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Opened 6 years ago
Closed 6 years ago
#2268 closed defect (can't reproduce)
Error opening mmCIF: basic_string::_M_construct null not valid
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-4.15.0-54-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.9 (2019-06-05) Description opening a .cif file from a Phenix refinement doesn't work. The same file can be opened with Chimera or PyMol Log: UCSF ChimeraX version: 0.9 (2019-06-05) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/NCL12_smallermap_apply_ncs_40_real_space_refined.pdb Chain information for NCL12_smallermap_apply_ncs_40_real_space_refined.pdb #1 --- Chain | Description A C E G | No description available B F | No description available D H | No description available I | No description available J N R W | No description available K M O Q S V X Z | No description available L P T Y | No description available > hide selAtoms ribbons > hide selAtoms > show selAtoms ribbons > select :42,58,61,62,191,193 11760 atoms, 10800 bonds selected > color sel yellow > show sel atoms > select clear Expected a keyword > select :39,97,114,138,177 10320 atoms, 9360 bonds selected > color sel red > show sel atoms Expected a keyword Expected a keyword > select :5,104,108,158,168 6480 atoms, 5760 bonds selected > color sel red > show sel atoms > select :39,97,114,138,177 10320 atoms, 9360 bonds selected > color sel orange > show sel atoms > cartoon style all modeHelix default arrows false xsection oval width 1 thickness 1 > select clear > undo > select :39,97,114,138,177 10320 atoms, 9360 bonds selected > color sel orange > show sel atoms > select :39,97,114,138,177 10320 atoms, 9360 bonds selected > color sel red > show sel atoms > select :39,97,114,138,177 10320 atoms, 9360 bonds selected > color sel orange > show sel atoms > select :5,104,108,158,168 6480 atoms, 5760 bonds selected > color sel red > show sel atoms > select :5,104,108,158,168 6480 atoms, 5760 bonds selected > color sel red > show sel atoms > select :42,58,61,62,191,193 11760 atoms, 10800 bonds selected > color sel yellow > show sel atoms > save session /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/cage_with_mutations.cxs > select clear > style selAtoms stick Changed 286320 atom styles > color selAtoms byhetero > select /A:42 189 atoms, 162 bonds selected > view > open 1hqk 1hqk title: Crystal structure analysis of lumazine synthase from aquifex aeolicus [more info...] Chain information for 1hqk #2 --- Chain | Description A B C D E | 6,7-dimethyl-8-ribityllumazine synthase 1hqk mmCIF Assemblies --- 1| author_and_software_defined_assembly Unknown command: selete solvent > delete solvent > delete #2/E > view > align #2/A@CA:10-40 toAtoms #1/A@CA:123-153 Unequal number of atoms to pair, 361 and 9847 > align #2/A:10-40@CA toAtoms #1/A:123-153@CA Unequal number of atoms to pair, 31 and 837 > align #2/A:10-40@CA toAtoms #1.1/A:123-153@CA Unequal number of atoms to pair, 31 and 0 > select clear > select /A 33376 atoms, 33947 bonds selected > select /AB Nothing selected > select /a 33376 atoms, 33947 bonds selected > align #2/A:10-40@CA toAtoms #1.1/X:123-153@CA Unequal number of atoms to pair, 31 and 0 > align #2/A:10-40@CA toAtoms #1/X:123-153@CA RMSD between 31 atom pairs is 0.432 angstroms > select clear > hide selAtoms > undo > ~select #2 Nothing selected > show #!2 models > select #2 4708 atoms, 4780 bonds selected > hide selAtoms > show selAtoms ribbons > preset cartoons/nucleotides ribbons/slabs Changed 4708 atom styles Preset expands to these ChimeraX commands: surf hide; style (protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20; cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x rect; nucleotides tube/slab shape box > cartoon style all modeHelix default arrows false xsection oval width 1 thickness 1 > select clear > select #2/A:3 8 atoms, 7 bonds selected > select up 29 atoms, 29 bonds selected > select up 1177 atoms, 1195 bonds