vdx_attrs.py script needs revision

[rkrishnan@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.8.dev202404110651 (2024-04-11 06:51:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warnings | No presets found in custom preset folder L:/Graphics/BCRX001/GraphicsBackup\\.temp  
No presets found in custom preset folder
L:/Graphics/BCRX001/GraphicsBackup\4161-prodrugs  
No presets found in custom preset folder
L:/Graphics/BCRX001/GraphicsBackup\7atf  
No presets found in custom preset folder
L:/Graphics/BCRX001/GraphicsBackup\alternate pathway animations  
No presets found in custom preset folder
L:/Graphics/BCRX001/GraphicsBackup\azasugar-publiation  
26 messages similar to the above omitted  
  
developer warning: toolbar 'Medical Image' depends on non-existent 'map'  

> cd L:/Graphics/BCRX001/GraphicsBackup/kallikrein/7353-xray/docking-movie-
> for-babu-mar2024

Current working directory is:
L:\Graphics\BCRX001\GraphicsBackup\kallikrein\7353-xray\docking-movie-for-
babu-mar2024  
UCSF ChimeraX version: 1.8.dev202404110651 (2024-04-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Compositor returned null texture  

> open L:/Graphics/BCRX001/GraphicsBackup/chimerax-test/facd_june3.mol2

Opened facd_june3.mol2 containing 97 structures (3145 atoms, 3439 bonds)  

> viewdockx #1.1-97

> open "C:/Users/RKrishnan/Desktop/chimerax recipe .py/vdx_attrs.py"

The following numeric ViewDockX attributes were registered: vdx_BCX_num,
vdx_EA, vdx_HA, vdx_MolWeight, vdx_viewdockx_rating  
The following non-numeric ViewDockX attributes were registered:
vdx_Registration_Number  
executed vdx_attrs.py  

> tile spacingFactor 1.8

97 models tiled  
Compositor returned null texture  
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')  

> hide #1.1-97 models

JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')  

> show #1.1-97 models

JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')  

> hide #1.1-97 models

> show #1.1-97 models

> label #1 residues byattribut text" {0.structure.vdx_BCX_num}

Expected a keyword  

> label #1 residues byattribut text "{0.structure.vdx_BCX_num}"

Expected a keyword  

> label #1 residues attribute text "{0.structure.vdx_BCX_num}"

Expected a keyword  

> label #1 residues text "{0.structure.vdx_Registration_Number}, EA
> (nM){0.structure.vdx_EA}" offset -8,-8,1 height 1.5

> label #1 residues text "{0.structure.vdx_BCX_num}, EA
> (nM){0.structure.vdx_EA}" offset -8,-8,1 height 1.5

> label #1 residues text "{0.structure.vdx_BCX_num}, EA
> (nM){0.structure.vdx_EA}" offset -8,-8,1 height 1.8

> label #1 residues text "{0.structure.vdx_BCX_num}, EA (nM)
> {0.structure.vdx_EA}" offset -8,-8,1 height 1.8

> label #1 residues text "{0.structure.vdx_BCX_num} EA (nM)
> {0.structure.vdx_EA}" offset -8,-8,1 height 1.8

JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')  

> hide #!1.1-97 models

JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')  

> show #!1.1-97 models

> hide #!1.1-97 models

> show #!1.1-97 models

JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')  

> hide #!1.1-97 models

JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')  

> show #!1.97 models

> hide #!1.97 models

> show #!1.1-97 models

> close session

> open L:\Graphics\BCRX001\GraphicsBackup\chimerax-test\facd_june3.mol2 format
> mol2

Opened facd_june3.mol2 containing 96 structures (3104 atoms, 3394 bonds)  

> viewdockx #1.1-96

> tile spacingFactor 1.8

96 models tiled  

> label #1 residues text "{0.structure.vdx_BCX_num} EA (nM)
> {0.structure.vdx_EA}" offset -8,-8,1 height 1.8

> open "C:/Users/RKrishnan/Desktop/chimerax recipe .py/vdx_attrs.py"

The following numeric ViewDockX attributes were registered: vdx_BCX_num,
vdx_EA, vdx_HA, vdx_MolWeight, vdx_viewdockx_rating  
The following non-numeric ViewDockX attributes were registered:  
executed vdx_attrs.py  

