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Opened 18 months ago
Closed 17 months ago
#15362 closed defect (fixed)
vdx_attrs.py script needs revision
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Attachments (1)
Change History (5)
comment:1 by , 18 months ago
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → vdx_attrs.py script needs revision |
comment:2 by , 18 months ago
comment:3 by , 17 months ago
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
comment:4 by , 17 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Hi Krish,
--Eric