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#14462 closed defect (fixed)

Clipper: HKLs must be an nx3 Numpy array

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

Description

The following bug report has been submitted:
Platform:        Linux-5.15.0-91-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
installed clipper to open mtz files but I get a error related to Numpy array. This was working on ChimeraX 1.3 but it doesn't in 1.4,1.6,1.7 versions

Log:
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  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb

71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb title:  
\--- [more info...]  
  
Chain information for 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
BMA — (BMA)  
CA — (CA)  
G21 — (G21)  
GOL — (GOL)  
IOD — (IOD)  
NAG — (NAG)  
PO4 — (PO4)  
SCN — (SCN)  
ZN — (ZN)  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_fphiout_prosmart_refmac.mtz

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 563, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1918, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/__init__.py", line 244, in open  
return open_structure_factors(session, data, **kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 52, in open_structure_factors  
raise e  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/map_mgr.py", line 292, in add_xmapset_from_file  
mtzdata = ReflectionDataContainer(self.session, sffile,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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.  
  

> coot

Unknown command: coot  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb

71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb title:  
\--- [more info...]  
  
Chain information for 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
BMA — (BMA)  
CA — (CA)  
G21 — (G21)  
GOL — (GOL)  
IOD — (IOD)  
NAG — (NAG)  
PO4 — (PO4)  
SCN — (SCN)  
ZN — (ZN)  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_fphiout_prosmart_refmac.mtz

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 563, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1918, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/__init__.py", line 244, in open  
return open_structure_factors(session, data, **kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 52, in open_structure_factors  
raise e  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/map_mgr.py", line 292, in add_xmapset_from_file  
mtzdata = ReflectionDataContainer(self.session, sffile,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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.  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_fphiout_prosmart_refmac.mtz

Reflection data must be associated with an atomic structure, provided via the
structure_model argument.  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb

71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb title:  
\--- [more info...]  
  
Chain information for 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
BMA — (BMA)  
CA — (CA)  
G21 — (G21)  
GOL — (GOL)  
IOD — (IOD)  
NAG — (NAG)  
PO4 — (PO4)  
SCN — (SCN)  
ZN — (ZN)  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_diffphiout_prosmart_refmac.mtz

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 563, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1918, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/__init__.py", line 244, in open  
return open_structure_factors(session, data, **kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 52, in open_structure_factors  
raise e  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/map_mgr.py", line 292, in add_xmapset_from_file  
mtzdata = ReflectionDataContainer(self.session, sffile,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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.  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb

71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb title:  
\--- [more info...]  
  
Chain information for 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
BMA — (BMA)  
CA — (CA)  
G21 — (G21)  
GOL — (GOL)  
IOD — (IOD)  
NAG — (NAG)  
PO4 — (PO4)  
SCN — (SCN)  
ZN — (ZN)  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_abcdout_prosmart_refmac.mtz

Summary of feedback from opening /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_abcdout_prosmart_refmac.mtz  
---  
notes | Discarding unrecognised/unsupported data array
/unknown/unknown150124/HLA A  
Discarding unrecognised/unsupported data array /unknown/unknown150124/HLB A  
Discarding unrecognised/unsupported data array /unknown/unknown150124/HLC A  
Discarding unrecognised/unsupported data array /unknown/unknown150124/HLD A  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 563, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1918, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/__init__.py", line 244, in open  
return open_structure_factors(session, data, **kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/map_mgr.py", line 292, in add_xmapset_from_file  
mtzdata = ReflectionDataContainer(self.session, sffile,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/clipper_mtz.py", line 430, in load_hkl_data  
(hklinfo, free, expt, calc) = load_mtz_data(  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/clipper_mtz.py", line 538, in load_mtz_data  
if len(crystal_dict) == 2:  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/clipper_mtz.py", line 538, in load_mtz_data  
if len(crystal_dict) == 2:  
  
See log for complete Python traceback.  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb

71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb title:  
\--- [more info...]  
  
Chain information for 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
BMA — (BMA)  
CA — (CA)  
G21 — (G21)  
GOL — (GOL)  
IOD — (IOD)  
NAG — (NAG)  
PO4 — (PO4)  
SCN — (SCN)  
ZN — (ZN)  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_fphiout_prosmart_refmac.map

MRC header value nsymbt (1094795585) is invalid  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_fphiout_prosmart_refmac.mtz

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 563, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1918, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/__init__.py", line 244, in open  
return open_structure_factors(session, data, **kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 52, in open_structure_factors  
raise e  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/map_mgr.py", line 292, in add_xmapset_from_file  
mtzdata = ReflectionDataContainer(self.session, sffile,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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.  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb

71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb title:  
\--- [more info...]  
  
Chain information for 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
BMA — (BMA)  
CA — (CA)  
G21 — (G21)  
GOL — (GOL)  
IOD — (IOD)  
NAG — (NAG)  
PO4 — (PO4)  
SCN — (SCN)  
ZN — (ZN)  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_fphiout_prosmart_refmac.mtz

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 563, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1918, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/__init__.py", line 244, in open  
return open_structure_factors(session, data, **kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 52, in open_structure_factors  
raise e  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/map_mgr.py", line 292, in add_xmapset_from_file  
mtzdata = ReflectionDataContainer(self.session, sffile,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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.  
  

> toolshed show

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb

71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb title:  
\--- [more info...]  
  