> label #1 residues text "{0.structure.vdx_BCX_num} EA (nM)
> {0.structure.vdx_EA}" offset -8,-8,1 height 1.8

> color byatrribut vdx_EA

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byattribute vdx_EA palette redblue

3104 atoms, 96 residues, atom vdx_EA range 13 to 145  
Fetching compressed palette greenwhitered from
https://www.colourlovers.com/api/palettes?keywords=greenwhitered&format=json&numResults=100  
Could not find palette greenwhitered at COLOURlovers.com using keyword search  
Fetching compressed palette greenred from
https://www.colourlovers.com/api/palettes?keywords=greenred&format=json&numResults=100  
Found 8 ColourLover palettes with name "greenred", using palette id 3264453 by
author normalachance with most views (34). To choose a different one use "name
by author" or id number.  

> color byattribute vdx_EA palette greenred

3104 atoms, 96 residues, atom vdx_EA range 13 to 145  
Fetching compressed palette redgreen from
https://www.colourlovers.com/api/palettes?keywords=redgreen&format=json&numResults=100  
Found 11 ColourLover palettes with name "redgreen", using palette id 1277402
by author rififie with most views (53). To choose a different one use "name by
author" or id number.  

> color byattribute vdx_EA palette redgreen

3104 atoms, 96 residues, atom vdx_EA range 13 to 145  

> color byattribute vdx_EA palette bluered

3104 atoms, 96 residues, atom vdx_EA range 13 to 145  
Fetching compressed palette range from
https://www.colourlovers.com/api/palettes?keywords=range&format=json&numResults=100  
Found 2 ColourLover palettes with name "range", using palette id 1009217 by
author alpen with most views (118). To choose a different one use "name by
author" or id number.  

> color byattribute vdx_EA palette range 13,145

Expected a keyword  
Compositor returned null texture  

> hide #!1.5 models

> show #!1.5 models

> hide #!1.1-96 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.20 models

> show #!1.19 models

> show #!1.18 models

> hide #!1.18-20 models

> show #!1.17 models

JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')  

> hide #!1.17 models

> show #!1.1 models

> show #!1.2 models

> show #!1.3 models

> show #!1.4 models

> show #!1.5 models

> show #!1.6 models

> show #!1.22 models

> show #!1.21 models

> show #!1.20 models

> show #!1.19 models

> show #!1.18 models

> show #!1.17 models

> show #!1.16 models

> hide #!1.1-6,16-22 models

> show #!1.15 models

> show #!1.14 models

> show #!1.13 models

> show #!1.12 models

> show #!1.11 models

> show #!1.10 models

> show #!1.9 models

> show #!1.8 models

> show #!1.7 models

> show #!1.6 models

> show #!1.5 models

> show #!1.4 models

> show #!1.3 models

> show #!1.2 models

> show #!1.1 models

Drag select of 449 atoms, 492 bonds  

> color sel byelement

> select clear

> select carbonyl

Nothing selected  

> select carboxylate

294 atoms, 196 bonds, 96 residues, 96 models selected  

> style (#!1.1-15 & sel) ball

Changed 48 atom styles  

> select clear

> undo

> ui tool show "Color Actions"

> set bgColor white

Drag select of 420 atoms, 460 bonds  

> color sel forest green

> color sel byhetero

> graphics silhouettes true

> graphics silhouettes false

> set bgColor gray

> set bgColor black

> select clear

> help help:user

> select #1 & vdx_EA >10

Expected a keyword  

> select #1 & 0.structure.vdx_EA >10

Expected a keyword  

> select #1 & {0.structure.vdx_EA}>10

Expected a keyword  

> :: & vdx_EA>10

Unknown command: :: & vdx_EA>10  

> :: & {0.structure.vdx_EA}>10

Unknown command: :: & {0.structure.vdx_EA}>10  

> select :: & vdx_EA>10

Expected an objects specifier or a keyword  
Drag select of 41 atoms, 45 bonds  

> ui tool show "Selection Inspector"

> select {0.structure.vdx_EA}>10

Expected an objects specifier or a keyword  

> select#1 residues {0.structure.vdx_EA}>10

Unknown command: select#1 residues {0.structure.vdx_EA}>10  

> select #1 residues {0.structure.vdx_EA}>10

Invalid "residues" argument: Expected true or false (or 1 or 0)  

