Render By Attribute: switching attributes does not preserve marker radius

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
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  
---  
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 7t6x format mmcif fromDatabase pdb

7t6x title:  
Cryo-EM structure of full-length hepatitis C virus E1E2 glycoprotein in
complex with AR4A, AT12009, and IGH505 Fabs [more info...]  
  
Chain information for 7t6x #1  
---  
Chain | Description | UniProt  
A | IGH505, heavy chain |   
B | IGH505, lambda light chain |   
C | AT12009 CrossMab, heavy chain |   
D | AT12009 crossMab, light kappa chain |   
E | Envelope glycoprotein E1 | A0A159UHX2_9HEPC 192-383  
H | AR4A Fab, heavy chain |   
L | AR4A, kappa light chain |   
U | Envelope glycoprotein E2 | A0A159UHX2_9HEPC 384-746  
  
Non-standard residues in 7t6x #1  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> set bgColor white

> select /H

1093 atoms, 1125 bonds, 140 residues, 1 model selected  

> color sel light gray

> select /L

802 atoms, 820 bonds, 106 residues, 1 model selected  

> color sel light gray

> select /C

1059 atoms, 1085 bonds, 144 residues, 1 model selected  

> color sel light gray

> select /D

788 atoms, 807 bonds, 105 residues, 1 model selected  

> color sel light gray

> select /E

929 atoms, 958 bonds, 1 pseudobond, 119 residues, 2 models selected  

> select /E

929 atoms, 958 bonds, 1 pseudobond, 119 residues, 2 models selected  

> color (#!1 & sel) hot pink

> select /U

2406 atoms, 2502 bonds, 303 residues, 1 model selected  

> color sel cornflower blue

> select /A

960 atoms, 989 bonds, 122 residues, 1 model selected  

> color sel light gray

> select /B

785 atoms, 806 bonds, 107 residues, 1 model selected  

> color sel light gray

> select none

Expected an objects specifier or a keyword  

> deselect all

Unknown command: deselect all  

> select ::name="BMA"

77 atoms, 77 bonds, 7 residues, 1 model selected  

> color sel bypolymer

[Repeated 1 time(s)]

> show sel surfaces

> hide sel surfaces

> show sel cartoons

[Repeated 1 time(s)]

> show sel atoms

> hide sel atoms

> select ::name="MAN"

66 atoms, 67 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select ::name="NAG"

336 atoms, 345 bonds, 24 residues, 1 model selected  

> style sel sphere

Changed 336 atom styles  

> color sel lime

> select /H

1093 atoms, 1125 bonds, 140 residues, 1 model selected  

> color sel bypolymer

> show sel surfaces

> transparency (#!1 & sel) 60

> transparency (#!1 & sel) 20

> set bgColor black

> set bgColor transparent

> select /L

802 atoms, 820 bonds, 106 residues, 1 model selected  

> show sel surfaces

> transparency (#!1 & sel) 40

> select /H

1093 atoms, 1125 bonds, 140 residues, 1 model selected  

> select /H

1093 atoms, 1125 bonds, 140 residues, 1 model selected  

> transparency (#!1 & sel) 20

> select /L

802 atoms, 820 bonds, 106 residues, 1 model selected  

> show sel surfaces

> transparency (#!1 & sel) 20

> select /C

1059 atoms, 1085 bonds, 144 residues, 1 model selected  

> show sel surfaces

> transparency (#!1 & sel) 20

> select /D

788 atoms, 807 bonds, 105 residues, 1 model selected  

> show sel surfaces

> transparency (#!1 & sel) 20

> select /E

929 atoms, 958 bonds, 1 pseudobond, 119 residues, 2 models selected  

> show sel surfaces

> select /U

2406 atoms, 2502 bonds, 303 residues, 1 model selected  

> show sel surfaces

> select /A

960 atoms, 989 bonds, 122 residues, 1 model selected  

> show sel surfaces

> transparency (#!1 & sel) 20

> select /B

785 atoms, 806 bonds, 107 residues, 1 model selected  

> show sel surfaces

> transparency (#!1 & sel) 20

> select /H

1093 atoms, 1125 bonds, 140 residues, 1 model selected  

> color (#!1 & sel) light gray

> select ::name="NAG"

336 atoms, 345 bonds, 24 residues, 1 model selected  

> show sel surfaces

> select all

9217 atoms, 9518 bonds, 1 pseudobond, 1177 residues, 2 models selected  

> color sel bypolymer

> undo

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> transparency sel 0

> cartoon style (#!1 & sel) modeHelix tube sides 20

> hide sel surfaces

> show sel cartoons

> cartoon style (#!1 & sel) modeHelix tube sides 20

> hide (#!1 & sel-residues & (protein|nucleic)) target a

> cartoon hide (#!1 & sel-residues)

> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> undo

[Repeated 3 time(s)]

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1

> cartoon #0

> show sel cartoons

> worm #0

No known/registered numeric attribute #0  

> worm sel cartoons

> cartoon byattribute sel cartoons

Expected attr-value:radius pair, repeatable or a keyword  

> worm all

No known/registered numeric attribute all  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 740, in _select_marker_cb  
self._set_sel_marker(marker, drag_start=event)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
All 'occupancy' values are 1  
[Repeated 1 time(s)]No attribute chosen for rendering  

> select /H

1093 atoms, 1125 bonds, 140 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> hide sel surfaces

> select /L

802 atoms, 820 bonds, 106 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> hide sel surfaces

> select /C

1059 atoms, 1085 bonds, 144 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> select /D

788 atoms, 807 bonds, 105 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> select /A

960 atoms, 989 bonds, 122 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> select /A