selected > select up 4708 atoms, 4780 bonds selected > select up 291028 atoms, 296020 bonds selected > select down 4708 atoms, 4780 bonds selected > select down 1177 atoms, 1195 bonds selected Expected fewer arguments > select ~sel 289851 atoms, 294825 bonds selected > delete #2/B-D > select clear Expected a keyword > save /home/hilvertg/Desktop/1hqk.pdb format pdb models #2 relModel #1 > open /home/hilvertg/Desktop/1hqk.pdb Chain information for 1hqk.pdb #3 --- Chain | Description A | No description available > open /home/hilvertg/Desktop/1hqk.pdb Chain information for 1hqk.pdb #4 --- Chain | Description A | No description available > open /home/hilvertg/Desktop/1hqk.pdb Chain information for 1hqk.pdb #5 --- Chain | Description A | No description available > align #2/A:10-40@CA toAtoms #1/Y:123-153@CA RMSD between 31 atom pairs is 0.408 angstroms > align #3/A:10-40@CA toAtoms #1/Z:123-153@CA RMSD between 31 atom pairs is 0.441 angstroms > align #4/A:10-40@CA toAtoms #1/W:123-153@CA RMSD between 31 atom pairs is 0.413 angstroms > align #3/A:10-40@CA toAtoms #1/V:123-153@CA RMSD between 31 atom pairs is 0.449 angstroms Missing or invalid "match_atoms" argument: empty atom specifier > mmaker #2 to #1/V 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 NCL12_smallermap_apply_ncs_40_real_space_refined.pdb, chain V (#1) with 1hqk, chain A (#2), sequence alignment score = 368.3 RMSD between 78 pruned atom pairs is 0.705 angstroms; (across all 80 pairs: 0.788) > mmaker #3 to #1/w 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 NCL12_smallermap_apply_ncs_40_real_space_refined.pdb, chain W (#1) with 1hqk.pdb, chain A (#3), sequence alignment score = 348.5 RMSD between 76 pruned atom pairs is 0.638 angstroms; (across all 80 pairs: 0.921) > mmaker #4 to #1/x 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 NCL12_smallermap_apply_ncs_40_real_space_refined.pdb, chain X (#1) with 1hqk.pdb, chain A (#4), sequence alignment score = 344.9 RMSD between 76 pruned atom pairs is 0.639 angstroms; (across all 80 pairs: 0.941) > mmaker #5 to #1/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 NCL12_smallermap_apply_ncs_40_real_space_refined.pdb, chain Y (#1) with 1hqk.pdb, chain A (#5), sequence alignment score = 359.3 RMSD between 74 pruned atom pairs is 0.627 angstroms; (across all 80 pairs: 1.355) > save 1hqk_fitRSR41_4chains.pdb format pdb models #2-5 relModel #1 > open /home/hilvertg/tetterst/NCL12_phenix_2/run_class001_croppedByHalf_shifted.mrc Opened run_class001_croppedByHalf_shifted.mrc, grid size 301,301,301, pixel 1.1, shown at level 0.035, step 2, values float32 > fitmap #2-5 inMap #6 Fit molecules 1hqk (#2), 1hqk.pdb (#3), 1hqk.pdb (#4), 1hqk.pdb (#5) to map run_class001_croppedByHalf_shifted.mrc (#6) using 4708 atoms average map value = 0.02049, steps = 40 shifted from previous position = 0.103 rotated from previous position = 0.262 degrees atoms outside contour = 3030, contour level = 0.02614 Position of 1hqk (#2) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.51390946 -0.79120081 -0.33150919 357.86300466 -0.29067269 0.52418934 -0.80045920 432.34719003 0.80709755 -0.31500289 -0.49936633 108.80614181 Axis 0.36359724 -0.85279408 0.37488573 Axis point 230.05125285 0.00000000 245.85756855 Rotation angle (degrees) 138.11988074 Shift along axis -197.79525407 Position of 1hqk.pdb (#3) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.97391357 0.22670061 -0.00995960 302.63182078 0.19420644 0.81000828 -0.55332671 91.18356372 -0.11737214 -0.54082661 -0.83290477 416.53345192 Axis 0.11070458 0.95127721 -0.28777799 Axis point 152.19688771 0.00000000 217.56587201 Rotation angle (degrees) 176.76353051 Shift along axis 0.37441455 Position of 1hqk.pdb (#4) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation 0.99981410 -0.01613991 -0.01054813 6.14298660 0.01614149 0.99986972 0.00006453 -2.77597737 0.01054572 -0.00023478 0.99994436 -1.97602260 Axis -0.00776154 -0.54699276 0.83710135 Axis point 181.24620797 