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Opened 7 years ago
Closed 7 years ago
#1498 closed defect (fixed)
Atom spec parsing: '<' not supported between instances of 'int' and 'NoneType'
| Reported by: | Owned by: | Conrad Huang | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-15.3.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-11-26) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.8 (2018-11-26) How to cite UCSF ChimeraX Opened ATP-Jun-F0.mrc, grid size 64,64,64, pixel 5.2, shown at level 7.86e-06, step 1, values float32 > open /Users/jliu/Desktop/T7-Ian/Useful-T7-20181101.cxs opened ChimeraX session Opened ATP-Jun-F0.mrc, grid size 64,64,64, pixel 5.2, shown at level 7.86e-06, step 1, values float32 > ui mousemode rightMode translate > select #36 7 models selected > ui mousemode rightMode zoom > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode rotate and select > ui mousemode rightMode zoom > ui mousemode rightMode translate > ui mousemode rightMode rotate > ui mousemode rightMode rotate and select > ui mousemode rightMode select > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate > ui mousemode rightMode translate > ui mousemode rightMode translate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > open /Users/jliu/Desktop/T7-Ian/maps/ATP-Jun.mrc Opened ATP-Jun.mrc, grid size 64,64,64, pixel 5.2, shown at level 0.168, step 1, values float32 > ~select #36 Nothing selected > select #36.1 3 models selected > select #37 2 models selected > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > show #!33.1 models > hide #!33.1 models > show #!33.1 models > hide #!33.1 models > show #!33.1 models > hide #!29.1 models > show #!29.1 models > hide #!30.1 models > show #!30.1 models > fitmap #37.1 inMap #30.1 No atoms or maps for #37.1 > hide #!30.1 models > show #!30.1 models > fitmap #37.1 inMap #30.1 No atoms or maps for #37.1 > fitmap #37.1 inMap #30.1 No atoms or maps for #37.1 Missing or invalid "atoms_or_map" argument: invalid objects specifier > fitmap #37 inMap #30.1 Fit map ATP-Jun.mrc in map ATPase-seg-X-ray-F1.mrc using 2623 points correlation = 0.7051, correlation about mean = 0.09516, overlap = 39.17 steps = 108, shift = 14.3, angle = 20.8 degrees Position of ATP-Jun.mrc (#37) relative to ATPase-seg-X-ray-F1.mrc (#30.1) coordinates: Matrix rotation and translation 0.99888012 -0.03917541 0.02652867 -6.12279643 0.02746690 0.02360873 -0.99934387 1.22970695 0.03852340 0.99895339 0.02465831 -5.59250201 Axis 0.99942638 -0.00599904 0.03333042 Axis point 0.00000000 3.35330455 -2.08366978 Rotation angle (degrees) 88.64920827 Shift along axis -6.31306177 > fitmap #36.1 inMap #37 Fit map ATP-Jun-F0.mrc in map ATP-Jun.mrc using 2673 points correlation = 0.8143, correlation about mean = 0.6747, overlap = 25.68 steps = 80, shift = 12.7, angle = 9.92 degrees Position of ATP-Jun-F0.mrc (#36.1) relative to ATP-Jun.mrc (#37) coordinates: Matrix rotation and translation -0.54610217 0.83384413 0.08047616 27.76920214 -0.11577253 -0.17026620 0.97857354 192.79491805 0.82968016 0.52508420 0.18951898 -66.52658195 Axis -0.35105399 -0.57997186 -0.73511478 Axis point 67.30160855 122.07719078 0.00000000 Rotation angle (degrees) 139.76704816 Shift along axis -72.65944203 > fitmap #36.2 inMap #37 Fit map ATP-Jun-F1.mrc in map ATP-Jun.mrc using 2624 points correlation = 0.9685, correlation about mean = 0.8064, overlap = 75.56 steps = 56, shift = 12.6, angle = 10.2 degrees Position of ATP-Jun-F1.mrc (#36.2) relative to ATP-Jun.mrc (#37) coordinates: Matrix rotation and translation -0.54904598 0.83154611 0.08414038 27.99623719 -0.11637859 -0.17575336 