> select #1

3104 atoms, 3394 bonds, 96 residues, 193 models selected  

> select clear

> select #1 residues

Missing "residues" keyword's argument  

> select #1::

Expected an objects specifier or a keyword  

> @@display

Unknown command: @@display  

> select #!1.1-96::num_atoms>=33.329 & ::num_atoms<=37.671

617 atoms, 671 bonds, 18 residues, 18 models selected  

> select #!1.1-96::vdx_EA>=10

Nothing selected  

> select #!1.1-96::0.structure.vdx_EA>=10

Expected an objects specifier or a keyword  

> select #!1.1-96::{0.structure.vdx_EA}>=10

Expected an objects specifier or a keyword  

> select #!1.1-96 & {0.structure.vdx_EA}>=10

Expected a keyword  

> select #!1.1-96

3104 atoms, 3394 bonds, 96 residues, 96 models selected  

> select #!1.1-96 & vdx_EA>10;

Expected a keyword  

> select #!1.1-96 & {0.structure.vdx_EA}>10;

Expected a keyword  

> select #!1.1-96 & byattribut {0.structure.vdx_EA}>10;

Expected a keyword  

> select #!1.1-96 & ::vdx_EA>10

Nothing selected  

> select #!1.1-96 & #1 byattribute vdx_EA>10;

Expected a keyword  

> select #!1.1-96

3104 atoms, 3394 bonds, 96 residues, 96 models selected  

> select #!1.1-96 vdx_EA>15

Expected a keyword  

> select #!1.1-96 by attribut vdx_EA>15

Expected a keyword  

> color byattribute vdx_EA>10

No known/registered numeric attribute vdx_EA>10  

> open "C:/Users/RKrishnan/Desktop/chimerax recipe .py/vdx_attrs.py"

The following numeric ViewDockX attributes were registered: vdx_BCX_num,
vdx_EA, vdx_HA, vdx_MolWeight, vdx_viewdockx_rating  
The following non-numeric ViewDockX attributes were registered:  
executed vdx_attrs.py  

> color byattribute vdx_EA>10

No known/registered numeric attribute vdx_EA>10  

> color byattribute {0.structure.vdx_EA}>10

No known/registered numeric attribute {0.structure.vdx_EA}>10  

> color byattribute vdx_EA palette redblue

3104 atoms, 96 residues, atom vdx_EA range 13 to 145  

> select byattribut vdx_EA>10

Expected an objects specifier or a keyword  

> select #1 byattribut vdx_EA>10

Expected a keyword  

> select #!=1.1-96 byattribut vdx_EA>10

Expected an objects specifier or a keyword  

> select #!1.1-96 &

Expected a keyword  

> select clear

> select #!1.1-96

3104 atoms, 3394 bonds, 96 residues, 96 models selected  

> select #!1.1-96 & ::vdx_EA>10;

Nothing selected  

> select #!1.1-96 & ::vdx_EA =13;

Nothing selected  

> select #!1.1-96 & ##vdx_EA =13;

Nothing selected  

> select #!1.1-96 & 0.structure.vdx_EA>10;

Expected a keyword  

> select #!1.1-96 & by attribut 0.structure.vdx_EA>10;

Expected a keyword  

> select #!1.1-96 & by attribut vdx_EA>10;

Expected a keyword  

> select #!1.1-96 & byattribut vdx_EA>10;

Expected a keyword  

> select #!1.1-96 & element C

Expected a keyword  

> select #!1.1-96 & :vdx_EA>10

Expected a keyword  

> select #!1.1-96 & ::vdx_EA>10

Nothing selected  

> select #!1.1-96 & ::vdx_EA=10

Nothing selected  

> select #!1.1-96 & ::vdx_EA=100

Nothing selected  

> select #!1.1-96 & 0.structure.vdx_EA=10

Expected a keyword  

> select #!1.1-96 & ::0.structure.vdx_EA=10

Expected a keyword  

> select #!1.1-96 & :0.structure.vdx_EA=10

Expected a keyword  

> select #!1.1-96 & :vdx_EA=10

Expected a keyword  

> select #!1.1-96 & :vdx_EA>10;

Expected a keyword  
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')  