960 atoms, 989 bonds, 122 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> select /B

785 atoms, 806 bonds, 107 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> select /E

929 atoms, 958 bonds, 1 pseudobond, 119 residues, 2 models selected  

> hide sel surfaces

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> show sel worm

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> worm sel

No known/registered numeric attribute sel  

> ui tool show "Render/Select by Attribute"

No attribute chosen for rendering  
All 'worm_radius' values are 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
All 'worm_radius' values are 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
All 'occupancy' values are 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> hide sel surfaces

> show sel surfaces

> worm sel surface

> cartoon byattribute sel surface

Expected attr-value:radius pair, repeatable or a keyword  

> alias

Missing or invalid "name" argument: Expected a text string  

> alias licorice cartoon 7t6x modeh default arrows f xsect oval width 1 thick
> 1

> color sel bypolymer

> undo

> alias licorice cartoon /E modeh default arrows f xsect oval width 1 thick 1

> hide sel surfaces

> show sel surfaces

> show sel cartoons

> hide sel surfaces

> alias licorice cartoon /E modeh default arrows f xsect oval width 1 thick 1

> alias worm cartoon /E modeh default arrows f xsect oval width 1 thick 1

FYI: alias is hiding existing command: "worm"  

> cartoon /E modeh default arrows f xsect oval width 1 thick 1

Expected fewer arguments  

> cartoon /E

Expected fewer arguments  

> worm

> cartoon /E modeh default arrows f xsect oval width 1 thick 1

Expected a keyword  

> worm

> cartoon /E modeh default arrows f xsect oval width 1 thick 1

Expected a keyword  

> /E

Expected fewer arguments  

> ~worm

> show sel surfaces

> style sel stick

Changed 929 atom styles  

> undo

> hide sel surfaces

> hide sel cartoons

> show sel cartoons

> show sel atoms

> hide sel cartoons

> hide sel atoms

> show sel surfaces

> bfactor min:0.2 max:2.5

Expected fewer arguments  

> bfactor

Expected fewer arguments  

> worm

> cartoon /E modeh default arrows f xsect oval width 1 thick 1

Expected a keyword  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
All 'occupancy' values are 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 348, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self._dispatch(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 586, in _dispatch  
self.render(apply=apply)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
AttributeError: 'HistogramMarker' object has no attribute 'radius'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 426, in render  
vals.append((marker.xy[0], getattr(marker, "rgba" if method == "color" else
"radius")))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
All 'worm_radius' values are 1  

> cartoon | worm

Expected an atoms specifier or a keyword  

> /E worm

Unknown command: /E worm  

> ribbon

> show sel cartoons

[Repeated 1 time(s)]

> hide sel surfaces

> show sel surfaces

> hide sel cartoons

> cartoon

> cartoon /E

> /E

Expected fewer arguments  

> cartoon /E worm

Expected a keyword  

> cartoon byattribute (worm)

No known/registered numeric attribute (worm)  

> cartoon byattribute worm

No known/registered numeric attribute worm  

> cartoon byattribute /E worm

Expected attr-value:radius pair, repeatable or a keyword  

> cartoon byattribute ribbon

No known/registered numeric attribute ribbon  

> cartoon byattribute (ribbon)

No known/registered numeric attribute (ribbon)  

> cartoon byattribute /E ribbon

Expected attr-value:radius pair, repeatable or a keyword  

> (cartoon byattribute | worm)

Unknown command: (cartoon byattribute | worm)  

> cartoon byattribute bfactor #1 min:0.2 max:2.5

1140 residues, residue bfactor range 11.6 to 578  

> hide sel surfaces

> show sel surfaces

> byattr bfactor #1 min:0.2 max:2.5

Expected fewer arguments  

> bfactor #1 min:0.2 max:2.5

Expected fewer arguments  

> byattribute bfactor #1 min:0.2 max:2.5

Expected fewer arguments  

> byattribute bfactor /E min:0.2 max:2.5

Expected fewer arguments  

> bfactor /E min:0.2 max:2.5

Expected fewer arguments  

> hide sel surfaces

> select /H

1093 atoms, 1125 bonds, 140 residues, 1 model selected  

> select /U

2406 atoms, 2502 bonds, 303 residues, 1 model selected  

> cartoon hide (#!1 & sel)

> hide sel surfaces

> hide sel cartoons

> select /U

2406 atoms, 2502 bonds, 303 residues, 1 model selected  

> hide sel cartoons

> hide sel surfaces

> hide sel atoms

> hide sel cartoons

> show sel atoms

> undo

> select ::name="NAG"

336 atoms, 345 bonds, 24 residues, 1 model selected  

> hide sel atoms

> worm

> cartoon /E modeh default arrows f xsect oval width 1 thick 1

Expected a keyword  

> cartoon /E bfactor

Expected fewer arguments  

> cartoon /E 2

Expected fewer arguments  

> ui tool show "Render/Select by Attribute"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 740, in _select_marker_cb  
self._set_sel_marker(marker, drag_start=event)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\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 "C:\Program Files\ChimeraX 1.9\bin\Lib\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: 3.3.0 - Build 32.0.101.5768
OpenGL renderer: Intel(R) Arc(TM) Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: HP
Model: HP Spectre x360 2-in-1 Laptop 14-eu0xxx
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,500,387,840
MaxProcessMemory: 137,438,953,344
CPU: 22 Intel(R) Core(TM) Ultra 7 155H
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    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: 2024.8.30
    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
    comtypes: 1.4.5
    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
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    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
    pywin32: 306
    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
    WMI: 1.5.1

[Eric Pettersen]

Duplicate of #16536