id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2370 (atomic) model: self.positions is None sitins07@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.91 (2019-08-30) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-08-30) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4v95 4v95 title: Crystal structure of YAEJ bound to the 70S ribosome [more info...] Chain information for 4v95 #1 --- Chain | Description AA CA | 16S Ribosomal RNA AB CB | 30S Ribosomal Protein S2 AC CC | 30S Ribosomal Protein S3 AD CD | 30S Ribosomal Protein S4 AE CE | 30S Ribosomal Protein S5 AF CF | 30S Ribosomal Protein S6 AG CG | 30S Ribosomal Protein S7 AH CH | 30S Ribosomal Protein S8 AI CI | 30S Ribosomal Protein S9 AJ CJ | 30S Ribosomal Protein S10 AK CK | 30S Ribosomal Protein S11 AL CL | 30S Ribosomal Protein S12 AM CM | 30S Ribosomal Protein S13 AN CN | 30S Ribosomal Protein S14 AO CO | 30S Ribosomal Protein S15 AP CP | 30S Ribosomal Protein S16 AQ CQ | 30S Ribosomal Protein S17 AR CR | 30S Ribosomal Protein S18 AS CS | 30S Ribosomal Protein S19 AT CT | 30S Ribosomal Protein S20 AU CU | 30S Ribosomal Protein THX AV CV | P-site fMet-tRNA AX CX | mRNA AY | YAEJ B0 D0 | 50S Ribosomal Protein L27 B1 D1 | 50S Ribosomal Protein L28 B2 D2 | 50S Ribosomal Protein L29 B3 D3 | 50S Ribosomal Protein L30 B4 D4 | 50S Ribosomal Protein L31 B5 D5 | 50S Ribosomal Protein L32 B6 D6 | 50S Ribosomal Protein L33 B7 D7 | 50S Ribosomal Protein L34 B8 D8 | 50S Ribosomal Protein L35 B9 D9 | 50S Ribosomal Protein L36 BA DA | 23S Ribosomal RNA BB DB | 5S Ribosomal RNA BD DD | 50S Ribosomal Protein L2 BE DE | 50S Ribosomal Protein L3 BF DF | 50S Ribosomal Protein L4 BG DG | 50S Ribosomal Protein L5 BH DH | 50S Ribosomal Protein L6 BI DI | 50S Ribosomal Protein L9 BN DN | 50S Ribosomal Protein L13 BO DO | 50S Ribosomal Protein L14 BP DP | 50S Ribosomal Protein L15 BQ DQ | 50S Ribosomal Protein L16 BR DR | 50S Ribosomal Protein L17 BS DS | 50S Ribosomal Protein L18 BT DT | 50S Ribosomal Protein L19 BU DU | 50S Ribosomal Protein L20 BV DV | 50S Ribosomal Protein L21 BW DW | 50S Ribosomal Protein L22 BX DX | 50S Ribosomal Protein L23 BY DY | 50S Ribosomal Protein L24 BZ DZ | 50S Ribosomal Protein L25 Non-standard residues in 4v95 #1 --- MG — magnesium ion ZN — zinc ion 4v95 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > open Z:/ALL/Niels/Valik/For_Poster/4v95_phases_2mFo-DFc.ccp4 Opened 4v95_phases_2mFo-DFc.ccp4, grid size 398,450,568, pixel 0.778,0.779,0.78, shown at level 0.562, step 2, values float32 > cd Z:/ALL/Niels/Valik/For_Poster/ Current working directory is: Z:\ALL\Niels\Valik\For_Poster > save 4v95.pdb models #1 > close #2 > close #1 > open Z:/ALL/Niels/Valik/For_Poster/X-ray.mrc Z:/ALL/Niels/Valik/For_Poster/4v95_70SArfB.pdb Summary of feedback from opening files --- warnings | Ignored bad PDB record found on line 148062 END CONECT record to nonexistent atom: (363, 31840) CONECT record to nonexistent atom: (949, 31552) CONECT record to nonexistent atom: (1056, 31567) CONECT record to nonexistent atom: (1874, 31592) CONECT record to nonexistent atom: (1874, 31593) 201 messages similar to the above omitted CONECT record for nonexistent atom: 31515 Bad residue range for secondary structure: HELIX 24 24 ASN A 199 ARG A 209 1 11 Bad residue range for secondary structure: HELIX 28 28 ASN A 127 ARG A 140 1 14 Bad residue range for secondary structure: HELIX 39 39 ASP A 4 ARG A 18 1 15 Bad residue range for secondary structure: HELIX 40 40 SER A 29 GLU A 42 1 14 Bad residue range for secondary structure: HELIX 45 45 GLU A 48 VAL A 53 1 6 45 messages similar to the above omitted Start residue of secondary structure not found: HELIX 160 160 ASN C 25 ARG C 30 1 6 Start residue of secondary structure not found: HELIX 161 161 ASP C 43 MET C 63 1 21 Start residue of secondary structure not found: HELIX 162 162 LYS C 74 GLY C 89 1 16 Start residue of secondary structure not found: HELIX 163 163 ASN C 104 GLU C 116 1 13 Start residue of secondary structure not found: HELIX 164 164 LYS C 132 ARG C 153 1 22 153 messages similar to the above omitted Bad residue range for secondary structure: SHEET 22 22 1 VAL A 41 ALA A 48 0 Bad residue range for secondary structure: SHEET 28 28 1 ARG A 2 LEU A 10 0 Bad residue range for secondary structure: SHEET 37 37 1 TYR A 85 MET A 89 0 Bad residue range