> hide #!1.1-15 models

> show #!1.1-96 models

> label #1 residues text "{0.structure.vdx_BCX_num} HA (nM)
> {0.structure.vdx_HA}" offset -8,-8,1 height 1.8

[Repeated 1 time(s)]

> select #1 residues;

Invalid "residues" argument: Expected true or false (or 1 or 0)  

> label #1 residues text "{0.structure.vdx_BCX_num} HA (nM)
> {0.structure.vdx_HA}" offset -8,-8,1 height 1.8

> select #1 ::;

Expected a keyword  

> label #1 residues text "{0.structure.vdx_BCX_num} HA (nM)
> {0.structure.vdx_HA}" offset -8,-8,1 height 1.8

> select #!11.1-96

Nothing selected  
Drag select of 71 atoms, 78 bonds  

> select #!1.1-96

3104 atoms, 3394 bonds, 96 residues, 96 models selected  

> ui tool show "Selection Inspector"

> select #!1.1-96 & vdx_HA>10

Expected a keyword  

> select #!1.1-96 & 0.structure.vdx_HA>10

Expected a keyword  

> select #!1.1-96 & #1 residues attribut 0.structure.vdx_HA>10

Invalid "residues" argument: Expected true or false (or 1 or 0)  

> select #!1.1-96 & #1 attribut 0.structure.vdx_HA>10

Expected a keyword  

> select #!1.1-96 & #1.1 attribut vdx_HA>10

Expected a keyword  

> select #!1.1-96 & #1 residues attribut 0.structure .vdx_HA>10

Invalid "residues" argument: Expected true or false (or 1 or 0)  

> select #!1.1-96 & attribut 0.structure .vdx_HA>10

Expected a keyword  

> select #1 residues

Missing "residues" keyword's argument  

> select #1

3104 atoms, 3394 bonds, 96 residues, 193 models selected  

> ui tool show "Selection Inspector"

> setattr sel structures name "-- multiple --"

Assigning name attribute to 96 items  

> setattr sel struct display false

Assigning display attribute to 96 items  

> setattr sel struct display true

Assigning display attribute to 96 items  

> setattr sel structures autochain false

Assigning autochain attribute to 96 items  

> setattr sel structures autochain true

Assigning autochain attribute to 96 items  

> select clear

> open "C:/Users/RKrishnan/Desktop/chimerax recipe .py/vdx_attrs.py"

The following numeric ViewDockX attributes were registered: vdx_BCX_num,
vdx_EA, vdx_HA, vdx_MolWeight, vdx_viewdockx_rating  
The following non-numeric ViewDockX attributes were registered:  
executed vdx_attrs.py  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 534, in _new_select_attr  
self._update_select_widget(attr_name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 657, in _update_select_widget  
self._update_histogram(self.select_histogram, attr_name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 692, in _update_histogram  
histogram.data_source = (min_val, max_val, lambda num_bins:  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 350, in data_source  
self._new_data()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 611, in _new_data  
self._redraw_cb()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 634, in _redraw_cb  
filled_range = self._max_val - self._min_val  
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~  
TypeError: unsupported operand type(s) for -: 'numpy.str_' and 'numpy.str_'  
  
TypeError: unsupported operand type(s) for -: 'numpy.str_' and 'numpy.str_'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\histogram.py", line 634, in _redraw_cb  
filled_range = self._max_val - self._min_val  
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 517.40
OpenGL renderer: Quadro P5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: To Be Filled By O.E.M.
Model: B550M-C
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 17,047,228,416
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5700                               
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56.1
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202404110651
    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
    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: 1.1.9
    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
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    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: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    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: 2.1
    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: 1.0
    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: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    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: 1.37.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.3.1
    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: 3.13.3
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    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: 0.1.6
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    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
    pywin32: 306
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.2.0
    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: 2.0.0
    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
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

[pett]

Hi Krish,

Due to changes in ViewDockX, the vdx_attrs.py script needs some revision. I will let you know when I have a new version.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[pett]

In addition to the revised script (which I've attached and will be updating the Recipes page with), you will need to get tomorrow's release candidate build or daily build.

--Eric

vdx_attrs.py​

[pett]

Added by email2trac

[pett]

Fix: ​https://github.com/RBVI/ChimeraX/commit/4c450ede3ca339e87efd86e78ca8fa79689b0b20