id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3578 Clipper: failure in French&Wilson treatment of intensities roger.b.sutton@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-112-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.93 (2020-04-03) Description Isolde doesn't seem to like my data Log: UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show ISOLDE > set selectionWidth 4 Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. Done loading forcefield Traceback (most recent call last): File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1271, in _choose_reflections_file self.add_xtal_data(filename) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1297, in add_xtal_data map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py"", line 174, in get_map_mgr sh = get_symmetry_handler(structure, create=create, auto_add_to_session=auto_add_to_session) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py"", line 159, in get_symmetry_handler sh = _get_symmetry_handler(structure, create) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py"", line 166, in _get_symmetry_handler p = structure.parent AttributeError: 'NoneType' object has no attribute 'parent' AttributeError: 'NoneType' object has no attribute 'parent' File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py"", line 166, in _get_symmetry_handler p = structure.parent See log for complete Python traceback. > open2 ""/media/rosutton/Dnase1L3 refine 26/DNAse1L3_refine_26-coot-0.pdb"" Summary of feedback from opening <_io.textiowrapper name=""/media/rosutton/Dnase1L3 refine 26/DNAse1L3_refine_26-coot-0.pdb"" mode=""rt"" encoding=""utf-8""> --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2020-01-04 Time 13:55:52 CST -0600 (1578167752.03 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 : /home/rosutton/Projects/DNAse1L3/Refine_25/DNAse1L3_re 27 messages similar to the above omitted Chain information for DNAse1L3_refine_26-coot-0.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available Chain information for DNAse1L3_refine_26-coot-0.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-cispro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-transpro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-gly-sym data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-prepro-noGP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-ileval-nopreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-general-noGPIVpreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Failed on HKL = ( -23, -5, 1) N_bins: 60 Imean: -10.338729306497815 I: 27.850000381469727 sigI: 26.019224166870117 eobs_sq: -2.69375467292351 sig_eobs_sq: -2.5166752504601537 Traceback (most recent call last): File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1271, in _choose_reflections_file self.add_xtal_data(filename) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1299, in add_xtal_data auto_choose_reflection_data=False) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/maps/map_mgr.py"", line 279, in add_xmapset_from_mtz auto_choose_reflection_data) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/maps/map_mgr.py"", line 301, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/maps/xmapset.py"", line 189, in __init__ fill_with_fcalc, exclude_missing_reflections) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/maps/xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 113, in french_wilson_analytical e_xpct = _expected_E_FW_acen(eobs_sq, sig_eobs_sq) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 195, in _expected_E_FW_acen pbdv(-1.5, -x)[0] / # Scipy parabolic cylinder function returns value *and* derivative ValueError: math domain error ValueError: math domain error File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 195, in _expected_E_FW_acen pbdv(-1.5, -x)[0] / # Scipy parabolic cylinder function returns value *and* derivative See log for complete Python traceback. Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Failed on HKL = ( -23, -5, 1) N_bins: 60 Imean: -10.338729306497815 I: 27.850000381469727 sigI: 26.019224166870117 eobs_sq: -2.69375467292351 sig_eobs_sq: -2.5166752504601537 Traceback (most recent call last): File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1271, in _choose_reflections_file self.add_xtal_data(filename) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1299, in add_xtal_data auto_choose_reflection_data=False) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/maps/map_mgr.py"", line 279, in add_xmapset_from_mtz auto_choose_reflection_data) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/maps/map_mgr.py"", line 301, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/maps/xmapset.py"", line 189, in __init__ fill_with_fcalc, exclude_missing_reflections) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/maps/xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 113, in french_wilson_analytical e_xpct = _expected_E_FW_acen(eobs_sq, sig_eobs_sq) File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 195, in _expected_E_FW_acen pbdv(-1.5, -x)[0] / # Scipy parabolic cylinder function returns value *and* derivative ValueError: math domain error ValueError: math domain error File ""/home/rosutton/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 195, in _expected_E_FW_acen pbdv(-1.5, -x)[0] / # Scipy parabolic cylinder function returns value *and* derivative See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 450.36.06 OpenGL renderer: Quadro P5000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision 7920 Tower OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 48 Intel(R) Xeon(R) Silver 4116 CPU @ 2.10GHz Cache Size: 16896 KB Graphics: 73:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P5000] [10de:1bb0] (rev a1) Subsystem: Dell GP104GL [Quadro P5000] [1028:11b2] Kernel driver in use: nvidia }}} " defect assigned normal Third Party all ChimeraX