id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2728 Clipper: math domain error mbk@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-72-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.91 (2019-12-23) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > isolde start > set selectionWidth 4 WARNING: no OpenCL or compatible CUDA drivers detected! While it is theoretically possible to run ISOLDE using CPU only, in practice it is prohibitively slow. If you have a suitable GPU in your machine, please check that you have the recommended drivers from the manufacturer installed. The current required CUDA version is 10.1 - if installed, please make sure this is on your library path before starting ChimeraX. Done loading forcefield > open /home/bashir/Documents/MRage_1674/Dean_Test_MR_P6122_1.1.pdb Chain information for Dean_Test_MR_P6122_1.1.pdb #1 --- Chain | Description A | No description available Chain information for Dean_Test_MR_P6122_1.1.pdb --- Chain | Description 1.1/A | No description available Discarding unrecognised/unsupported data array /NULL_xname194033/NULL_dname/FOM W No free flags detected in this dataset! Automatically generated a new random set with 171 free from 3541 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Failed on HKL = ( 0, 0, 60) N_bins: 60 Imean: -1437.5044896467866 I: -8858.0 sigI: 9269.0 eobs_sq: 1.027011285158551 sig_eobs_sq: -1.0746633102432388 Traceback (most recent call last): File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 1271, in _choose_reflections_file self.add_xtal_data(filename) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 1299, in add_xtal_data auto_choose_reflection_data=False) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/map_mgr.py"", line 279, in add_xmapset_from_mtz auto_choose_reflection_data) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/map_mgr.py"", line 301, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/xmapset.py"", line 189, in __init__ fill_with_fcalc, exclude_missing_reflections) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 110, in french_wilson_analytical e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 281, in _expected_E_FW_cen e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio ValueError: math domain error ValueError: math domain error File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 281, in _expected_E_FW_cen e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio See log for complete Python traceback. Discarding unrecognised/unsupported data array /NULL_xname194033/NULL_dname/FOM W No free flags detected in this dataset! Automatically generated a new random set with 193 free from 3541 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Failed on HKL = ( 0, 0, 60) N_bins: 60 Imean: -1437.5044896467866 I: -8858.0 sigI: 9269.0 eobs_sq: 1.027011285158551 sig_eobs_sq: -1.0746633102432388 Traceback (most recent call last): File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 1271, in _choose_reflections_file self.add_xtal_data(filename) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 1299, in add_xtal_data auto_choose_reflection_data=False) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/map_mgr.py"", line 279, in add_xmapset_from_mtz auto_choose_reflection_data) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/map_mgr.py"", line 301, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/xmapset.py"", line 189, in __init__ fill_with_fcalc, exclude_missing_reflections) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 110, in french_wilson_analytical e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 281, in _expected_E_FW_cen e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio ValueError: math domain error ValueError: math domain error File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 281, in _expected_E_FW_cen e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio See log for complete Python traceback. Discarding unrecognised/unsupported data array /NULL_xname194033/NULL_dname/FOM W No free flags detected in this dataset! Automatically generated a new random set with 182 free from 3541 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Failed on HKL = ( 0, 0, 60) N_bins: 60 Imean: -1437.5044896467866 I: -8858.0 sigI: 9269.0 eobs_sq: 1.027011285158551 sig_eobs_sq: -1.0746633102432388 Traceback (most recent call last): File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 1271, in _choose_reflections_file self.add_xtal_data(filename) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 1299, in add_xtal_data auto_choose_reflection_data=False) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/map_mgr.py"", line 279, in add_xmapset_from_mtz auto_choose_reflection_data) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/map_mgr.py"", line 301, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/xmapset.py"", line 189, in __init__ fill_with_fcalc, exclude_missing_reflections) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 110, in french_wilson_analytical e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 281, in _expected_E_FW_cen e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio ValueError: math domain error ValueError: math domain error File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 281, in _expected_E_FW_cen e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio See log for complete Python traceback. Discarding unrecognised/unsupported data array /NULL_xname194033/NULL_dname/FOM W No free flags detected in this dataset! Automatically generated a new random set with 189 free from 3541 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Failed on HKL = ( 0, 0, 60) N_bins: 60 Imean: -1437.5044896467866 I: -8858.0 sigI: 9269.0 eobs_sq: 1.027011285158551 sig_eobs_sq: -1.0746633102432388 Traceback (most recent call last): File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 1271, in _choose_reflections_file self.add_xtal_data(filename) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 1299, in add_xtal_data auto_choose_reflection_data=False) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/map_mgr.py"", line 279, in add_xmapset_from_mtz auto_choose_reflection_data) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/map_mgr.py"", line 301, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/xmapset.py"", line 189, in __init__ fill_with_fcalc, exclude_missing_reflections) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/maps/xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 110, in french_wilson_analytical e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq) File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 281, in _expected_E_FW_cen e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio ValueError: math domain error ValueError: math domain error File ""/home/bashir/.local/share/ChimeraX/0.91/site- packages/chimerax/clipper/reflection_tools/french_wilson.py"", line 281, in _expected_E_FW_cen e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio See log for complete Python traceback. OpenGL version: 3.3 (Core Profile) Mesa 19.0.8 OpenGL renderer: AMD JUNIPER (DRM 2.50.0 / 4.15.0-72-generic, LLVM 8.0.0) OpenGL vendor: X.Org }}} " defect assigned normal Third Party all ChimeraX