id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3966 Clipper: Failure to read BUSTER MTZ file erwin.pannecoucke@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description I tried to load the mtz file corresponding to my structure. The mtz file is the output from BUSTER, so should be in a classical format. Log: Startup Messages --- warnings | QWebEngineUrlScheme::registerScheme: Scheme ""cxcmd"" already registered QWebEngineUrlScheme::registerScheme: Scheme ""help"" already registered QWebEngineUrlScheme::registerScheme: Scheme ""cxcmd"" already registered QWebEngineUrlScheme::registerScheme: Scheme ""help"" already registered QWebEngineUrlScheme::registerScheme: Scheme ""cxcmd"" already registered 8 messages similar to the above omitted Replacing file-saver for 'DCD coordinates' from MD-crds bundle with that from MDcrds bundle Replacing opener for 'Gromacs full-precision coordinates' from MD-crds bundle with that from MDcrds bundle Replacing opener for 'Gromacs compressed coordinates' from MD-crds bundle with that from MDcrds bundle Replacing opener for 'DCD coordinates' from MD-crds bundle with that from MDcrds bundle notes | Replacing data format 'Gromacs full-precision coordinates' as defined by ChimeraX-MD-crds bundle with definition from ChimeraX-MDcrds bundle Replacing data format 'Gromacs compressed coordinates' as defined by ChimeraX- MD-crds bundle with definition from ChimeraX-MDcrds bundle Replacing data format 'DCD coordinates' as defined by ChimeraX-MD-crds bundle with definition from ChimeraX-MDcrds bundle UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /mnt/DATA1/Erwin/20170904_Petra3_P14/phenix/Refine_37/20_buster/refine37-buster20.pdb > format pdb Summary of feedback from opening /mnt/DATA1/Erwin/20170904_Petra3_P14/phenix/Refine_37/20_buster/refine37-buster20.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 = Thu Oct 4 11:57:23 CEST 2018 Ignored bad PDB record found on line 11 REMARK Files used: Ignored bad PDB record found on line 12 REMARK PDB = ./pdbchk.pdb Ignored bad PDB record found on line 13 REMARK MTZ = /mnt/data1/ErwinP/20170904_Petra3_P14/T343I-hFL/phen 16 messages similar to the above omitted Chain information for refine37-buster20.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available > ui tool show ISOLDE > set selectionWidth 4 Chain information for refine37-buster20.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 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | 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 ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 1283, in _choose_reflections_file self.add_xtal_data(filename) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 1311, in add_xtal_data auto_choose_reflection_data=False) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/maps/map_mgr.py"", line 284, in add_xmapset_from_mtz auto_choose_reflection_data) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/maps/map_mgr.py"", line 293, in add_xmapset_from_file auto_choose_reflection_data=auto_choose_reflection_data) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/clipper_mtz.py"", line 53, in __init__ self._init_from_hkl_file(hklfile, free_flag_label, auto_choose_reflection_data) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/clipper_mtz.py"", line 61, in _init_from_hkl_file auto_choose_reflection_data=auto_choose_reflection_data) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/clipper_mtz.py"", line 422, in load_hkl_data load_map_coeffs = load_map_coeffs) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/clipper_mtz.py"", line 491, in load_mtz_data hklinfo, crystal_dict = mtz_read.load_mtz_data(session, filename, load_map_coeffs=load_map_coeffs) File ""/home/erwinp/.local/share/ChimeraX/1.1/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 ""/home/erwinp/.local/share/ChimeraX/1.1/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. 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 ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 1283, in _choose_reflections_file self.add_xtal_data(filename) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 1311, in add_xtal_data auto_choose_reflection_data=False) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/maps/map_mgr.py"", line 284, in add_xmapset_from_mtz auto_choose_reflection_data) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/maps/map_mgr.py"", line 293, in add_xmapset_from_file auto_choose_reflection_data=auto_choose_reflection_data) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/clipper_mtz.py"", line 53, in __init__ self._init_from_hkl_file(hklfile, free_flag_label, auto_choose_reflection_data) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/clipper_mtz.py"", line 61, in _init_from_hkl_file auto_choose_reflection_data=auto_choose_reflection_data) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/clipper_mtz.py"", line 422, in load_hkl_data load_map_coeffs = load_map_coeffs) File ""/home/erwinp/.local/share/ChimeraX/1.1/site- packages/chimerax/clipper/clipper_mtz.py"", line 491, in load_mtz_data hklinfo, crystal_dict = mtz_read.load_mtz_data(session, filename, load_map_coeffs=load_map_coeffs) File ""/home/erwinp/.local/share/ChimeraX/1.1/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 ""/home/erwinp/.local/share/ChimeraX/1.1/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 450.36.06 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Supermicro Model: SYS-7049GP-TRT OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 64 Intel(R) Xeon(R) Gold 5218 CPU @ 2.30GHz Cache Size: 22528 KB Memory: total used free shared buff/cache available Mem: 251G 16G 150G 1.6G 84G 232G Swap: 4.0G 59M 3.9G Graphics: 05:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41) Subsystem: Super Micro Computer Inc Device [15d9:096d] Kernel driver in use: ast PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atom-Search: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-Bug-Reporter: 1.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-Cage-Builder: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 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1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Third Party fixed all ChimeraX