for secondary structure: SHEET 39 39 1 ILE A 45 GLU A 49 0 Bad residue range for secondary structure: SHEET 41 41 1 HIS A 82 ARG A 85 0 61 messages similar to the above omitted Start residue of secondary structure not found: SHEET 256 256 1 ILE C 32 ARG C 36 0 Start residue of secondary structure not found: SHEET 257 257 1 ILE C 39 ILE C 42 0 Start residue of secondary structure not found: SHEET 258 258 1 PHE C 70 VAL C 71 0 Start residue of secondary structure not found: SHEET 259 259 1 TYR C 92 VAL C 93 0 Start residue of secondary structure not found: SHEET 260 260 1 ILE C 162 VAL C 164 0 243 messages similar to the above omitted Opened X-ray.mrc, grid size 398,450,568, pixel 0.778,0.779,0.78, shown at level 0.562, step 2, values float32 Chain information for 4v95_70SArfB.pdb --- Chain | Description 1.2/A | No description available 1.2/A | No description available 1.2/B | No description available 1.2/B | No description available > open Z:/ALL/Niels/Valik/For_Poster/Model_3_major_state_Mg- wz.Q28-coot-0_Niels.pdb Summary of feedback from opening Z:/ALL/Niels/Valik/For_Poster/Model_3_major_state_Mg-wz.Q28-coot-0_Niels.pdb --- warning | Ignored bad PDB record found on line 147722 END Chain information for Model_3_major_state_Mg-wz.Q28-coot-0_Niels.pdb #2 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 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 I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available 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 i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available w | No description available x | No description available y | No description available z | No description available > open Z:/ALL/Niels/Valik/For_Poster/X-ray_resampled.mrc Opened X-ray_resampled.mrc, grid size 512,512,512, pixel 0.652, shown at level 0.481, step 2, values float32 > hide #!2 models > select #1.2/A:104 108 atoms, 99 bonds, 1 model selected > select up 40236 atoms, 44299 bonds, 1 model selected > select down 108 atoms, 99 bonds, 1 model selected > open Z:/ALL/Niels/Valik/For_Poster/4v95.cif 4v95.cif title: Crystal structure of YAEJ bound to the 70S ribosome [more info...] Chain information for 4v95.cif #4 --- Chain | Description AA CA | 16S Ribosomal RNA AB CB | 30S Ribosomal Protein S2 AC CC | 30S Ribosomal Protein S3 AD CD | 30S Ribosomal Protein S4 AE CE | 30S Ribosomal Protein S5 AF CF | 30S Ribosomal Protein S6 AG CG | 30S Ribosomal Protein S7 AH CH | 30S Ribosomal Protein S8 AI CI | 30S Ribosomal Protein S9 AJ CJ | 30S Ribosomal Protein S10 AK CK | 30S Ribosomal Protein S11 AL CL | 30S Ribosomal Protein S12 AM CM | 30S Ribosomal Protein S13 AN CN | 30S Ribosomal Protein S14 AO CO | 30S Ribosomal Protein S15 AP CP | 30S Ribosomal Protein S16 AQ CQ | 30S Ribosomal Protein S17 AR CR | 30S Ribosomal Protein S18 AS CS | 30S Ribosomal Protein S19 AT CT | 30S Ribosomal Protein S20 AU CU | 30S Ribosomal Protein THX AV CV | P-site fMet-tRNA AX CX | mRNA AY | YAEJ B0 D0 | 50S Ribosomal Protein L27 B1 D1 | 50S Ribosomal Protein L28 B2 D2 | 50S Ribosomal Protein L29 B3 D3 | 50S Ribosomal Protein L30 B4 D4 | 50S Ribosomal Protein L31 B5 D5 | 50S Ribosomal Protein L32 B6 D6 | 50S Ribosomal Protein L33 B7 D7 | 50S Ribosomal Protein L34 B8 D8 | 50S Ribosomal Protein L35 B9 D9 | 50S Ribosomal Protein L36 BA DA | 23S Ribosomal RNA BB DB | 5S Ribosomal RNA BD DD | 50S Ribosomal Protein L2 BE DE | 50S Ribosomal Protein L3 BF DF | 50S Ribosomal Protein L4 BG DG | 50S Ribosomal Protein L5 BH DH | 50S Ribosomal Protein L6 BI DI | 50S Ribosomal Protein L9 BN DN | 50S Ribosomal Protein L13 BO DO | 50S Ribosomal Protein L14 BP DP | 50S Ribosomal Protein L15 BQ DQ | 50S Ribosomal Protein L16 BR DR | 50S Ribosomal Protein L17 BS DS | 50S Ribosomal Protein L18 BT DT | 50S Ribosomal Protein L19 BU DU | 50S Ribosomal Protein L20 BV DV | 50S Ribosomal Protein L21 BW DW | 50S Ribosomal Protein L22 BX DX | 50S Ribosomal Protein L23 BY DY | 50S Ribosomal Protein L24 BZ DZ | 50S Ribosomal Protein L25 Non-standard residues in 4v95.cif #4 --- MG — magnesium ion ZN — zinc ion 4v95.cif mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > close #4 > open Z:/ALL/Niels/Valik/For_Poster/4v95.cif 4v95.cif title: Crystal structure of YAEJ bound to the 70S ribosome [more info...] Chain information for 4v95.cif #4 --- Chain | Description AA CA | 16S