0.97753097 192.88886428 0.82765002 0.52691731 0.19327084 -65.90130349 Axis -0.35033329 -0.57804767 -0.73697183 Axis point 66.93543148 121.66843891 0.00000000 Rotation angle (degrees) 139.97503079 Shift along axis -72.73956846 > fitmap #36.3 inMap #37 Fit map ATP-Jun-Stalk.mrc in map ATP-Jun.mrc using 2627 points correlation = 0.8285, correlation about mean = 0.6675, overlap = 21.28 steps = 96, shift = 8.56, angle = 10.1 degrees Position of ATP-Jun-Stalk.mrc (#36.3) relative to ATP-Jun.mrc (#37) coordinates: Matrix rotation and translation -0.54849067 0.83226132 0.08061701 26.77825296 -0.11586466 -0.17113290 0.97841143 193.19261123 0.82809021 0.52730887 0.19029448 -66.35172892 Axis -0.35000200 -0.57995041 -0.73563314 Axis point 66.67484982 122.41190273 0.00000000 Rotation angle (degrees) 139.87715747 Shift along axis -72.60404573 > hide #!36.3 models > hide #!36.2 models > hide #!36.1 models > hide #!30.1 models > hide #!37 models > show #!37 models > show #!36.3 models > hide #!36.3 models > show #!36.3 models > hide #!36.3 models > show #!36.3 models > show #!36.2 models > show #!36.1 models > select #36.1 3 models selected > select #36.2 3 models selected > ~select #36.3 3 models selected > select #36.1 3 models selected > select #36.3 3 models selected > select #36.2 3 models selected > select #36.1 3 models selected > select #36.2 3 models selected > select #36.3 3 models selected > ~select #32 3 models selected > ~select #31 3 models selected > select #36.1 3 models selected > select #36 7 models selected > ui mousemode rightMode rotate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > fitmap #36.1 inMap #37 Fit map ATP-Jun-F0.mrc in map ATP-Jun.mrc using 2673 points correlation = 0.8138, correlation about mean = 0.6736, overlap = 25.61 steps = 92, shift = 33.5, angle = 20.2 degrees Position of ATP-Jun-F0.mrc (#36.1) relative to ATP-Jun.mrc (#37) coordinates: Matrix rotation and translation -0.74493467 0.66456426 0.05853816 53.49201285 0.06051868 -0.02006819 0.99796532 165.51292458 0.66438683 0.74696161 -0.02526906 -113.29777602 Axis -0.28152479 -0.67951752 -0.67749519 Axis point 18.02370014 -0.00000000 -132.37422835 Rotation angle (degrees) 153.52589749 Shift along axis -50.76956239 Expected a keyword Expected a keyword > hide #!36.1 models > show #!36.1 models > ~select #36.2 5 models selected > ~select #36.3 3 models selected Expected a keyword > fitmap #36.1 inMap #37 Fit map ATP-Jun-F0.mrc in map ATP-Jun.mrc using 2673 points correlation = 0.8142, correlation about mean = 0.6743, overlap = 25.66 steps = 104, shift = 41.9, angle = 28.2 degrees Position of ATP-Jun-F0.mrc (#36.1) relative to ATP-Jun.mrc (#37) coordinates: Matrix rotation and translation -0.84643705 0.48772978 -0.21369139 84.89389703 0.02211141 0.43315426 0.90104856 137.47165198 0.53202954 0.75795586 -0.37742220 -148.66144371 Axis -0.16064900 -0.83721478 -0.52274593 Axis point 53.86196357 0.00000000 -106.48543065 Rotation angle (degrees) 153.55374210 Shift along axis -51.01925388 > ~select #36.3 3 models selected > ui mousemode rightMode translate selected models > hide #!36.1 models > fitmap #36.1 inMap #37 Fit map ATP-Jun-F0.mrc in map ATP-Jun.mrc using 2673 points correlation = 0.8138, correlation about mean = 0.6737, overlap = 25.61 steps = 220, shift = 80.6, angle = 54.8 degrees Position of ATP-Jun-F0.mrc (#36.1) relative to ATP-Jun.mrc (#37) coordinates: Matrix rotation and translation -0.89531677 0.03513207 -0.44404240 161.96914110 -0.04784519 0.98353213 0.17428544 70.76454034 0.44285297 0.17728597 -0.87889189 -187.75513490 Axis 0.00336845 -0.99564621 -0.09315191 Axis point 103.83734681 