id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2611 mmCIF: local variable '_1to3' referenced before assignment d.mann@… Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.4.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 0.9 (2019-06-06) Description ISOLDE Plugin: ""Save current model as..."" option in the main GUI does not work. Throws the following error: UnboundLocalError: local variable '_1to3' referenced before assignment File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-packages/chimerax/atomic/mmcif/mmcif_write.py"", line 347, in save_structure seq_entities[chars] = (eid, _1to3, [c]) See log for complete Python traceback. Log: Startup Errors --- error | Bundle 'ChimeraX-Registration' custom initialization failed warnings | 'clip' is a prefix of an existing command 'clipper' Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 432, in initialize api._api_caller.initialize(api, session, self) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1447, in initialize return cls._get_func(api, ""initialize"")(session, bi) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/registration/__init__.py"", line 41, in initialize nag(session) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/registration/nag.py"", line 29, in nag _check_usage(session) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/registration/nag.py"", line 167, in _check_usage usage = _get_usage() File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/registration/nag.py"", line 204, in _get_usage usage[""dates""].append(datetime.strptime(value, TimeFormat)) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/_strptime.py"", line 577, in _strptime_datetime tt, fraction, gmtoff_fraction = _strptime(data_string, format) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/_strptime.py"", line 359, in _strptime (data_string, format)) ValueError: time data 'Wed Sep 25 09:33:02 2019' does not match format '%a %b %d %H:%M:%S %Y' 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 15_S16_BP_v3-coot-0.pdb Chain information for 15_S16_BP_v3-coot-0.pdb #1 --- Chain | Description B | No description available > open /Users/mann/Desktop/ribosome/v2/cryosparc.mrc Opened cryosparc.mrc, grid size 360,360,360, pixel 1.19, shown at level 2.09, step 2, values float32 > toolshed show ISOLDE > set selectionWidth 4 Chain information for 15_S16_BP_v3-coot-0.pdb --- Chain | Description 1.3/B | No description available Done loading forcefield Bad residue number: 1 Adding hydrogens Summary of feedback from adding hydrogens to 15_S16_BP_v3-coot-0.pdb #1.3 --- notes | No usable SEQRES records for 15_S16_BP_v3-coot-0.pdb (#1.3) chain B; guessing termini instead Chain-initial residues that are actual N termini: /B ALA 2 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /B ALA 118 65 hydrogen bonds /B ALA 118 is not terminus, removing H atom from 'C' 946 hydrogens added Alignment identifier is 1.3.B > select #1 1851 atoms, 1867 bonds, 16 models selected > select #1 1851 atoms, 1867 bonds, 16 models selected > select #1.1 6 models selected > ~select #1.1 Nothing selected > set bgColor white QWidget::repaint: Recursive repaint detected Missing filename suffix /Users/mann/Desktop/ribosome/v2/built/isolde_v2 Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1139, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1152, in save_cif_file save.save(self.session, filename, [model]) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 61, in save_file return mmcif_write.write_mmcif(session, path, models=models) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 108, in write_mmcif save_structure(session, f, models, used_data_names) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 347, in save_structure seq_entities[chars] = (eid, _1to3, [c]) UnboundLocalError: local variable '_1to3' referenced before assignment UnboundLocalError: local variable '_1to3' referenced before assignment File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 347, in save_structure seq_entities[chars] = (eid, _1to3, [c]) See log for complete Python traceback. Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1139, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1152, in save_cif_file save.save(self.session, filename, [model]) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 61, in save_file return mmcif_write.write_mmcif(session, path, models=models) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 108, in write_mmcif save_structure(session, f, models, used_data_names) File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 347, in save_structure seq_entities[chars] = (eid, _1to3, [c]) UnboundLocalError: local variable '_1to3' referenced before assignment UnboundLocalError: local variable '_1to3' referenced before assignment File ""/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif_write.py"", line 347, in save_structure seq_entities[chars] = (eid, _1to3, [c]) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: GeForce RTX 2070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Input/Output fixed Tristan Croll all ChimeraX