Chain information for 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
BMA — (BMA)  
CA — (CA)  
G21 — (G21)  
GOL — (GOL)  
IOD — (IOD)  
NAG — (NAG)  
PO4 — (PO4)  
SCN — (SCN)  
ZN — (ZN)  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_fphiout_prosmart_refmac.mtz

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 563, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1918, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/__init__.py", line 244, in open  
return open_structure_factors(session, data, **kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 52, in open_structure_factors  
raise e  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/map_mgr.py", line 292, in add_xmapset_from_file  
mtzdata = ReflectionDataContainer(self.session, sffile,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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.  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb

71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb title:  
\--- [more info...]  
  
Chain information for 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in 71_zatx-glpg21-1_xyzout_prosmart_refmac.pdb #1  
---  
BMA — (BMA)  
CA — (CA)  
G21 — (G21)  
GOL — (GOL)  
IOD — (IOD)  
NAG — (NAG)  
PO4 — (PO4)  
SCN — (SCN)  
ZN — (ZN)  
  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_fphiout_prosmart_refmac.map

MRC header value nsymbt (1094795585) is invalid  

> open /mnt/home/r.borza/CCP4I2_PROJECTS/ZATX-
> GLPG21-1/CCP4_JOBS/job_71/71_zatx-glpg21-1_fphiout_prosmart_refmac.mtz

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 121, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 563, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1918, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/__init__.py", line 244, in open  
return open_structure_factors(session, data, **kw)  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 52, in open_structure_factors  
raise e  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/site-
packages/chimerax/clipper/maps/map_mgr.py", line 292, in add_xmapset_from_file  
mtzdata = ReflectionDataContainer(self.session, sffile,  
File "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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 "/mnt/home/r.borza/.local/share/ChimeraX/1.6/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: 3.3.0 NVIDIA 470.223.02
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Hewlett-Packard
Model: HP Z640 Workstation
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
Cache Size: 20480 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       5.1Gi        18Gi       105Mi        39Gi        56Gi
	Swap:          2.0Gi       1.0Mi       2.0Gi

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117 [GeForce GTX 1650] [10de:1f82] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] TU117 [GeForce GTX 1650] [1462:3870]	
	Kernel driver in use: nvidia

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
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    certifi: 2023.5.7
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    ChimeraX-AddCharge: 1.5.9.1
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    ChimeraX-AlignmentHdrs: 3.3.1
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    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
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    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
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    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
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    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: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    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-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    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-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-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    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-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
    distro: 1.7.0
    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: 2022.9.26
    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
    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
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    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    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
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    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
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    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
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    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
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    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
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    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
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    sphinxcontrib-serializinghtml: 1.1.5
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    wheel-filename: 1.4.1
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Change History (5)

comment:1 by pett, 21 months ago

Cc:	Tom Goddard added
Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Clipper: HKLs must be an nx3 Numpy array

Reported by Razvan

comment:2 by Tristan Croll, 21 months ago

Hmm… this is the second of these reported recently. Something’s clearly
going wrong with finding the free flags array in REFMAC MTZ files - either
I broke something and didn’t notice (can’t think what, though - I haven’t
touched this code in some time) or something has changed in how REFMAC
arranges its MTZ output (I *wish* people could settle on a standard for
things like this!).

I wonder if you might be willing to help me with a test case to work on
fixing this. Just run a refinement on some non-confidential structure
(something from the PDB), check if the output MTZ triggers this bug, and if
so attach it here? One of the downsides of working in a company is that
legal & licensing make it a bit more complicated for me to do this myself.
Meanwhile, a question: is there a specific reason you’re using the
pre-calculated map structure factors from REFMAC? If you just give Clipper
an MTZ containing only the experimental F/sigF and free flag arrays it will
generate its own maps. In the absence of nasty crystal pathologies like
tNCS or twinning these are in my experience just as good as any other, and
come with the advantage that the maps will automatically recalculate in
response to changes in the model.

On Wed, 24 Jan 2024 at 17:42, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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comment:3 by Tristan Croll, 21 months ago

Resolution:	→ fixed
Status:	assigned → closed

Never mind. As luck would have it, I just received a MTZ file triggering the same bug. Silliness on my part - comes up when you provide a MTZ file containing *only* map coefficients with no free flags or experimental data (something I generally never do, which is why I missed it). If experimental data is present but no free flags, then a new free set is automatically generated. Anyway, the offending code (aimed at filtering missing reflections out of the free flags array) was failing to check if the array wasn't empty before proceeding.

comment:4 by r.borza@…, 21 months ago

Hi,

Sorry for the delay
It is solved then?
Do you still need some help from me?

Thank you for your time

Razvan


-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: donderdag 25 januari 2024 10:35
To: tcroll@altoslabs.com; Razvan Borza <r.borza@nki.nl>
Cc: goddard@cgl.ucsf.edu
Subject: Re: [ChimeraX] #14462: Clipper: HKLs must be an nx3 Numpy array

#14462: Clipper: HKLs must be an nx3 Numpy array
----------------------------------+---------------------------
          Reporter:  r.borza@\u2026    |      Owner:  Tristan Croll
              Type:  defect       |     Status:  closed
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:  fixed        |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------
Changes (by Tristan Croll):

 * resolution:   => fixed
 * status:  assigned => closed

Comment:

 Never mind. As luck would have it, I just received a MTZ file triggering  the same bug. Silliness on my part - comes up when you provide a MTZ file  containing *only* map coefficients with no free flags or experimental data  (something I generally never do, which is why I missed it). If  experimental data is present but no free flags, then a new free set is  automatically generated. Anyway, the offending code (aimed at filtering  missing reflections out of the free flags array) was failing to check if  the array wasn't empty before proceeding.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/14462#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:5 by Tristan Croll, 21 months ago

No, thanks. I've got this from here. Will try to put a fix out tomorrow.

On Thu, Jan 25, 2024 at 9:37 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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