Ribosomal RNA AB CB | 30S Ribosomal Protein S2 AC CC | 30S Ribosomal Protein S3 AD CD | 30S Ribosomal Protein S4 AE CE | 30S Ribosomal Protein S5 AF CF | 30S Ribosomal Protein S6 AG CG | 30S Ribosomal Protein S7 AH CH | 30S Ribosomal Protein S8 AI CI | 30S Ribosomal Protein S9 AJ CJ | 30S Ribosomal Protein S10 AK CK | 30S Ribosomal Protein S11 AL CL | 30S Ribosomal Protein S12 AM CM | 30S Ribosomal Protein S13 AN CN | 30S Ribosomal Protein S14 AO CO | 30S Ribosomal Protein S15 AP CP | 30S Ribosomal Protein S16 AQ CQ | 30S Ribosomal Protein S17 AR CR | 30S Ribosomal Protein S18 AS CS | 30S Ribosomal Protein S19 AT CT | 30S Ribosomal Protein S20 AU CU | 30S Ribosomal Protein THX AV CV | P-site fMet-tRNA AX CX | mRNA AY | YAEJ B0 D0 | 50S Ribosomal Protein L27 B1 D1 | 50S Ribosomal Protein L28 B2 D2 | 50S Ribosomal Protein L29 B3 D3 | 50S Ribosomal Protein L30 B4 D4 | 50S Ribosomal Protein L31 B5 D5 | 50S Ribosomal Protein L32 B6 D6 | 50S Ribosomal Protein L33 B7 D7 | 50S Ribosomal Protein L34 B8 D8 | 50S Ribosomal Protein L35 B9 D9 | 50S Ribosomal Protein L36 BA DA | 23S Ribosomal RNA BB DB | 5S Ribosomal RNA BD DD | 50S Ribosomal Protein L2 BE DE | 50S Ribosomal Protein L3 BF DF | 50S Ribosomal Protein L4 BG DG | 50S Ribosomal Protein L5 BH DH | 50S Ribosomal Protein L6 BI DI | 50S Ribosomal Protein L9 BN DN | 50S Ribosomal Protein L13 BO DO | 50S Ribosomal Protein L14 BP DP | 50S Ribosomal Protein L15 BQ DQ | 50S Ribosomal Protein L16 BR DR | 50S Ribosomal Protein L17 BS DS | 50S Ribosomal Protein L18 BT DT | 50S Ribosomal Protein L19 BU DU | 50S Ribosomal Protein L20 BV DV | 50S Ribosomal Protein L21 BW DW | 50S Ribosomal Protein L22 BX DX | 50S Ribosomal Protein L23 BY DY | 50S Ribosomal Protein L24 BZ DZ | 50S Ribosomal Protein L25 Non-standard residues in 4v95.cif #4 --- MG — magnesium ion ZN — zinc ion 4v95.cif mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > mmaker #4/AY to #2/y Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Model_3_major_state_Mg-wz.Q28-coot-0_Niels.pdb, chain y (#2) with 4v95.cif, chain AY (#4), sequence alignment score = 634.5 RMSD between 82 pruned atom pairs is 0.762 angstroms; (across all 132 pairs: 2.902) > select #4 284877 atoms, 303230 bonds, 14000 pseudobonds, 4 models selected > style sel stick Changed 284877 atom styles > hide sel atoms > select #1.2 140349 atoms, 152485 bonds, 10 pseudobonds, 3 models selected > hide sel cartoons > hide sel atoms > select #4/y Nothing selected > select #4/AY 1034 atoms, 1043 bonds, 1 model selected > show sel atoms > color zone #3 near sel distance 2 sharpEdges true > volume splitbyzone #3 > save session Z:/ALL/Niels/Valik/For_Poster/X-ray.cxs > save session Z:/ALL/Niels/Valik/For_Poster/X-ray.cxs includeMaps true > view sel > save session Z:/ALL/Niels/Valik/For_Poster/X-ray.cxs includeMaps true > close #1.2 > close #1 > show #!2 models > select #2 147646 atoms, 159894 bonds, 1 model selected > style sel stick Changed 147646 atom styles > hide sel atoms > hide sel cartoons > select #2/y 1047 atoms, 1059 bonds, 1 model selected > show sel atoms > open Z:/ALL/Niels/Valik/For_Poster/Volumes/gs/gs_arfb.mrc Opened gs_arfb.mrc, grid size 512,512,512, pixel 0.652, shown at level 0.00126, step 2, values float32 > hide #!1 models > hide #!4 models > save session Z:/ALL/Niels/Valik/For_Poster/X-ray.cxs includeMaps true Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 2394, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 164, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\models.py"", line 275, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 769, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 532, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 2394, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 164, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\models.py"", line 275, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 141, in lambda e, what=what, self=self: self.handle_scheme(what), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 84, in handle_scheme cmd(self.session) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 166, in _file_save session.ui.main_window.file_save_cb(session) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\ui\gui.py"", line 601, in file_save_cb self.save_dialog.display(self, session) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\ui\save_dialog.py"", line 