0.00000000 -78.05323244 Rotation angle (degrees) 153.55191139 Shift along axis -52.42111183 > fitmap #36.2 inMap #37 Fit map ATP-Jun-F1.mrc in map ATP-Jun.mrc using 2624 points correlation = 0.9685, correlation about mean = 0.8067, overlap = 75.57 steps = 68, shift = 9.33, angle = 20.1 degrees Position of ATP-Jun-F1.mrc (#36.2) relative to ATP-Jun.mrc (#37) coordinates: Matrix rotation and translation -0.75015776 0.65836425 0.06180522 55.93293724 0.05482529 -0.03122052 0.99800776 166.16735704 0.65898221 0.75205174 -0.01267469 -110.89872197 Axis -0.27824539 -0.67557503 -0.68277220 Axis point 72.90859554 130.87897346 0.00000000 Rotation angle (degrees) 153.76992291 Shift along axis -52.10303477 > hide #!36.2 models > show #!36.2 models > select #36.2 3 models selected > select #36 7 models selected > ~select #36 Nothing selected > select #36.2 3 models selected > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > close #36.1,2,3,0 > ~select #9.1 Nothing selected > ~select #9.1 Nothing selected > ~select #9.1 Nothing selected > show #!30.1 models > close #37 > close #36 > open /Users/jliu/Desktop/T7-Ian/maps/ATP-Jun-seg.mrc Opened ATP-Jun-seg.mrc, grid size 48,49,48, pixel 5.2,5.2,5.2, shown at level 0.211, step 1, values float32 > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > ~select #32 2 models selected > ~select #32 2 models selected > hide #!33.1 models > show #!33.1 models > hide #!29.1 models > show #!29.1 models > hide #!30.1 models > show #!30.1 models > hide #!30.1 models > show #!30.1 models Expected a keyword Expected a keyword Expected a keyword > hide #!30.1 models > show #!30.1 models > fitmap #36.1 inMap #30.1 No atoms or maps for #36.1 > fitmap #36 inMap #30.1 Fit map ATP-Jun-seg.mrc in map ATPase-seg-X-ray-F1.mrc using 6045 points correlation = 0.6982, correlation about mean = 0.3576, overlap = 48.6 steps = 224, shift = 6.1, angle = 29.3 degrees Position of ATP-Jun-seg.mrc (#36) relative to ATPase-seg-X-ray-F1.mrc (#30.1) coordinates: Matrix rotation and translation 0.99876133 -0.04477584 0.02170332 -5.90125196 0.02268382 0.02150681 -0.99951139 1.57212453 0.04428716 0.99876566 0.02249589 -6.13420973 Axis 0.99936691 -0.01129450 0.03373754 Axis point 0.00000000 3.78252881 -2.19927622 Rotation angle (degrees) 88.77480768 Shift along axis -6.12222541 > hide #!30.1 models > open /Users/jliu/Desktop/T7-Ian/maps/ATP-Jun-seg.mrc Opened ATP-Jun-seg.mrc, grid size 48,49,48, pixel 5.2,5.2,5.2, shown at level 0.211, step 1, values float32 > open /Users/jliu/Desktop/T7-Ian/maps/ATP-Jun-seg.mrc Opened ATP-Jun-seg.mrc, grid size 48,49,48, pixel 5.2,5.2,5.2, shown at level 0.211, step 1, values float32 > open /Users/jliu/Desktop/T7-Ian/maps/ATP-Jun-seg.mrc Opened ATP-Jun-seg.mrc, grid size 48,49,48, pixel 5.2,5.2,5.2, shown at level 0.211, step 1, values float32 > open /Users/jliu/Desktop/T7-Ian/maps/ATP-Jun-seg.mrc Opened ATP-Jun-seg.mrc, grid size 48,49,48, pixel 5.2,5.2,5.2, shown at level 0.211, step 1, values float32 > open /Users/jliu/Desktop/T7-Ian/maps/ATP-Jun-seg.mrc Opened ATP-Jun-seg.mrc, grid size 48,49,48, pixel 5.2,5.2,5.2, shown at level 0.211, step 1, values float32 > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > fitmap #36 inMap #30.1 Fit map ATP-Jun-seg.mrc in map ATPase-seg-X-ray-F1.mrc using 6045 points correlation = 0.6982, correlation about mean = 0.3576, overlap = 48.59 steps = 72, shift = 13.4, angle = 0.422 degrees Position of ATP-Jun-seg.mrc (#36) relative to ATPase-seg-X-ray-F1.mrc (#30.1) coordinates: Matrix rotation and translation 0.99862745 -0.04362735 0.02898218 -5.90595443 0.02992192 0.02104298 -0.99933077 