id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1913 Clipper: name '_f_sigf_chooser' is not defined jared.sampson@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-16.7.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-12-17) Description 1. Load a phenix-output model. 2. Open Isolde. 3. Click ""Load crystallographic dataset"" Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.8 (2018-12-17) How to cite UCSF ChimeraX Updating list of available bundles failed: 'list' object has no attribute 'split' > cd ~/projects/vrc42/refine_uca_complex/4_phenix Current working directory is: /Users/jared/Dropbox/Projects/vrc42/refine_uca_complex/4_phenix > open /Users/jared/Dropbox/Projects/vrc42/refine_uca_complex/4_phenix/4_phenix_001.pdb Summary of feedback from opening /Users/jared/Dropbox/Projects/vrc42/refine_uca_complex/4_phenix/4_phenix_001.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2019-05-01 Time 13:11:08 EDT -0400 (1556730668.19 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 : ../VRC42UCA_refine_19.mtz 76 messages similar to the above omitted Chain information for 4_phenix_001.pdb #1 --- Chain | Description A L | No description available B H | No description available C T | No description available > toolshed show ISOLDE Chain information for 4_phenix_001.pdb --- Chain | Description 1.3/A 1.3/L | No description available 1.3/B 1.3/H | No description available 1.3/C 1.3/T | No description available Traceback (most recent call last): File ""/Users/jared/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 1179, in _choose_reflections_file self.add_xtal_data(filename) File ""/Users/jared/Library/Application Support/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 ""/Users/jared/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/maps/map_mgr.py"", line 239, in add_xmapset_from_mtz return XmapSet(self, mtzdata) File ""/Users/jared/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/maps/xmapset.py"", line 169, in __init__ choice = self._choose_fsigf(crystal_data) File ""/Users/jared/Library/Application Support/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 ""/Users/jared/Library/Application Support/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: 4.1 INTEL-10.25.22 OpenGL renderer: Intel(R) Iris(TM) Graphics 540 OpenGL vendor: Intel Inc. }}} " defect closed normal Third Party fixed Conrad Huang all ChimeraX