378.43271433 0.00000000 Rotation angle (degrees) 1.10482595 Shift along axis -0.18337072 Position of 1hqk.pdb (#5) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.48811192 0.47002647 0.73540592 63.93027042 0.22594772 0.88192717 -0.41370532 49.92570445 -0.84302692 -0.03577121 -0.53668057 401.05229801 Axis 0.23026539 0.96169795 -0.14871082 Axis point 135.00452964 0.00000000 187.22166255 Rotation angle (degrees) 124.85019002 Shift along axis 3.09356176 > fitmap #2-5 inMap #6 Fit molecules 1hqk (#2), 1hqk.pdb (#3), 1hqk.pdb (#4), 1hqk.pdb (#5) to map run_class001_croppedByHalf_shifted.mrc (#6) using 4708 atoms average map value = 0.02049, steps = 40 shifted from previous position = 0.0028 rotated from previous position = 0.015 degrees atoms outside contour = 3028, contour level = 0.02614 Position of 1hqk (#2) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.51383847 -0.79114586 -0.33175029 357.88197457 -0.29060801 0.52436358 -0.80036855 432.31755641 0.80716604 -0.31485086 -0.49935150 108.78654139 Axis 0.36356425 -0.85284072 0.37481161 Axis point 230.03769638 0.00000000 245.84416454 Rotation angle (degrees) 138.10872164 Shift along axis -197.81046751 Position of 1hqk.pdb (#3) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.97389329 0.22677681 -0.01020450 302.63151950 0.19440797 0.80998859 -0.55328476 91.15029454 -0.11720663 -0.54082416 -0.83292967 416.50636138 Axis 0.11077752 0.95127233 -0.28776604 Axis point 152.17114904 0.00000000 217.56395104 Rotation angle (degrees) 176.77589326 Shift along axis 0.37713663 Position of 1hqk.pdb (#4) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation 0.99981901 -0.01593881 -0.01038774 6.05667092 0.01593987 0.99987295 0.00001871 -2.72954150 0.01038612 -0.00018429 0.99994605 -1.96005303 Axis -0.00533509 -0.54595430 0.83779797 Axis point 180.56205412 377.88304904 0.00000000 Rotation angle (degrees) 1.09013405 Shift along axis -0.18423641 Position of 1hqk.pdb (#5) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.48820166 0.47019812 0.73523660 63.91919465 0.22608631 0.88183432 -0.41382751 49.94119364 -0.84293779 -0.03580435 -0.53681834 401.06151793 Axis 0.23035096 0.96167121 -0.14875118 Axis point 134.97434285 0.00000000 187.23524199 Rotation angle (degrees) 124.86137425 Shift along axis 3.09248218 > fitmap #2-5 inMap #6 Fit molecules 1hqk (#2), 1hqk.pdb (#3), 1hqk.pdb (#4), 1hqk.pdb (#5) to map run_class001_croppedByHalf_shifted.mrc (#6) using 4708 atoms average map value = 0.02049, steps = 40 shifted from previous position = 0.0193 rotated from previous position = 0.0237 degrees atoms outside contour = 3030, contour level = 0.02614 Position of 1hqk (#2) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.51372723 -0.79135148 -0.33143200 357.84587266 -0.29071125 0.52401225 -0.80056114 432.37254837 0.80719967 -0.31491904 -0.49925414 108.76520228 Axis 0.36370074 -0.85272918 0.37493295 Axis point 230.08218634 0.00000000 245.88045414 Rotation angle (degrees) 138.11484557 Shift along axis -197.76822023 Position of 1hqk.pdb (#3) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.97396947 0.22645931 -0.00998234 302.72879211 0.19400890 0.81001131 -0.55339157 91.22148424 -0.11723487 -0.54092315 -0.83286141 416.52689555 Axis 0.11058879 0.95127812 -0.28781948 Axis point 152.23936900 0.00000000 217.57557408 Rotation angle (degrees) 176.76836003 Shift along axis 0.37085720 Position of 1hqk.pdb (#4) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation 0.99981259 -0.01633366 -0.01039215 6.19288304 0.01633598 0.99986655 0.00013805 -2.82711840 0.01038851 -0.00030779 0.99994599 -1.92921851 Axis -0.01151412 -0.53667262 0.84371199 Axis point 182.11173455 376.93088495 0.00000000 Rotation angle (degrees) 1.10935315 Shift along axis -0.18177335 Position of 1hqk.pdb (#5) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.48828719 0.46985001 0.73540233 64.03282726 0.22578944 0.88201551 -0.41360340 49.91621339 -0.84296782 -0.03591116 -0.53676405 401.08609939 Axis 0.23013467 