The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Would be useful if the ChimeraX clipper command documentation were online. Google cannot find it, although the "help clipper" command shows it.
Log:
Startup Errors
---
error | Bundle 'ChimeraX-ISOLDE' custom initialization failed
warning | Traceback (most recent call last):
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module
m = importlib.import_module(self.package_name)
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py",
line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "/Users/goddard/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>
__version__ = _version()
File "/Users/goddard/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 49, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 956, in require
needed = self.resolve(parse_requirements(requirements))
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 815, in resolve
dist = self._resolve_dist(
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 861, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-Clipper 0.21.0
(/Users/goddard/Library/Application Support/ChimeraX/1.6/site-packages),
Requirement.parse('ChimeraX-Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize
api = self._get_api(session.logger)
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api
m = self.get_module()
File
"/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Clipper 0.21.0 (/Users/goddard/Library/Application
Support/ChimeraX/1.6/site-packages), Requirement.parse('ChimeraX-
Clipper~=0.20.0'), {'ChimeraX-ISOLDE'})
Could not find tool "Tabbed Toolbar"
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Successfully installed
'ChimeraX_Clipper-0.21.0-cp39-cp39-macosx_10_13_universal2.whl'
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing
/Users/goddard/Library/Caches/ChimeraX/1.6/installers/ChimeraX_Clipper-0.21.0-cp39-cp39-macosx_10_13_universal2.whl
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Clipper==0.21.0) (1.1)
Requirement already satisfied: ChimeraX-Core<1.7,>=1.6.dev202303162359 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Clipper==0.21.0) (1.6.1)
Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Clipper==0.21.0) (10.0.6)
Requirement already satisfied: ChimeraX-Atomic~=1.36 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Clipper==0.21.0) (1.43.10)
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.0.3)
Requirement already satisfied: ChimeraX-PDB~=2.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.7.2)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.3)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.1.1)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.12)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.0.1)
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.0.2)
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (1.10.1)
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (1.5.1)
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (1.2.3)
Requirement already satisfied: ChimeraX-UI~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (1.28.4)
Requirement already satisfied: ChimeraX-Surface~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (1.0.1)
Requirement already satisfied: ChimeraX-IO~=1.0.1 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.21.0) (1.0.1)
Requirement already satisfied: ChimeraX-MapData~=2.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.0)
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.10.3)
Requirement already satisfied: ChimeraX-Map~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.1.4)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.2)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.0)
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.1.1)
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.0.1)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.0.1)
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.0)
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (2.0)
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in
./ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.21.0) (1.4)
Installing collected packages: ChimeraX-Clipper
Attempting uninstall: ChimeraX-Clipper
Found existing installation: ChimeraX-Clipper 0.20.0
Uninstalling ChimeraX-Clipper-0.20.0:
Successfully uninstalled ChimeraX-Clipper-0.20.0
Successfully installed ChimeraX-Clipper-0.21.0
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
chimerax-isolde 1.6.dev0 requires ChimeraX-Clipper~=0.20.0, but you have
chimerax-clipper 0.21.0 which is incompatible.