1.61597620 0.04298826 0.99882636 0.02231954 -6.08020176 Axis 0.99929874 -0.00700458 0.03678274 Axis point 0.00000000 3.77874032 -2.12765762 Rotation angle (degrees) 88.79698770 Shift along axis -6.13677852 > ~select #36.1 1 model selected > select #36 2 models selected > select #36.1 2 models selected > ~select #36 Nothing selected > select #36.1 2 models selected > ~select #36.1 Nothing selected > select #37 2 models selected > ~select #38 2 models selected > select #38.1 2 models selected > select #37 2 models selected > select #38 2 models selected > select #37 2 models selected > select #39.1 2 models selected > select #38.1 2 models selected > ~select #38 Nothing selected > select #41.1 2 models selected > select #37 2 models selected > ~select #41.1 2 models selected > show #37-41 target m > select #38 2 models selected > show #37-41 target m > select #37.1 2 models selected > select #38 2 models selected > select #37 2 models selected > select #38 2 models selected > ui mousemode rightMode rotate selected models > show #37-41 target m > ui mousemode rightMode translate selected models > ~select #38.1 1 model selected > select #38 2 models selected > select #39 2 models selected > 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 > ui mousemode rightMode rotate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate 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 > 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 translate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode translate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > hide #!25.1 models > show #!25.1 models > hide #!25.1 models > show #!25.1 models > hide #!25.1 models > show #!25.1 models > hide #!38 models > show #!38 models > hide #!38 models > show #!38 models > fitmap #38 inMap #35.1 Fit map ATP-Jun-seg.mrc in map ATPase-seg-X-ray-F1.mrc using 6974 points correlation = 0.6738, correlation about mean = 0.3841, overlap = 47.44 steps = 2000, shift = 86.8, angle = 77.6 degrees Position of ATP-Jun-seg.mrc (#38) relative to ATPase-seg-X-ray-F1.mrc (#35.1) coordinates: Matrix rotation and translation -0.56604061 -0.05739011 -0.82237729 -17.58830434 -0.81204967 0.21068967 0.54422902 -6.05110912 0.14203305 0.97586694 -0.16586253 -5.78932286 Axis 0.33243171 -0.74275350 -0.58121114 Axis point -9.00155280 0.00000000 -5.05910114 Rotation angle (degrees) 139.51771496 Shift along axis 2.01239132 > hide #!35.1 models > show #!35.1 models > hide #!35.1 models > show #!35.1 models > hide #!35.2 models > show #!35.2 models > hide #!35.2 models > hide #!35.1 models > show #!35.1 models > hide #!35.1 models > hide #!34 models > show #!34 models > show #!30.1 models > hide #!30.1 models > hide #!29.1 models > show #!29.1 models > hide #!29.1 models > hide #!33.1 models > hide #!34.1 models > show #!35.1 models > hide #!35.1 models > show #!35.1 models > hide #!35.1 models > hide #!25.1 models > show #!25.1 models > hide #!25.1 models > show #!25.1 models > fitmap #38 inMap #25.1 Fit map ATP-Jun-seg.mrc in map ATPase-seg-X-ray-F1.mrc using 6974 points correlation = 0.6738, correlation about mean = 0.3841, overlap = 47.44 steps = 1784, shift = 104, angle = 59.4 degrees Position of ATP-Jun-seg.mrc (#38) relative to ATPase-seg-X-ray-F1.mrc (#25.1) coordinates: Matrix rotation and translation -0.56740806 -0.05733875 -0.82143799 -17.64258785 -0.81128096 0.20970363 0.54575418 -6.10964218 0.14096568 0.97608233 -0.16550536 -5.77744422 Axis 0.33202198 -0.74254768 -0.58170813 Axis point -9.05002079 0.00000000 -5.03356024 Rotation angle (degrees) 139.60588628 Shift along axis 2.03975993 > ui mousemode rightMode