0.96172929 -0.14871049 Axis point 135.05247472 0.00000000 187.21264918 Rotation angle (degrees) 124.85613916 Shift along axis 3.09634812 > fitmap #2-5 inMap #6 Fit molecules 1hqk (#2), 1hqk.pdb (#3), 1hqk.pdb (#4), 1hqk.pdb (#5) to map run_class001_croppedByHalf_shifted.mrc (#6) using 4708 atoms average map value = 0.02049, steps = 40 shifted from previous position = 0.0138 rotated from previous position = 0.0072 degrees atoms outside contour = 3028, contour level = 0.02614 Position of 1hqk (#2) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.51370890 -0.79133774 -0.33149320 357.83863525 -0.29077182 0.52408631 -0.80049065 432.37079905 0.80718952 -0.31483029 -0.49932652 108.77841768 Axis 0.36370835 -0.85275316 0.37487103 Axis point 230.07665518 0.00000000 245.86733746 Rotation angle (degrees) 138.11398686 Shift along axis -197.77878754 Position of 1hqk.pdb (#3) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.97396441 0.22647832 -0.01004465 302.71682893 0.19407102 0.81005789 -0.55330160 91.18948393 -0.11717407 -0.54084544 -0.83292043 416.50572822 Axis 0.11060849 0.95129046 -0.28777112 Axis point 152.22680262 0.00000000 217.56310817 Rotation angle (degrees) 176.77211543 Shift along axis 0.37241976 Position of 1hqk.pdb (#4) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation 0.99981384 -0.01628282 -0.01035113 6.15897042 0.01628401 0.99986741 0.00003118 -2.79909103 0.01034925 -0.00019973 0.99994643 -1.94831795 Axis -0.00598358 -0.53642363 0.84392766 Axis point 180.87065282 376.11586777 0.00000000 Rotation angle (degrees) 1.10557915 Shift along axis -0.17959351 Position of 1hqk.pdb (#5) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.48831029 0.46989340 0.73535927 64.01813030 0.22590482 0.88199546 -0.41358314 49.89801122 -0.84292353 -0.03583570 -0.53683864 401.07028918 Axis 0.23017980 0.96172412 -0.14867405 Axis point 135.03278263 0.00000000 187.20776939 Rotation angle (degrees) 124.86024953 Shift along axis 3.09505586 > fitmap #2-5 inMap #6 Fit molecules 1hqk (#2), 1hqk.pdb (#3), 1hqk.pdb (#4), 1hqk.pdb (#5) to map run_class001_croppedByHalf_shifted.mrc (#6) using 4708 atoms average map value = 0.02049, steps = 28 shifted from previous position = 0.00806 rotated from previous position = 0.0257 degrees atoms outside contour = 3026, contour level = 0.02614 Position of 1hqk (#2) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.51402784 -0.79106620 -0.33164686 357.89062880 -0.29055484 0.52435673 -0.80039235 432.31334061 0.80706459 -0.31506235 -0.49938207 108.81389347 Axis 0.36349253 -0.85284881 0.37486276 Axis point 230.02394415 0.00000000 245.84282683 Rotation angle (degrees) 138.11845314 Shift along axis -197.81707015 Position of 1hqk.pdb (#3) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.97386364 0.22691232 -0.01002102 302.56474706 0.19441493 0.80995461 -0.55333205 91.16437699 -0.11744128 -0.54081820 -0.83290049 416.54044806 Axis 0.11081676 0.95126308 -0.28778150 Axis point 152.15976137 0.00000000 217.56738621 Rotation angle (degrees) 176.76324958 Shift along axis 0.37791631 Position of 1hqk.pdb (#4) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation 0.99981682 -0.01592476 -0.01061731 6.08466344 0.01592646 0.99987316 0.00007580 -2.73513767 0.01061476 -0.00024489 0.99994363 -1.98869738 Axis -0.00837738 -0.55464318 0.83204613 Axis point 181.33023587 379.90319907 0.00000000 Rotation angle (degrees) 1.09672527 Shift along axis -0.18863603 Position of 1hqk.pdb (#5) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.48800496 0.47021869 0.73535403 63.85539692 0.22604514 0.88182570 -0.41386837 49.95773867 -0.84306272 -0.03574661 -0.53662596 401.04314726 Axis 0.23037385 0.96166363 -0.14876478 Axis point 134.96648214 0.00000000 187.24005294 Rotation angle (degrees) 124.84809209 Shift along axis 3.09205852 > fitmap #2-5 inMap #6 Fit molecules 1hqk (#2), 1hqk.pdb (#3), 1hqk.pdb (#4), 1hqk.pdb (#5) to map run_class001_croppedByHalf_shifted.mrc (#6) using 4708 atoms average map value = 0.02049, steps = 28 shifted from previous position = 0.00774 rotated from previous position = 0.00637 degrees atoms outside contour = 3024, contour level = 0.02614 Position of 1hqk (#2) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.51407484 -0.79103633 -0.33164527 357.88949366 -0.29046279 0.52434861 -0.80043107 432.30564665 0.80706779 -0.31515087 -0.49932105 108.81202749 Axis 0.36345345 -0.85284581 0.37490748 Axis point 230.00997275 0.00000000 245.85105333 Rotation angle (degrees) 138.11819949 Shift along axis -197.81944613 Position of 1hqk.pdb (#3) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.97385253 0.22696107 -0.00999646 302.53922738 0.19443095 0.80989622 -0.55341189 91.18783800 -0.11750686 -0.54088519 -0.83284774 416.56873273 Axis 0.11083575 0.95124766 -0.28782518 Axis point 152.15045063 0.00000000 217.58384755 Rotation angle (degrees) 176.76047777 Shift along axis 0.37540900 Position of 1hqk.pdb (#4) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation 0.99981675 -0.01589669 -0.01066544 6.07665599 0.01589944 0.99987358 0.00017229 -2.74361867 0.01066136 -0.00034183 0.99994311 -1.96565012 Axis -0.01342723 -0.55698732 0.83041245 Axis point 182.08877705 380.00324501 0.00000000 Rotation angle (degrees) 1.09698218 Shift along axis -0.18573219 Position of 1hqk.pdb (#5) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.48795803 0.47024515 0.73536825 63.82946742 0.22597773 0.88180907 -0.41394062 49.98640569 -0.84310795 -0.03580880 -0.53655075 401.06390458 Axis 0.23036967 0.96165681 -0.14881531 Axis point 134.96504555 0.00000000 187.25941494 Rotation angle (degrees) 124.84440925 Shift along axis 3.08969120 > fitmap #2-5 inMap #6 Fit molecules 1hqk (#2), 1hqk.pdb (#3), 1hqk.pdb (#4), 1hqk.pdb (#5) to map run_class001_croppedByHalf_shifted.mrc (#6) using 4708 atoms average map value = 0.02049, steps = 40 shifted from previous position = 0.022 rotated from previous position = 0.0259 degrees atoms outside contour = 3031, contour level = 0.02614 Position of 1hqk (#2) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.51369773 -0.79128397 -0.33163885 357.86243275 -0.29061142 0.52416411 -0.80049797 432.34247268 0.80725439 -0.31483595 -0.49921807 108.74997214 Axis 0.36364964 -0.85277025 0.37488909 Axis point 230.06274008 0.00000000 245.87206843 Rotation angle (degrees) 138.10551649 Shift along axis -197.78307493 Position of 1hqk.pdb (#3) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.97394453 0.22655791 -0.01017694 302.71228573 0.19419614 0.80996706 -0.55339066 91.20239625 -0.11713204 -0.54094813 -0.83285966 416.51792127 Axis 0.11066481 0.95126670 -0.28782800 Axis point 152.21137866 0.00000000 217.58137768 Rotation angle (degrees) 176.77729291 Shift along axis 0.37187979 Position of 1hqk.pdb (#4) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation 0.99981681 -0.01614132 -0.01028631 6.11400602 0.01614363 0.99986967 0.00014128 -2.78966440 0.01028269 -0.00030731 0.99994708 -1.90669252 Axis -0.01171749 -0.53728535 0.84331913 Axis point 181.85847795 376.58465731 0.00000000 Rotation angle (degrees) 1.09679955 Shift along axis -0.18074527 Position of 1hqk.pdb (#5) relative to run_class001_croppedByHalf_shifted.mrc (#6) coordinates: Matrix rotation and translation -0.48833295 0.47001590 0.73526593 64.00674558 0.22588235 0.88192505 -0.41374554 49.94303181 -0.84291642 -0.03596198 -0.53684135 401.10243655 Axis 0.23021117 0.96170202 -0.14876844 Axis point 135.02426549 0.00000000 187.23374042 Rotation angle (degrees) 124.86359370 Shift along axis 3.09399989 > save 1hqk_fitMap_4chains.pdb format pdb models #2-5 relModel #1 > close #6 > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > ui mousemode rightMode clip Unknown command: depthCueEend 1.7 Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a keyword > lighting depthCueEnd 1.7 > lighting depthCueStart 0.5 > save session /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/cage_with_mutations2.cxs > close > open 1hqk format mmCIF fromDatabase pdb 1hqk