | Description
G | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb H
#6.4
---
Chain | Description
H | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb I
#6.5
---
Chain | Description
I | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb J
#6.6
---
Chain | Description
J | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb K
#6.7
---
Chain | Description
K | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb L
#6.8
---
Chain | Description
L | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb M
#6.9
---
Chain | Description
M | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb N
#6.10
---
Chain | Description
N | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb O
#6.11
---
Chain | Description
O | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb P
#6.12
---
Chain | Description
P | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb V
#6.13
---
Chain | Description
V | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb W
#6.14
---
Chain | Description
W | No description available
Chain information for FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb X
#6.15
---
Chain | Description
X | No description available
Associated FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb E (6.1)
chain E to FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb, chain E
with 0 mismatches
Associated FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb F (6.2)
chain F to
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A with 1 mismatch
Associated FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb G (6.3)
chain G to FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb, chain E
with 0 mismatches
Associated FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb I (6.5)
chain I to
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A with 1 mismatch
Associated FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb K (6.7)
chain K to FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb, chain E
with 0 mismatches
Associated FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb N (6.10)
chain N to
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A with 1 mismatch
Chains used in RMSD evaluation for alignment 1:
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1/A, FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb E #6.1/E,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb F #6.2/F,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb G #6.3/G,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb I #6.5/I,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb K #6.7/K,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb N #6.10/N
> hide #6.4 models
> hide #6.5 models
> hide #6.6 models
> hide #6.8 models
> hide #6.9 models
> hide #6.10 models
> hide #6.11 models
> hide #6.12 models
> hide #6.13 models
> hide #6.14 models
> hide #6.15 models
> close #6.8-15
Chains used in RMSD evaluation for alignment 1:
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1/A, FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb E #6.1/E,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb F #6.2/F,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb G #6.3/G,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb I #6.5/I,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb K #6.7/K
> close #6.4-6
Chains used in RMSD evaluation for alignment 1:
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1/A, FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb E #6.1/E,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb F #6.2/F,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb G #6.3/G,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb K #6.7/K
> combine #6.1-3 +#6.7
Expected a keyword
> combine #6.1-3 \+ #6.7
Expected a keyword
> combine #6.1-3 & #6.7
No structures specified
> combine #6.1-3, #6.7
Expected a keyword
> combine #6.1-3
Associated combination chain E to
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb, chain E with 0
mismatches
Associated combination chain G to
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb, chain E with 0
mismatches
Associated combination chain F to
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A with 1 mismatch
Chains used in RMSD evaluation for alignment 1:
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1/A, FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb E #6.1/E,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb F #6.2/F,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb G #6.3/G,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb K #6.7/K, combination
#7/E
> combine #6.1-3 and #6.7
Expected a keyword
> combine #6.1,#6.2
Expected a keyword
> combine #6.1 #6.2
Associated combination chain E to
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb, chain E with 0
mismatches
Associated combination chain F to
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A with 1 mismatch
Chains used in RMSD evaluation for alignment 1:
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1/A, FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb E #6.1/E,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb F #6.2/F,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb G #6.3/G,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb K #6.7/K, combination
#7/E, combination #8/E
> combine #6.1 #6.2 #6.3 #6.7
Associated combination chain E to
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb, chain E with 0
mismatches
Associated combination chain G to
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb, chain E with 0
mismatches
Associated combination chain K to
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb, chain E with 0
mismatches
Associated combination chain F to
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A with 1 mismatch
Chains used in RMSD evaluation for alignment 1:
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1/A, FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb E #6.1/E,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb F #6.2/F,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb G #6.3/G,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb K #6.7/K, combination
#7/E, combination #8/E, combination #9/E
> close #7-8
Chains used in RMSD evaluation for alignment 1:
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1/A, FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb E #6.1/E,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb F #6.2/F,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb G #6.3/G,
FluB_GSK2115_SD83_5A7_trimer_rosetta_coot_phenix_8.pdb K #6.7/K, combination
#9/E
> rename #9 gsk_combination
> hide #!6 models
> hide #6.1 models
> hide #6.2 models
> hide #6.3 models
> hide #6.7 models
> view
> mmaker #1 to #9
Computing secondary structure
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 gsk_combination, chain E (#9) with
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 1739
RMSD between 330 pruned atom pairs is 0.661 angstroms; (across all 349 pairs:
1.379)
> mmaker #1 to #9 show true
Computing secondary structure
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 gsk_combination, chain E (#9) with
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#1), sequence alignment score = 1739
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
bfd_uniref_hits_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1/A, gsk_combination #9/E
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 330 pruned atom pairs is 0.661 angstroms; (across all 349 pairs:
1.379)
> hide #9 models
> select add #1
12444 atoms, 12684 bonds, 1638 residues, 1 model selected
> ui tool show "Render/Select by Attribute"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 181, in <lambda>
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 740, in _select_marker_cb
self._set_sel_marker(marker, drag_start=event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 760, in _set_sel_marker
self._select_callback(self._prev_markers, self._prev_marker,
self._active_markers, marker)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 728, in _render_sel_marker_cb
value_entry.setText("%g" % cur_marker.radius)
^^^^^^^^^^^^^^^^^
AttributeError: 'HistogramMarker' object has no attribute 'radius'
AttributeError: 'HistogramMarker' object has no attribute 'radius'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 728, in _render_sel_marker_cb
value_entry.setText("%g" % cur_marker.radius)
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 181, in <lambda>
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 740, in _select_marker_cb
self._set_sel_marker(marker, drag_start=event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 760, in _set_sel_marker
self._select_callback(self._prev_markers, self._prev_marker,
self._active_markers, marker)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 728, in _render_sel_marker_cb
value_entry.setText("%g" % cur_marker.radius)
^^^^^^^^^^^^^^^^^
AttributeError: 'HistogramMarker' object has no attribute 'radius'
AttributeError: 'HistogramMarker' object has no attribute 'radius'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 728, in _render_sel_marker_cb
value_entry.setText("%g" % cur_marker.radius)
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 181, in <lambda>
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 740, in _select_marker_cb
self._set_sel_marker(marker, drag_start=event)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 760, in _set_sel_marker
self._select_callback(self._prev_markers, self._prev_marker,
self._active_markers, marker)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 728, in _render_sel_marker_cb
value_entry.setText("%g" % cur_marker.radius)
^^^^^^^^^^^^^^^^^
AttributeError: 'HistogramMarker' object has no attribute 'radius'
AttributeError: 'HistogramMarker' object has no attribute 'radius'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 728, in _render_sel_marker_cb
value_entry.setText("%g" % cur_marker.radius)
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3T/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 5 days, 4 hours, 27 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
C27F398:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Render By Attribute: switching attributes does not preserve marker radius |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate of #16536