id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2219 Errors and warnings opening mmCIF saved by ChimeraX sitins07@… Greg Couch "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.9 (2019-05-22) Description saved model as cif file w/o indication relModel and tryed to open it. Log: UCSF ChimeraX version: 0.9 (2019-05-22) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""D:\\\Projects\\\Ribo\\\SecY\\\LepB75\\\run_class001.mrc"" Opened run_class001.mrc, grid size 64,64,64, pixel 5.8, shown at level 0.208, step 1, values float32 > close #1 > open Z:/ALL/Niels/Valik/ArfB_ModelRefinement/3d512_ptrna_arfb_26A.ccp4 Opened 3d512_ptrna_arfb_26A.ccp4, grid size 512,512,512, pixel 0.652, shown at level 4.85, step 2, values float32 > ui mousemode rightMode select > select #1 2 models selected > select clear > open 5lza #2.1 File not found: #2.1 > open 5lza mode l#2.1 File not found: mode > open 5lza Summary of feedback from opening 5lza fetched from pdb --- note | Fetching compressed mmCIF 5lza from http://files.rcsb.org/download/5lza.cif 5lza title: Structure of the 70S ribosome with SECIS-mRNA and P-site tRNA (Initial complex, IC) [more info...] Chain information for 5lza #2 --- Chain | Description 0 | 50S ribosomal protein L32 1 | 50S ribosomal protein L33 2 | 50S ribosomal protein L34 3 | 50S ribosomal protein L35 4 | 50S ribosomal protein L36 6 | 50S ribosomal protein L31 A | 23S ribosomal RNA B | 5S ribosomal RNA C | 50S ribosomal protein L2 D | 50S ribosomal protein L3 E | 50S ribosomal protein L4 F | 50S ribosomal protein L5 G | 50S ribosomal protein L6 H | 50S ribosomal protein L9 I | 50S ribosomal protein L11 J | 50S ribosomal protein L13 K | 50S ribosomal protein L14 L | 50S ribosomal protein L15 M | 50S ribosomal protein L16 N | 50S ribosomal protein L17 O | 50S ribosomal protein L18 P | 50S ribosomal protein L19 Q | 50S ribosomal protein L20 R | 50S ribosomal protein L21 S | 50S ribosomal protein L22 T | 50S ribosomal protein L23 U | 50S ribosomal protein L24 V | 50S ribosomal protein L25 W | 50S ribosomal protein L27 X | 50S ribosomal protein L28 Y | 50S ribosomal protein L29 Z | 50S ribosomal protein L30 a | 16S ribosomal RNA b | 30S ribosomal protein S2 c | 30S ribosomal protein S3 d | 30S ribosomal protein S4 e | 30S ribosomal protein S5 f | 30S ribosomal protein S6 g | 30S ribosomal protein S7 h | 30S ribosomal protein S8 i | 30S ribosomal protein S9 j | 30S ribosomal protein S10 k | 30S ribosomal protein S11 l | 30S ribosomal protein S12 m | 30S ribosomal protein S13 n | 30S ribosomal protein S14 o | 30S ribosomal protein S15 p | 30S ribosomal protein S16 q | 30S ribosomal protein S17 r | 30S ribosomal protein S18 s | 30S ribosomal protein S19 t | 30S ribosomal protein S20 u | 30S ribosomal protein S21 v | fMet-tRNAfMet x | SECIS mRNA Non-standard residues in 5lza #2 --- 3TD — (1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono- D-ribitol ZN — zinc ion > select clear > select #2 145925 atoms, 158589 bonds, 4705 pseudobonds, 3 models selected > show selAtoms > hide selAtoms ribbons > hide selAtoms > show selAtoms ribbons > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode select > fitmap #2 inMap #1 resolution 3 metric correlation Fit map 5lza map 3 in map 3d512_ptrna_arfb_26A.ccp4 using 1470649 points correlation = 0.7513, correlation about mean = 0.441, overlap = 3.751e+06 steps = 156, shift = 3.38, angle = 7.09 degrees Position of 5lza map 3 (#3) relative to 3d512_ptrna_arfb_26A.ccp4 (#1) coordinates: Matrix rotation and translation 0.98141202 -0.12295256 0.14735371 7.45722239 0.12039961 0.99238088 0.02615572 -12.80825658 -0.14944692 -0.00792821 0.98873796 36.92764472 Axis -0.08845584 0.77026764 0.63155628 Axis point 195.55171456 -0.00000000 -33.62136457 Rotation angle (degrees) 11.10810164 Shift along axis 12.79646554 > select #1 2 models selected > hide #!1 models > select /x:107 20 atoms, 21 bonds selected > select up 1025 atoms, 1145 bonds selected > delete sel > delete sel > select /v:10 23 atoms, 25 bonds selected > select up 1644 atoms, 1836 bonds selected > delete sel > hide #!2 models > show #!1 models > close #3 > select #1 2 models selected > select clear > open 4rb7 Summary of feedback from opening 4rb7 fetched from pdb --- warning | 4RB7 has been replaced by 4W2F notes | Fetching compressed mmCIF 4rb7 from http://files.rcsb.org/download/4rb7.cif Fetching CCD UAM from http://ligand-expo.rcsb.org/reports/U/UAM/UAM.cif 4rb7 