id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2336 ChimeraX bug report submission ash@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-48-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.9 (2019-06-06) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /u/azsha/AS/CVI03/Buster/corrected_test7_moreloop120_added400_built_deleted_n3N100_210819/refine- coot-1.pdb Summary of feedback from opening /u/azsha/AS/CVI03/Buster/corrected_test7_moreloop120_added400_built_deleted_n3N100_210819/refine- coot-1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK --------------------- added by autoBUSTER ------------------------------- Ignored bad PDB record found on line 2 REMARK run at = Wed Aug 21 12:15:40 CEST 2019 Ignored bad PDB record found on line 16 REMARK Files used: Ignored bad PDB record found on line 17 REMARK PDB = /u/azsha/AS/CVI03/Buster/corrected_test7_moreloop120 Ignored bad PDB record found on line 18 REMARK MTZ = /u/azsha/AS/CVI03/090819/xscale_CVI03Sy7_merged_p21_ 81 messages similar to the above omitted Chain information for refine-coot-1.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl Error parsing /u/azsha/Downloads/ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl: No such file: /u/azsha/Downloads/ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl Bundle saved as /u/azsha/Downloads/ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl Successfully installed ChimeraX-Clipper-0.9.7 ChimeraX-ISOLDE-1.0b3 Installed ChimeraX-Clipper (0.9.7) Installed ChimeraX-ISOLDE (1.0b3) 'clip' is a prefix of an existing command 'clipper' > toolshed show ISOLDE > set selectionWidth 4 Chain information for refine-coot-1.pdb --- Chain | Description 1.3/A | No description available 1.3/B | No description available 1.3/C | No description available Done loading forcefield Discarding unrecognised/unsupported data array /HKL_base/HKL_base/FOM W Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLA A Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLB A Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLC A Discarding unrecognised/unsupported data array /HKL_base/HKL_base/HLD A Traceback (most recent call last): File ""/u/azsha/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 1256, in _choose_reflections_file self.add_xtal_data(filename) File ""/u/azsha/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 1283, in add_xtal_data xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate) File ""/u/azsha/.local/share/ChimeraX/0.9/site- packages/chimerax/clipper/maps/map_mgr.py"", line 271, in add_xmapset_from_mtz return self.add_xmapset_from_file(mtzfile, oversampling_rate) File ""/u/azsha/.local/share/ChimeraX/0.9/site- packages/chimerax/clipper/maps/map_mgr.py"", line 276, in add_xmapset_from_file shannon_rate = oversampling_rate) File ""/u/azsha/.local/share/ChimeraX/0.9/site- packages/chimerax/clipper/clipper_mtz.py"", line 48, in __init__ hklinfo, free, exp, calc = load_hkl_data(session, hklfile, free_flag_label=free_flag_label) File ""/u/azsha/.local/share/ChimeraX/0.9/site- packages/chimerax/clipper/clipper_mtz.py"", line 325, in load_hkl_data load_map_coeffs = load_map_coeffs) File ""/u/azsha/.local/share/ChimeraX/0.9/site- packages/chimerax/clipper/clipper_mtz.py"", line 393, in load_mtz_data hklinfo, crystal_dict = mtz_read.load_mtz_data(session, filename, load_map_coeffs=load_map_coeffs) File ""/u/azsha/.local/share/ChimeraX/0.9/site- packages/chimerax/clipper/io/mtz_read.py"", line 103, in load_mtz_data ncryst, ndat, nname, ndtype = _parse_column_path(column_paths[i+1]) IndexError: list index out of range IndexError: list index out of range File ""/u/azsha/.local/share/ChimeraX/0.9/site- packages/chimerax/clipper/io/mtz_read.py"", line 103, in load_mtz_data ncryst, ndat, nname, ndtype = _parse_column_path(column_paths[i+1]) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.40.04 OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party fixed Conrad Huang all ChimeraX