rotate selected models > ui mousemode rightMode translate selected models > fitmap #38 inMap #25.1 Fit map ATP-Jun-seg.mrc in map ATPase-seg-X-ray-F1.mrc using 6974 points correlation = 0.6891, correlation about mean = 0.4064, overlap = 49.13 steps = 156, shift = 9.3, angle = 10.8 degrees Position of ATP-Jun-seg.mrc (#38) relative to ATPase-seg-X-ray-F1.mrc (#25.1) coordinates: Matrix rotation and translation 0.99886661 -0.04503581 0.01540461 -5.89421147 0.01643286 0.02255127 -0.99961063 1.56866206 0.04467089 0.99873083 0.02326578 -6.09368951 Axis 0.99942018 -0.01463680 0.03074201 Axis point 0.00000000 3.76271734 -2.19935794 Rotation angle (degrees) 88.71980113 Shift along axis -6.10108632 > fitmap #38 inMap #25.1 Fit map ATP-Jun-seg.mrc in map ATPase-seg-X-ray-F1.mrc using 6974 points correlation = 0.689, correlation about mean = 0.4064, overlap = 49.11 steps = 80, shift = 2.8, angle = 0.96 degrees Position of ATP-Jun-seg.mrc (#38) relative to ATPase-seg-X-ray-F1.mrc (#25.1) coordinates: Matrix rotation and translation 0.99856468 -0.04293755 0.03201514 -5.91292679 0.03299886 0.02240040 -0.99920434 1.68945323 0.04218624 0.99882664 0.02378513 -6.07385327 Axis 0.99926564 -0.00508683 0.03797771 Axis point 0.00000000 3.81814426 -2.07608799 Rotation angle (degrees) 88.71789394 Shift along axis -6.14784957 > show #!29.1 models > hide #!29.1 models > show #!29.1 models > fitmap #39 inMap #29.1 Fit map ATP-Jun-seg.mrc in map ATPase-seg-X-ray-F1.mrc using 5095 points correlation = 0.7083, correlation about mean = 0.2815, overlap = 47.75 steps = 184, shift = 4.89, angle = 21.5 degrees Position of ATP-Jun-seg.mrc (#39) relative to ATPase-seg-X-ray-F1.mrc (#29.1) coordinates: Matrix rotation and translation 0.99858249 -0.04493064 0.02853568 -5.88294905 0.02948242 0.02055094 -0.99935400 1.63342043 0.04431518 0.99877872 0.02184646 -6.16046667 Axis 0.99927615 -0.00789141 0.03721434 Axis point 0.00000000 3.82343195 -2.16113447 Rotation angle (degrees) 88.82593038 Shift along axis -6.12083837 > ~select #32 2 models selected > ~select #31 2 models selected > ~select #32 2 models selected > ~select #31 2 models selected > hide #!31 models > show #!31 models > show #!30.1 models > hide #!30.1 models > show #!30.1 models > hide #!36.1 models > show #!36.1 models > fitmap #36 inMap #30.1 Fit map ATP-Jun-seg.mrc in map ATPase-seg-X-ray-F1.mrc using 6045 points correlation = 0.6981, correlation about mean = 0.3574, overlap = 48.59 steps = 64, shift = 0.104, angle = 0.0767 degrees Position of ATP-Jun-seg.mrc (#36) relative to ATPase-seg-X-ray-F1.mrc (#30.1) coordinates: Matrix rotation and translation 0.99857995 -0.04401235 0.03001838 -5.95226364 0.03099819 0.02175069 -0.99928281 1.68776707 0.04332784 0.99879431 0.02308413 -6.14281835 Axis 0.99927393 -0.00665630 0.03751411 Axis point 0.00000000 3.84642745 -2.11771664 Rotation angle (degrees) 88.75616090 Shift along axis -6.18961850 > show #!33.1 models > fitmap #41 inMap #33.1 Fit map ATP-Jun-seg.mrc in map ATPase-seg-X-ray-F1.mrc using 5026 points correlation = 0.7094, correlation about mean = 0.276, overlap = 47.66 steps = 204, shift = 15.5, angle = 36 degrees Position of ATP-Jun-seg.mrc (#41) relative to ATPase-seg-X-ray-F1.mrc (#33.1) coordinates: Matrix rotation and translation 0.99868696 -0.04529662 0.02392775 -5.87534061 0.02488999 0.02079949 -0.99947377 1.60724000 0.04477510 0.99875699 0.02189961 -6.14898139 Axis 0.99932939 -0.01042590 0.03510082 Axis point 0.00000000 3.80442003 -2.18283831 Rotation angle (degrees) 88.81429199 Shift along axis -6.10399180 > hide #!33.3 models > show #!33.3 models > hide #!33.1 models > show #!33.1 