title: Crystal structure analysis of lumazine synthase from aquifex aeolicus [more info...] Chain information for 1hqk #1 --- Chain | Description A B C D E | 6,7-dimethyl-8-ribityllumazine synthase 1hqk mmCIF Assemblies --- 1| author_and_software_defined_assembly > sym #1 assembly 1 > view > ui mousemode rightMode clip > close > open /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/cage_with_mutations2.cxs format session opened ChimeraX session > close > open /home/hilvertg/tetterst/NCL12_phenix_2/run_class001_croppedByHalf_shifted.mrc Opened run_class001_croppedByHalf_shifted.mrc, grid size 301,301,301, pixel 1.1, shown at level 0.035, step 2, values float32 > close > open "/home/hilvertg/tetterst/NCL12 phenix/ChimeraX/fullcage_RSR98.csx.cxs" format session opened ChimeraX session > lighting depthCueStart 0.5 > lighting depthCueEnd 1.7 > lighting depthCueStart 0.8 > lighting depthCueStart 1.2 > lighting depthCueStart 1.5 > lighting depthCueStart 0.2 > lighting soft > lighting flat > lighting full > lighting simple > lighting simple > lighting soft > lighting full > lighting depthCueStart 0.3 > lighting depthCueStart 0.5 > lighting depthCueStart 0.6 > lighting soft > lighting full > lighting flat > lighting flat > lighting full > set silhouettes false > close > open "/home/hilvertg/tetterst/NCL12 phenix/ChimeraX/overlay chains licorice.cxs" format session opened ChimeraX session > close > open "/home/hilvertg/tetterst/1906 figures for Don/alpha2 filtered sdev3.cxs" format session opened ChimeraX session > close > open "/home/hilvertg/tetterst/NCL12 phenix/ChimeraX/mutation mapping.cxs" format session opened ChimeraX session > close > open "/home/hilvertg/tetterst/NCL12 phenix/ChimeraX/overlay chains.cxs" format session opened ChimeraX session > close > open "/home/hilvertg/tetterst/NCL12 phenix/ChimeraX/overlay chains licorice.cxs" format session opened ChimeraX session > close > open /home/hilvertg/tetterst/NCL12_phenix_2/run_class001_croppedByHalf_shifted.mrc Opened run_class001_croppedByHalf_shifted.mrc, grid size 301,301,301, pixel 1.1, shown at level 0.035, step 2, values float32 > close > open "/home/hilvertg/tetterst/NCL12 phenix/ChimeraX/overlay chains licorice.cxs" format session opened ChimeraX session > close > open /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/cage_with_mutations2.cxs format session opened ChimeraX session > ui mousemode rightMode clip > ui mousemode rightMode clip > ui mousemode rightMode clip > close > open "/home/hilvertg/tetterst/NCL12 phenix/ChimeraX/overlay chains licorice.cxs" format session opened ChimeraX session > close > open /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/cage_with_mutations2.cxs format session opened ChimeraX session Expected a keyword > select :5,59,104,108,158,168 8056 atoms, 7080 bonds selected > color sel red > show sel atoms > select clear > close > open 1hqk format mmCIF fromDatabase pdb 1hqk title: Crystal structure analysis of lumazine synthase from aquifex aeolicus [more info...] Chain information for 1hqk #1 --- Chain | Description A B C D E | 6,7-dimethyl-8-ribityllumazine synthase 1hqk mmCIF Assemblies --- 1| author_and_software_defined_assembly > sym #1 assembly 1 > view > hide selAtoms > show selAtoms ribbons > hide selAtoms > style selAtoms stick Changed 13370 atom styles > show selAtoms > color selAtoms byhetero > color selAtoms byhetero > select :95 90 atoms, 80 bonds selected > style selAtoms sphere Changed 90 atom styles > style selAtoms ball Changed 90 atom styles > color sel green > select clear > select :42 40 atoms, 30 bonds selected > color sel yellow > select clear > select up Nothing selected > select :95 90 atoms, 80 bonds selected > color sel yellow > color selAtoms byhetero > select :95,42 130 atoms, 110 bonds selected > color sel grey > color selAtoms byhetero > color sel grey > select :103 80 atoms, 70 bonds selected > color selAtoms byhetero > color selAtoms byhetero > select :104 60 atoms, 50 bonds