Opened 3 years ago

Last modified 3 years ago

#8282 assigned defect

Clipper: Cannot determine the correct value for the free reflections

Reported by: rruiz@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/rruiz/Library/CloudStorage/OneDrive-
> UniversityofMarylandSchoolofMedicine/TG2/Xray structure/TG2_refine_6.pdb"

Chain information for TG2_refine_6.pdb #1  
---  
Chain | Description  
A D G J M P | No description available  
B E H K N Q | No description available  
C F I L O R | No description available  
  

> show cartoons

> style sphere

Changed 30910 atom styles  

> style sphere

Changed 30910 atom styles  

> hide atoms

> select ::name="GDP"

40 atoms, 42 bonds, 1 residue, 1 model selected  

> rainbow sel

> select ::name="GDP"

40 atoms, 42 bonds, 1 residue, 1 model selected  

> color sel red

> select ::name="GDP"

40 atoms, 42 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 40 atom styles  

> open "/Users/rruiz/Library/CloudStorage/OneDrive-
> UniversityofMarylandSchoolofMedicine/TG2/Xray structure/TG2_refine_6.mtz"

Summary of feedback from opening /Users/rruiz/Library/CloudStorage/OneDrive-
UniversityofMarylandSchoolofMedicine/TG2/Xray structure/TG2_refine_6.mtz  
---  
warning | WARNING: multiple experimental reflection datasets found:  
(Original-experimental-data-mapped-to-asu) I-obs, SIGI-obs,  
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered  
Automatically choosing "(Experimental-data-used-in-refinement) F-obs-filtered,
SIGF-obs-filtered".  
  
Traceback (most recent call last):  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 116, in handle_drag_and_drop  
mw.dropEvent(event)  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 574, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1919, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/__init__.py", line 240, in open  
return open_structure_factors(session, data, **kw)  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/cmd.py", line 51, in open_structure_factors  
raise e  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling)  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/xmapset.py", line 252, in init_maps  
self._launch_live_xmap_mgr(crystal_data, fsigf_data)  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/xmapset.py", line 435, in _launch_live_xmap_mgr  
xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo,  
RuntimeError: Cannot determine the correct value for the free reflections in
the given FreeR_flag array. Please convert your reflection file to CCP4 or
PHENIX format using sftools or phenix.reflection_file_editor.  
  
RuntimeError: Cannot determine the correct value for the free reflections in
the given FreeR_flag array. Please convert your reflection file to CCP4 or
PHENIX format using sftools or phenix.reflection_file_editor.  
  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/xmapset.py", line 435, in _launch_live_xmap_mgr  
xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo,  
  
See log for complete Python traceback.  
  

> open "/Users/rruiz/Library/CloudStorage/OneDrive-
> UniversityofMarylandSchoolofMedicine/TG2/Xray structure/TG2_refine_6.mtz"

Summary of feedback from opening /Users/rruiz/Library/CloudStorage/OneDrive-
UniversityofMarylandSchoolofMedicine/TG2/Xray structure/TG2_refine_6.mtz  
---  
warning | WARNING: multiple experimental reflection datasets found:  
(Original-experimental-data-mapped-to-asu) I-obs, SIGI-obs,  
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered  
Automatically choosing "(Experimental-data-used-in-refinement) F-obs-filtered,
SIGF-obs-filtered".  
note |  
  
  
| Chain information for TG2_refine_6.pdb #1  
  
---  
  
  
Chain  
| Description  
  
  
  
  
  
  
A D G J M P  
| No description available  
  
  
  
  
B E H K N Q  
| No description available  
  
  
  
  
C F I L O R  
| No description available  
  
  
  
  
  
  
  
Traceback (most recent call last):  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 155, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/__init__.py", line 240, in open  
return open_structure_factors(session, data, **kw)  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/cmd.py", line 51, in open_structure_factors  
raise e  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling)  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/xmapset.py", line 187, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/xmapset.py", line 252, in init_maps  
self._launch_live_xmap_mgr(crystal_data, fsigf_data)  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/xmapset.py", line 435, in _launch_live_xmap_mgr  
xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo,  
RuntimeError: Cannot determine the correct value for the free reflections in
the given FreeR_flag array. Please convert your reflection file to CCP4 or
PHENIX format using sftools or phenix.reflection_file_editor.  
  
RuntimeError: Cannot determine the correct value for the free reflections in
the given FreeR_flag array. Please convert your reflection file to CCP4 or
PHENIX format using sftools or phenix.reflection_file_editor.  
  
File "/Users/rruiz/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/xmapset.py", line 435, in _launch_live_xmap_mgr  
xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo,  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.54
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
      OS Loader Version: 540.120.3~6

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 118 days 3:40

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Clipper: Cannot determine the correct value for the free reflections

Reported by Raquel Ruiz

in reply to:  2 ; comment:2 by Tristan Croll, 3 years ago 

Could you try updating to ChimeraX 1.5, installing ISOLDE 1.5 into that,
and see if this error still occurs? If it does, is there any chance you can
share the model and MTZ so I can debug?

On Wed, 11 Jan 2023 at 18:52, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:
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