[notice] A new release of pip is available: 23.0 -> 23.2.1
[notice] To update, run:
/Users/goddard/Desktop/ChimeraX-1.6.1.app/Contents/MacOS/ChimeraX -m pip
install --upgrade pip
> open /Users/goddard/ucsf/data/vrdemos/Jacobson maps/1949_refine_round5.pdb
'/Users/goddard/ucsf/data/vrdemos/Jacobson' has no suffix
> open /Users/goddard/ucsf/data/vrdemos/Jacobson\ maps/1949_refine_round5.pdb
'/Users/goddard/ucsf/data/vrdemos/Jacobson\' has no suffix
> open /Users/goddard/"ucsf/data/vrdemos/Jacobson maps/1949_refine_round5.pdb"
'/Users/goddard/"ucsf/data/vrdemos/Jacobson' has no suffix
> open "/Users/goddard/ucsf/data/vrdemos/Jacobson maps/1949_refine_round5.pdb"
Summary of feedback from opening /Users/goddard/ucsf/data/vrdemos/Jacobson
maps/1949_refine_round5.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2017-08-22 Time 14:59:02 PDT -0700 (1503439142.30 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /Users/Yang Yang/Desktop/1949_remodel_chain
B/1949_refine_round4.mtz
49 messages similar to the above omitted
Chain information for 1949_refine_round5.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/goddard/ucsf/data/vrdemos/Jacobson maps/1949_refine_round5.mtz"
> structureModel #1
Summary of feedback from opening /Users/goddard/ucsf/data/vrdemos/Jacobson
maps/1949_refine_round5.mtz
---
warning | WARNING: multiple experimental reflection datasets found:
(Original-experimental-data-mapped-to-asu) F-obs, SIGF-obs,
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered
Automatically choosing "(Original-experimental-data-mapped-to-asu) F-obs,
SIGF-obs".
notes | Launching live xmap mgr took 1.2309551239013672 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 42,34,38, pixel
0.71,0.746,0.676, shown at level 0.156, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 42,34,38, pixel 0.71,0.746,0.676,
shown at level -0.134,0.134, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 42,34,38, pixel
0.71,0.746,0.676, shown at level 0.529, step 1, values float32
Opened (STATIC) (Model-structure-factors-(bulk-solvent-and-all-scales-
included)) F-model, PHIF-model as #1.1.1.5, grid size 42,34,38, pixel
0.71,0.746,0.676, shown at level -0.416,0.416, step 1, values float32
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT as #1.1.1.6,
grid size 42,34,38, pixel 0.71,0.746,0.676, shown at level 0.322, step 1,
values float32
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill
as #1.1.1.7, grid size 42,34,38, pixel 0.71,0.746,0.676, shown at level 0.32,
step 1, values float32
Opened (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT as #1.1.1.8, grid
size 42,34,38, pixel 0.71,0.746,0.676, shown at level -0.211,0.211, step 1,
values float32
Chain information for 1949_refine_round5.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
Opened crystallographic dataset from /Users/goddard/ucsf/data/vrdemos/Jacobson
maps/1949_refine_round5.mtz
Found experimental reflection data:
(Original-experimental-data-mapped-to-asu) F-obs, SIGF-obs
Rwork: 0.3091; Rfree: 0.3648
Generated maps:
Reflection Data
(LIVE) 2mFo-DFc
(LIVE) mFo-DFc
(LIVE) 2mFo-DFc_sharp_29
(STATIC) (Model-structure-factors-(bulk-solvent-and-all-scales-included))
F-model, PHIF-model
(STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT
(STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill
(STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT
Any unwanted maps may be safely closed via the Model panel.
> usage clipper
Subcommands are:
* clipper associate
* clipper isolate
* clipper open
* clipper save
* clipper set autoCameraOrtho
* clipper set contourSensitivity
* clipper spotlight
* clipper symmetry
> help clipper
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 4.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 515.0.0.0.0
OS Loader Version: 577.140.2~15
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 6 days, 15 hours, 23 minutes
Graphics/Displays:
Radeon Pro 580:
Chipset Model: Radeon Pro 580
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1X-025
EFI Driver Version: 01.00.931
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
biopython: 1.81
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
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
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.1.7
ChimeraX-PickBlobs: 1.0.1
ChimeraX-PICKLUSTER: 0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.0
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RMF: 0.12
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StarMap: 1.2.15
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-StrudelScore: 0.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-TugLigands: 1.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
mrcfile: 1.4.3
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
opt-einsum: 3.3.0
packaging: 21.3
pandas: 2.0.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
pyqtgraph: 0.13.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
recordtype: 1.4
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
threed-strudel: 0.9.18
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
It would be very helpful to have the clipper command documentation online at say the ISOLDE web site. I was not able to find anything about it using Google although the ChimeraX "help clipper" gives useful documentation apparently generated from a .rst in the github repository.