selected > select :106 90 atoms, 80 bonds selected > select :145 90 atoms, 80 bonds selected Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel green > color sel green > select #2/C:24 10 atoms, 10 bonds selected > select up 148 atoms, 149 bonds selected > select up 1339 atoms, 1195 bonds selected > select up 6685 atoms, 5975 bonds selected > select down 1339 atoms, 1195 bonds selected > select down 148 atoms, 149 bonds selected > select down 10 atoms, 10 bonds selected Expected an objects specifier or a keyword > select :21 110 atoms, 100 bonds selected > select up 2 atoms, 1 bond selected > select up 8 atoms, 7 bonds selected > select up 148 atoms, 149 bonds selected > color sel yellow > style selAtoms stick Changed 148 atom styles > color selAtoms byhetero > select :21 110 atoms, 100 bonds selected > select #2/B:39 7 atoms, 6 bonds selected > select up 148 atoms, 149 bonds selected > select up 1337 atoms, 1195 bonds selected > select clear > select :21 110 atoms, 100 bonds selected > select #2/B:39 7 atoms, 6 bonds selected > select up 148 atoms, 149 bonds selected > select up 1337 atoms, 1195 bonds selected > color sel yellow > select :21 110 atoms, 100 bonds selected > select :57 140 atoms, 150 bonds selected > ui mousemode rightMode clip > ui mousemode rightMode clip > select #2/D:113@CB 1 atom selected > select up 11 atoms, 11 bonds selected > save 1hqk_cage.pdb format pdb models #2 > save 1hqk_cage.pdb format pdb models #2 relModel #1 > close > open /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/cage_with_mutations2.cxs format session opened ChimeraX session > view cofr false > view orient cofr false > set bgColor white > lighting full > set silhouettes true > zoom Pixel size at center of rotation is 0.475 > zoom 6 > view /X > view /X:50 > view /A:42 > view /X:42 > ui mousemode rightMode clip > ui mousemode rightMode clip > lighting simple > lighting soft > lighting full > set silhouettes false > set silhouettes true > close > open /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/NCL12_smallermap_apply_ncs_40_real_space_refined.cif Summary of feedback from opening /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/NCL12_smallermap_apply_ncs_40_real_space_refined.cif --- warnings | skipping chem_comp category: Missing column 'type' near line 3469 Unknown polymer entity '?' near line 3512 Bad residue range for secondary structure "4" near line 335 Bad residue range for secondary structure "8" near line 339 Bad residue range for secondary structure "12" near line 343 Bad residue range for secondary structure "16" near line 347 Bad residue range for secondary structure "20" near line 351 235 messages similar to the above omitted Invalid sheet range for strand "1 1" near line 2253 Invalid sheet range for strand "1 3" near line 2255 Invalid sheet range for strand "2 1" near line 2256 Invalid sheet range for strand "2 3" near line 2258 Invalid sheet range for strand "3 1" near line 2259 475 messages similar to the above omitted Skipping residue with duplicate label_seq_id 2 in chain CI Skipping residue with duplicate label_seq_id 4 in chain CI Skipping residue with duplicate label_seq_id 6 in chain CI Skipping residue with duplicate label_seq_id 8 in chain CI Skipping residue with duplicate label_seq_id 10 in chain CI 65 messages similar to the above omitted Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 484, in dropEvent _open_dropped_file(self.session, p) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 1332, in _open_dropped_file run(session, 'open %s' % quote_if_necessary(path)) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 64, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/models.py", line 601, in open session, filenames, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/io.py", line 477, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/io.py", line 433, in open_data models, status = open_func(*args, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py", line 