138, in display fmt.save(session, filename) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 1062, in save run(session, cmd) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2688, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 956, in save_session save(session, filename, **kw) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\commands\save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 769, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 532, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) See log for complete Python traceback. > save session Z:/ALL/Niels/Valik/For_Poster/X-ray-1.cxs includeMaps true Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 2394, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 164, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\models.py"", line 275, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 769, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 532, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 2394, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 164, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\models.py"", line 275, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 141, in lambda e, what=what, self=self: self.handle_scheme(what), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 84, in handle_scheme cmd(self.session) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 166, in _file_save session.ui.main_window.file_save_cb(session) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\ui\gui.py"", line 601, in file_save_cb self.save_dialog.display(self, session) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\ui\save_dialog.py"", line 138, in display fmt.save(session, filename) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 1062, in save run(session, cmd) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2688, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 956, in save_session save(session, filename, **kw) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\commands\save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 769, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 532, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) See log for complete Python traceback. > show #!3 models > hide #!3 models > close #3 > save session Z:/ALL/Niels/Valik/For_Poster/X-ray-1.cxs includeMaps true Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 2394, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 164, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\models.py"", line 275, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 769, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 532, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 2394, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\atomic\structure.py"", line 164, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\models.py"", line 275, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 141, in lambda e, what=what, self=self: self.handle_scheme(what), File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 84, in handle_scheme cmd(self.session) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 166, in _file_save session.ui.main_window.file_save_cb(session) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\ui\gui.py"", line 601, in file_save_cb self.save_dialog.display(self, session) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\ui\save_dialog.py"", line 138, in display fmt.save(session, filename) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 1062, in save run(session, cmd) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2688, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 956, in save_session save(session, filename, **kw) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\commands\save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 769, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 532, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' File ""C:\Program Files\ChimeraX_01092019\bin\lib\site- packages\chimerax\core\session.py"", line 258, in process raise RuntimeError(msg) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 397.93 OpenGL renderer: Quadro P4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Core can't reproduce Greg Couch all ChimeraX