id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2319 ISOLDE: name '_f_sigf_chooser' is not defined 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: 0.8 (2018-12-17) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | Traceback (most recent call last): File ""/opt/bioxray/programs/chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 338, in __init__ self.init_available_from_cache(logger) File ""/opt/bioxray/programs/chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 445, in init_available_from_cache abc.load_from_cache() File ""/opt/bioxray/programs/chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/available.py"", line 61, in load_from_cache b = _build_bundle(d) File ""/opt/bioxray/programs/chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/available.py"", line 242, in _build_bundle keywords = _extract_extra_keywords(keywords) File ""/opt/bioxray/programs/chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/installed.py"", line 270, in _extract_extra_keywords all_kwds = [k.strip() for k in kwds.split(',')] AttributeError: 'list' object has no attribute 'split' UCSF ChimeraX version: 0.8 (2018-12-17) How to cite UCSF ChimeraX > toolshed show ISOLDE > open /u/azsha/AS/CVI03/Buster/LoopC_test_120819/refine_all_140819.pdb Summary of feedback from opening /u/azsha/AS/CVI03/Buster/LoopC_test_120819/refine_all_140819.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 = Mon Aug 12 10:28:08 CEST 2019 Ignored bad PDB record found on line 14 REMARK Files used: Ignored bad PDB record found on line 15 REMARK PDB = /u/azsha/AS/CVI03/Buster/LoopC_test_120819/pdbchk.pd Ignored bad PDB record found on line 16 REMARK MTZ = /u/azsha/AS/CVI03/090819/xscale_CVI03Sy7_merged_p21_ 45 messages similar to the above omitted Chain information for refine_all_140819.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available Chain information for refine_all_140819.pdb --- Chain | Description 1.3/A | No description available 1.3/B | No description available 1.3/C | No description available > toolshed show ISOLDE Traceback (most recent call last): File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 1179, in _choose_reflections_file self.add_xtal_data(filename) File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 1206, in add_xtal_data xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate) File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/clipper/maps/map_mgr.py"", line 239, in add_xmapset_from_mtz return XmapSet(self, mtzdata) File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/clipper/maps/xmapset.py"", line 169, in __init__ choice = self._choose_fsigf(crystal_data) File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/clipper/maps/xmapset.py"", line 453, in _choose_fsigf choice = _f_sigf_chooser(list(fsigfs.keys())) NameError: name '_f_sigf_chooser' is not defined NameError: name '_f_sigf_chooser' is not defined File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/clipper/maps/xmapset.py"", line 453, in _choose_fsigf choice = _f_sigf_chooser(list(fsigfs.keys())) See log for complete Python traceback. Traceback (most recent call last): File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 1179, in _choose_reflections_file self.add_xtal_data(filename) File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 1206, in add_xtal_data xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate) File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/clipper/maps/map_mgr.py"", line 239, in add_xmapset_from_mtz return XmapSet(self, mtzdata) File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/clipper/maps/xmapset.py"", line 169, in __init__ choice = self._choose_fsigf(crystal_data) File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/clipper/maps/xmapset.py"", line 453, in _choose_fsigf choice = _f_sigf_chooser(list(fsigfs.keys())) NameError: name '_f_sigf_chooser' is not defined NameError: name '_f_sigf_chooser' is not defined File ""/u/azsha/.local/share/ChimeraX/0.8/site- packages/chimerax/clipper/maps/xmapset.py"", line 453, in _choose_fsigf choice = _f_sigf_chooser(list(fsigfs.keys())) 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 all ChimeraX