55, in open_file log_info=log_info, combine_sym_atoms=combine_sym_atoms) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 73, in open_mmcif pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets, atomic) ValueError: basic_string::_M_construct null not valid ValueError: basic_string::_M_construct null not valid File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 73, in open_mmcif pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets, atomic) See log for complete Python traceback. > open /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/NCL12_smallermap_apply_ncs_40_real_space_refined.cif Summary of feedback from opening /home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/NCL12_smallermap_apply_ncs_40_real_space_refined.cif --- warnings | skipping chem_comp category: Missing column 'type' near line 3469 Unknown polymer entity '?' near line 3512 Bad residue range for secondary structure "4" near line 335 Bad residue range for secondary structure "8" near line 339 Bad residue range for secondary structure "12" near line 343 Bad residue range for secondary structure "16" near line 347 Bad residue range for secondary structure "20" near line 351 235 messages similar to the above omitted Invalid sheet range for strand "1 1" near line 2253 Invalid sheet range for strand "1 3" near line 2255 Invalid sheet range for strand "2 1" near line 2256 Invalid sheet range for strand "2 3" near line 2258 Invalid sheet range for strand "3 1" near line 2259 475 messages similar to the above omitted Skipping residue with duplicate label_seq_id 2 in chain CI Skipping residue with duplicate label_seq_id 4 in chain CI Skipping residue with duplicate label_seq_id 6 in chain CI Skipping residue with duplicate label_seq_id 8 in chain CI Skipping residue with duplicate label_seq_id 10 in chain CI 65 messages similar to the above omitted Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 484, in dropEvent _open_dropped_file(self.session, p) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 1332, in _open_dropped_file run(session, 'open %s' % quote_if_necessary(path)) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 64, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/models.py", line 601, in open session, filenames, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/io.py", line 477, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/io.py", line 433, in open_data models, status = open_func(*args, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py", line 55, in open_file log_info=log_info, combine_sym_atoms=combine_sym_atoms) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 73, in open_mmcif pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets, atomic) ValueError: basic_string::_M_construct null not valid ValueError: basic_string::_M_construct null not valid File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 73, in open_mmcif pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets, atomic) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 396.54 OpenGL renderer: GeForce GTX 1060 6GB/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (4)
comment:1 by , 6 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Error opening mmCIF: basic_string::_M_construct null not valid |
comment:2 by , 6 years ago
| Status: | assigned → feedback |
|---|
Please try the current ChimeraX daily build. This bug should be already fixed. Please let me know if the fix works for your mmCIF file. If it doesn't work, then please send me the mmCIF file so I can fix it.
comment:3 by , 6 years ago
Have you tried a newer ChimeraX yet? If not, could you send me home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/NCL12_smallermap_apply_ncs_40_real_space_refined.cif so I could test if it is fixed?
comment:4 by , 6 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | feedback → closed |
No response and not able to reproduce.
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Reported by Stephan Tetter