title: Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin, mRNA and three deacylated tRNAs in the A, P and E sites [more info...] Chain information for 4rb7 #3 --- Chain | Description A | 16S Ribosomal RNA B | 30S Ribosomal Protein S2 C | 30S Ribosomal Protein S3 D | 30S Ribosomal Protein S4 E | 30S Ribosomal Protein S5 F | 30S Ribosomal Protein S6 G | 30S Ribosomal Protein S7 H | 30S Ribosomal Protein S8 I | 30S Ribosomal Protein S9 J | 30S Ribosomal Protein S10 K | 30S Ribosomal Protein S11 L | 30S Ribosomal Protein S12 M | 30S Ribosomal Protein S13 N | 30S Ribosomal Protein S14 O | 30S Ribosomal Protein S15 P | 30S Ribosomal Protein S16 Q | 30S Ribosomal Protein S17 R | 30S Ribosomal Protein S18 S | 30S Ribosomal Protein S19 T | 30S Ribosomal Protein S20 U | 30S Ribosomal Protein THX V | mRNA W Y | A/P-site tRNA X | E-site tRNA Non-standard residues in 4rb7 #3 --- MG — magnesium ion SF4 — iron/sulfur cluster UAM — Amicoumacin A ZN — zinc ion > select #3 56383 atoms, 60679 bonds, 2274 pseudobonds, 3 models selected > view cofr false > select clear > select #3/X:52@OP1 1 atom selected > select up 23 atoms, 25 bonds selected > select up 1625 atoms, 1815 bonds selected > select ~sel 198014 atoms, 214472 bonds, 6790 pseudobonds, 8 models selected > ~select #1 198014 atoms, 214472 bonds, 6790 pseudobonds, 6 models selected > ~select #2 54758 atoms, 58864 bonds, 2200 pseudobonds, 3 models selected > delete sel > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode select > select #1 2 models selected > select #3/X:46@OP2 1 atom selected > select up 23 atoms, 25 bonds selected > select up 1625 atoms, 1815 bonds selected > hide selAtoms > show selAtoms ribbons > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > fitmap sel inMap #1 resolution 3 metric correlation Fit map 4rb7 map 3 in map 3d512_ptrna_arfb_26A.ccp4 using 16004 points correlation = 0.7946, correlation about mean = 0.4409, overlap = 4.046e+04 steps = 160, shift = 2.4, angle = 17.5 degrees Position of 4rb7 map 3 (#4) relative to 3d512_ptrna_arfb_26A.ccp4 (#1) coordinates: Matrix rotation and translation -0.51006370 -0.32635529 0.79581860 362.26667041 0.31639986 0.78916258 0.52641577 288.37901093 -0.79982883 0.52030247 -0.29926442 313.70216794 Axis -0.00355373 0.92756683 0.37364040 Axis point 234.01739579 0.00000000 -12.87736775 Rotation angle (degrees) 120.66934318 Shift along axis 383.41521220 > close #4 > ui mousemode rightMode select > select #3/X:46 23 atoms, 25 bonds selected > select up 1625 atoms, 1815 bonds selected > hide selAtoms ribbons > show selAtoms > style selAtoms stick Changed 1625 atom styles > select clear > show #!2 models > select clear > select #1 2 models selected > open 4v95 Summary of feedback from opening 4v95 fetched from pdb --- note | Fetching compressed mmCIF 4v95 from http://files.rcsb.org/download/4v95.cif 4v95 title: Crystal structure of YAEJ bound to the 70S ribosome [more info...] Chain information for 4v95 #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 #4 --- MG — magnesium ion ZN — zinc ion 4v95 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > select #4/AY 1034 atoms, 1043 bonds selected > select ~sel 428724 atoms, 459610 bonds, 18664 pseudobonds, 9 models selected > ~select #3 427099 atoms, 457795 bonds, 18590 pseudobonds, 8 models selected > ~select #2 283843 atoms, 302187 bonds, 14000 pseudobonds, 5 models selected > select #1 2 models selected > select #1 2 models selected > select #1 2 models selected > ~select #1.1 1 model selected > select #1 2 models selected > select #1 2 models selected > ~select #1.1 1 model selected > select #4/AY 1034 atoms, 1043 bonds selected > ui mousemode rightMode ""translate selected models"" > select ~sel 428724 atoms, 459610 bonds, 18664 pseudobonds, 9 models selected > ~select #1.1 428724 atoms, 459610 bonds, 18664 pseudobonds, 8 models selected > ~select #2 285468 atoms, 304002 bonds, 14074 pseudobonds, 5 models selected > ~select #3 283843 atoms, 302187 bonds, 14000 pseudobonds, 4 models selected > delete sel > close #1 > open Z:/ALL/Niels/Valik/ArfB_ModelRefinement/3d512_ptrna_arfb_26A.ccp4 Opened 3d512_ptrna_arfb_26A.ccp4, grid size 512,512,512, pixel 0.652, shown at level 4.85, step 2, values float32 > ui mousemode rightMode select > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > style selAtoms stick Changed 1034 atom styles > style selAtoms ball Changed 1034 atom styles > ui mousemode rightMode ""translate selected models"" > fitmap