models > show #!34.1 models > select #34.1 3 models selected > fitmap #37 inMap #34.1 Fit map ATP-Jun-seg.mrc in map ATPase-seg-X-ray-F1.mrc using 5802 points correlation = 0.701, correlation about mean = 0.3397, overlap = 48.46 steps = 232, shift = 7.82, angle = 31.2 degrees Position of ATP-Jun-seg.mrc (#37) relative to ATPase-seg-X-ray-F1.mrc (#34.1) coordinates: Matrix rotation and translation 0.99876751 -0.04457261 0.02183287 -5.88169471 0.02281813 0.02171723 -0.99950372 1.58562224 0.04407635 0.99877005 0.02270755 -6.11415616 Axis 0.99936997 -0.01112433 0.03370323 Axis point 0.00000000 3.78073785 -2.18196862 Rotation angle (degrees) 88.76253580 Shift along axis -6.10169491 > hide #!33.2 models > show #!33.2 models > show #!35.1 models > hide #!35.1 models > hide #9.1,3,0 #1-3,6-7,17,24,26-28,31-32 #25.1,2,3,0 #29.1,2,3,0 #30.1,2,3,0 #33.1,2,3,0 #34.1,2,3,0 #35.1,2,3,0 #4 #5 #8 #10 #11 #12 #13 #14 #15 #16 #18 #19 #20 #21 #22 #23 target m > show #!2 models > hide #!2 models > show #!9.1 models > select #9 5 models selected > show #!9.3 models > hide #!9.3 models > show #!9.3 models > hide #!9.1 models > show #!9.1 models > hide #!9.1 models > show #!9.1 models > hide #!9.1 models > show #!9.1 models > show #!6 models > show #!7 models > hide #!7 models > hide #!6 models > hide #!9 models > hide #!9.1 models > hide #!9.3 models > ~select #2 5 models selected > show #!2 models > show #!2 models > show #!1 models > show #2 target m > select #23 5 models selected > show #9.1,3,0 #1-3,6-7,17 #4 #5 #8 #10 #11 #12 #13 #14 #15 #16 #18 #19 #20 #21 #22 #23 target m > hide #!3 models > show #!2 models > show #!2 models > hide #!4 models > hide #!5 models > show #!5 models > hide #!2 models > hide #!9.3 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!5 models > lighting flat > lighting flat > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17.1 models > hide #!17 models > hide #!16 models > show #!16 models > show #!17 models > hide #!6 models > hide #!1 models > hide #!21 models > hide #!23 models > hide #!22 models > show #!22 models > hide #!22 models > hide #!9.1 models > show #!9.1 models > hide #!30 models > hide #!29 models > hide #!25 models > hide #!33 models > hide #!34 models > hide #!35 models > ~select #28 3 models selected > ~select #27 3 models selected > ~select #26 3 models selected > hide #!10 models > hide #!11 models > hide #!12 models > hide #!14 models > hide #!16 models > hide #!17 models > hide #!15 models > hide #!13 models > hide #!9.1 models > show #!9.1 models > hide #!9.1 models > show #!9.1 models > show #!17 models > show #!17.1 models > hide #!17.1 models > hide #!17 models > show #!18 models > hide #!18 models > show #!18 models > fitmap #36 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 6045 points correlation = 0.5212, correlation about mean = -0.2163, overlap = 21.31 steps = 92, shift = 8.2, angle = 5.3 degrees Position of ATP-Jun-seg.mrc (#36) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation -0.43836744 0.00929223 0.89874789 92.95163266 0.89875175 0.01444388 0.43821998 46.07562111 -0.00890939 0.99985264 -0.01468310 -175.62186271 Axis 0.40422897 0.65327641 0.64017878 Axis point -13.23050080 0.00000000 -144.72738917 Rotation angle (degrees) 135.99698938 Shift along axis -44.75552962 > fitmap #37 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 6168 points correlation = 0.5239, correlation about mean = -0.2239, overlap = 21.9 steps = 144, shift = 22.9, angle = 8.76 degrees Position of ATP-Jun-seg.mrc (#37) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation -0.54352974 -0.01883838 -0.83917847 -86.28360844 -0.83937324 0.00590189 0.54352340 56.99817362 -0.00528636 0.99980511 -0.01902028 -175.72682743 Axis 0.36336104 -0.66407198 -0.65343490 Axis point 11.24111145 0.00000000 -143.24990270 Rotation angle (degrees) 141.10738438 Shift along axis 45.62305045 > fitmap #38 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 6974 points correlation = 0.5232, correlation about mean = -0.2761, overlap = 24.38 steps = 56, shift = 10.6, angle = 3.26 degrees Position of ATP-Jun-seg.mrc (#38) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation 0.99760536 0.00660362 -0.06884735 -6.17993674 -0.06870712 -0.01952125 -0.99744587 -103.15139404 -0.00793074 0.99978767 -0.01902079 -175.61053952 Axis 0.99882600 -0.03046469 -0.03766326 Axis point 0.00000000 34.39103456 -138.45824440 Rotation angle (degrees) 91.17283134 Shift along axis 3.58385897 > fitmap #39 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 6458 points correlation = 0.5226, correlation about mean = -0.2456, overlap = 22.78 steps = 112, shift = 10.7, angle = 4.36 degrees Position of ATP-Jun-seg.mrc (#39) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation -0.99765145 -0.00810446 0.06801420 6.10128594 0.06784873 0.01919133 0.99751104 103.37181218 -0.00938956 0.99978300 -0.01859638 -175.67128270 Axis 0.02094589 0.71360665 0.70023340 Axis point -1.15272071 0.00000000 -138.68850568 Rotation angle (degrees) 176.89108431 Shift along axis -49.11628967 > fitmap #40 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 6045 points correlation = 0.524, correlation about mean = -0.2143, overlap = 21.5 steps = 84, shift = 13.1, angle = 12 degrees Position of ATP-Jun-seg.mrc (#40) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation 0.55770466 0.01846586 0.82983406 86.22807846 0.83000537 -0.00334103 -0.55774545 -57.25187381 -0.00752677 0.99982394 -0.01719007 -175.63388588 Axis 0.80051418 0.43036235 0.41709146 Axis point 0.00000000 28.92125893 -132.40128516 Rotation angle (degrees) 103.38028785 Shift along axis -28.86764530 > fitmap #41 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 5802 points correlation = 0.5215, correlation about mean = -0.1883, overlap = 20.44 steps = 96, shift = 18.5, angle = 2.89 degrees Position of ATP-Jun-seg.mrc (#41) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation 0.44307676 -0.00723584 -0.89645447 -93.18819659 -0.89645106 -0.01210672 -0.44297734 -46.46403852 -0.00764781 0.99990052 -0.01185078 -175.69765035 Axis 0.75393891 -0.46442318 -0.46463666 Axis point 0.00000000 26.93821676 -131.88643259 Rotation angle (degrees) 106.88432247 Shift along axis 32.95633917 > fitmap #41 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 5802 points correlation = 0.5215, correlation about mean = -0.1882, overlap = 20.44 steps = 44, shift = 0.0633, angle = 0.195 degrees Position of ATP-Jun-seg.mrc (#41) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation 0.44003390 -0.00692808 -0.89795443 -93.20909008 -0.89794599 -0.01224513 -0.43993528 -46.42313937 -0.00794766 0.99990101 -0.01160931 -175.69981177 Axis 0.75270153 -0.46526780 -0.46579639 Axis point 0.00000000 26.76353865 -131.90546526 Rotation angle (degrees) 106.97235594 Shift along axis 33.28090469 > fitmap #40 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 6045 points correlation = 0.524, correlation about mean = -0.2143, overlap = 21.5 steps = 28, shift = 0.0685, angle = 0.158 degrees Position of ATP-Jun-seg.mrc (#40) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation 0.55541453 0.01831265 0.83137199 86.26272382 0.83154052 -0.00330481 -0.55545433 -57.21708572 -0.00742434 0.99982688 -0.01706326 -175.61481922 Axis 