Clipper: open MTZ file: HKLs must be an nx3 Numpy array!

[jae-hun.jeoung@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
> camera ortho

> cofr centerOfView

> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true

Saved volume settings  

> mousemode rightMode clip

> mousemode alt rightMode "contour level"

> mousemode alt leftMode "move picked models"

> alias cofron cofr centerofview showpivot true

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias cootmode surface cap false; surface style solid; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10
> position cofr; color ##~num_residues cornflower blue

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000

> alias map_unsphere surface unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> alias caps_off surface cap false

> alias caps_on surface cap true

> alias selbetween ks ri

> buttonpanel Shortcuts rows 3 columns 4

> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"

> buttonpanel Shortcuts add Model_Panel command "tool show Models"

> buttonpanel Shortcuts add Log command "tool show Log"

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add map_sphere command map_sphere_15

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add cootmode command cootmode

> buttonpanel Shortcuts add mark_cofr command "marker #10000 position cofr"

> buttonpanel Shortcuts add hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Volumes/Data/phenix/Rec_CODH2_22/Refine_1/refine_1.pdb

Summary of feedback from opening
/Volumes/Data/phenix/Rec_CODH2_22/Refine_1/refine_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2009-11-16 Time 13:26:14 CET +0100 (1258374374.93 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/jae-
hunjeoung/xtal/data/CODH/Rec_CODH2_22/Rec_CODH2_22.cv  
  
229 messages similar to the above omitted  
  
Chain information for refine_1.pdb #1  
---  
Chain | Description  
X | No description available  
  

> open /Volumes/Data/phenix/Rec_CODH2_22/Refine_1/refine_1_map_coeffs.mtz

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/adminjh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/clipper/__init__.py", line 244, in open  
return open_structure_factors(session, data, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/adminjh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/clipper/cmd.py", line 52, in open_structure_factors  
raise e  
File "/Users/adminjh/Library/Application Support/ChimeraX/1.7/lib/python/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/adminjh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/clipper/maps/map_mgr.py", line 292, in add_xmapset_from_file  
mtzdata = ReflectionDataContainer(self.session, sffile,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/adminjh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/clipper/clipper_mtz.py", line 54, in __init__  
self._init_from_hkl_file(hklfile, free_flag_label,
auto_choose_reflection_data,  
File "/Users/adminjh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/clipper/clipper_mtz.py", line 62, in _init_from_hkl_file  
hklinfo, free, exp, calc = load_hkl_data(self.session, hklfile,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/adminjh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/clipper/clipper_mtz.py", line 460, in load_hkl_data  
hklinfo, free, expt, calc = _filter_out_missing_free_flags(hklinfo, free,
expt, calc)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/adminjh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/clipper/clipper_mtz.py", line 479, in
_filter_out_missing_free_flags  
new_hklinfo.add_hkl_list(good)  
RuntimeError: HKLs must be an nx3 Numpy array!  
  
RuntimeError: HKLs must be an nx3 Numpy array!  
  
File "/Users/adminjh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/clipper/clipper_mtz.py", line 479, in
_filter_out_missing_free_flags  
new_hklinfo.add_hkl_list(good)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16R000QGD/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 14 days, 8 hours, 28 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U3223QE:
          Resolution: 6016 x 3384
          UI Looks like: 3008 x 1692 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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    ChimeraX-AddH: 2.2.5
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    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
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    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
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    ChimeraX-Bumps: 1.0
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    ChimeraX-Contacts: 1.0.1
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    ChimeraX-Crosslinks: 1.0
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    ChimeraX-FileHistory: 1.0.1
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    ChimeraX-gltf: 1.0
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[Tristan Croll]

Hmm... that's an interesting one. Will look into it, but in the meantime is there a specific reason you're using pre-calculated map coefficients rather than the experimental F/sigF data? Unless you're facing some nasty crystal pathologies like twinning or strong translational NCS, you're generally better off giving ISOLDE an MTZ containing just the F/sigF and free flags arrays. That way you'll get live maps that auto-update to reflect the model changes.

[jae-hun.jeoung@…]

Dear Tristan,
Thank you for your comments.
There is no specific reason of using the calculated map-coefficient.
As you recommended, use of the data with F/sigF worked well.

Thanks again.
Best wishes,
Jae-Hun

smime.p7s​

[jae-hun.jeoung@…]

Added by email2trac

[Tristan Croll]

Found the problem - was arising when trying to load an MTZ file containing *only* map coefficients with no free set or experimental data. That's something I essentially never do, which is why I missed it.