sel inMap #1 resolution 3 metric correlation Fit map 4v95 map 3 in map 3d512_ptrna_arfb_26A.ccp4 using 11320 points correlation = 0.3589, correlation about mean = 0.03981, overlap = 8294 steps = 124, shift = 3.33, angle = 9.42 degrees Position of 4v95 map 3 (#5) relative to 3d512_ptrna_arfb_26A.ccp4 (#1) coordinates: Matrix rotation and translation -0.08009276 -0.68535987 0.72378657 162.10850033 0.32622959 -0.70415289 -0.63066866 102.85090349 0.94189140 0.18560860 0.27998222 69.28655556 Axis 0.61931821 -0.16547844 0.76750364 Axis point 22.36142170 77.89368017 0.00000000 Rotation angle (degrees) 138.77537259 Shift along axis 136.55482265 > style selAtoms stick Changed 1034 atom styles > ui mousemode rightMode select > select clear > cd Z:/ALL/Niels/Valik/ArfB_ModelRefinement/ Current working directory is: Z:\ALL\Niels\Valik\ArfB_ModelRefinement > save sterting_model.cif format mmcif models #2,3,4 relModel #1 got an unexpected keyword argument 'rel_model' > save sterting_model.cif format mmcif models #2,3,4 relModel #2 got an unexpected keyword argument 'rel_model' > save sterting_model.cif format mmcif models #2,3,4 relModel #1 got an unexpected keyword argument 'rel_model' > save sterting_model.cif format mmcif models #2,3,4 relModel #1 got an unexpected keyword argument 'rel_model' Invalid ""relModel"" argument: invalid model specifier > save sterting_model.cif format mmcif models #2,3,4 relModel #4 got an unexpected keyword argument 'rel_model' Missing ""relModel"" keyword's argument > save sterting_model.cif format mmcif models #2,3,4 relModel #1.1 got an unexpected keyword argument 'rel_model' > save sterting_model.cif format mmcif models #2,3,4 relModel #2 got an unexpected keyword argument 'rel_model' > save sterting_model.cif format mmcif models #2,3,4 > hide #!2 models > hide #!3 models > hide #!4 models > open Z:/ALL/Niels/Valik/ArfB_ModelRefinement/sterting_model.cif Summary of feedback from opening Z:/ALL/Niels/Valik/ArfB_ModelRefinement/sterting_model.cif --- warnings | Duplicate polymer '1' near line 180314 Skipping residue with duplicate label_seq_id 3 in chain X Skipping residue with duplicate label_seq_id 5 in chain X Unable to connect G #4 in chain X and #5 in chain Skipping residue with duplicate label_seq_id 6 in chain X Unable to connect #5 in chain and G #7 in chain X Skipping residue with duplicate label_seq_id 8 in chain X Skipping residue with duplicate label_seq_id 10 in chain X Unable to connect G #9 in chain X and #10 in chain Duplicate polymer '1' near line 182575 Skipping residue with duplicate label_seq_id 3 in chain AY Skipping residue with duplicate label_seq_id 5 in chain AY Skipping residue with duplicate label_seq_id 7 in chain AY Skipping residue with duplicate label_seq_id 9 in chain AY Skipping residue with duplicate label_seq_id 11 in chain AY 61 messages similar to the above omitted Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 572, in _qt_safe run(session, ""open "" + quote_if_necessary(paths[0])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2632, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 64, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 602, in open session, filenames, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 477, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 433, in open_data models, status = open_func(*args, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\mmcif\\__init__.py"", line 55, in open_file log_info=log_info, combine_sym_atoms=combine_sym_atoms) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\mmcif\mmcif.py"", line 85, in open_mmcif for p in pointers] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\mmcif\mmcif.py"", line 85, in for p in pointers] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\structure.py"", line 2245, in __init__ self._set_chain_descriptions(self.session) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\structure.py"", line 2424, in _set_chain_descriptions mmcif_cid = ch.existing_residues.mmcif_chain_ids[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molc.py"", line 195, in get_prop cget(self._c_pointers, n, pointer(values)) RuntimeError: unknown C++ exception RuntimeError: unknown C++ exception File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molc.py"", line 195, in get_prop cget(self._c_pointers, n, pointer(values)) 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 Input/Output fixed Eric Pettersen all ChimeraX