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Opened 6 years ago
Closed 6 years ago
#2219 closed defect (fixed)
Errors and warnings opening mmCIF saved by ChimeraX
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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 <listcomp> 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
Change History (3)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Errors and warnings opening mmCIF saved by ChimeraX |
comment:2 by , 6 years ago
| Status: | assigned → feedback |
|---|
comment:3 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | feedback → closed |
User upgraded to daily build. And started a new ticket, #2230.
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Hello. The first thing to try is to update your version of Chimera to the latest daily build. There have been several mmCIF bug fixes since you installed your version. If that doesn't fix your problem, then please send me the problematic mmCIF file so I can figure out if the is writing or the reading that is the problem.