0.79954659 0.43121253 0.41806817 Axis point 0.00000000 28.78679568 -132.39943784 Rotation angle (degrees) 103.44293309 Shift along axis -29.12062348 > fitmap #39 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 6458 points correlation = 0.5225, correlation about mean = -0.2457, overlap = 22.78 steps = 28, shift = 0.129, angle = 0.238 degrees Position of ATP-Jun-seg.mrc (#39) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation -0.99736525 -0.00785896 0.07211674 6.16698110 0.07194973 0.01978916 0.99721194 103.33879102 -0.00926417 0.99977331 -0.01917157 -175.74606903 Axis 0.02246570 0.71378967 0.69999971 Axis point -1.36746158 0.00000000 -138.68949247 Rotation angle (degrees) 176.73201205 Shift along axis -49.12149090 > fitmap #38 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 6974 points correlation = 0.5232, correlation about mean = -0.2762, overlap = 24.38 steps = 28, shift = 0.0992, angle = 0.0466 degrees Position of ATP-Jun-seg.mrc (#38) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation 0.99758623 0.00609268 -0.06917091 -6.12986478 -0.06903629 -0.02006547 -0.99741234 -103.13773802 -0.00746485 0.99978014 -0.01959642 -175.69500356 Axis 0.99881728 -0.03085986 -0.03757280 Axis point 0.00000000 34.38927594 -138.46234969 Rotation angle (degrees) 91.20546757 Shift along axis 3.66155448 > fitmap #37 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 6168 points correlation = 0.524, correlation about mean = -0.2238, overlap = 21.89 steps = 28, shift = 0.142, angle = 0.23 degrees Position of ATP-Jun-seg.mrc (#37) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation -0.54678031 -0.01854915 -0.83707059 -86.25997861 -0.83725488 0.00499758 0.54678994 57.09367876 -0.00595915 0.99981545 -0.01826295 -175.64911383 Axis 0.36198543 -0.66409115 -0.65417849 Axis point 10.99677025 0.00000000 -143.16121940 Rotation angle (degrees) 141.26266723 Shift along axis 45.76561018 > fitmap #36 inMap #23.1 Fit map ATP-Jun-seg.mrc in map Chan-C6-IM.mrc using 6045 points correlation = 0.521, correlation about mean = -0.2164, overlap = 21.31 steps = 28, shift = 0.157, angle = 0.224 degrees Position of ATP-Jun-seg.mrc (#36) relative to Chan-C6-IM.mrc (#23.1) coordinates: Matrix rotation and translation -0.43487915 0.00974635 0.90043615 92.98170450 0.90044486 0.01459372 0.43472539 45.98229367 -0.00890375 0.99984614 -0.01512252 -175.71787183 Axis 0.40577443 0.65293458 0.63954948 Axis point -13.48686607 0.00000000 -144.86571079 Rotation angle (degrees) 135.86523796 Shift along axis -44.62724592 Chain information for F1.pdb #42.1 --- Chain | Description A | No description available B | No description available C | No description available D E F | No description available G | No description available H | No description available Chain information for Fo.pdb #42.2 --- Chain | Description M N O P Q R S T U V | No description available Chain information for Stalk.pdb #42.3 --- Chain | Description I J | No description available K | No description available L | No description available > toolshed show "Model Panel" > select #42 23568 atoms, 23553 bonds, 1 pseudobond, 2 models selected > ~select #42.1 7027 atoms, 7012 bonds, 1 pseudobond, 2 models selected > select #42.1 16541 atoms, 16541 bonds, 1 model selected > select #42.2 3650 atoms, 3640 bonds, 1 model selected > select #42.3 3377 atoms, 3372 bonds, 1 pseudobond, 2 models selected > select #42.2 3650 atoms, 3640 bonds, 1 model selected > select #42.1 16541 atoms, 16541 bonds, 1 model selected > select #42.2 3650 atoms, 3640 bonds, 1 model selected > select #42.3 3377 atoms, 3372 bonds, 1 pseudobond, 2 models selected > select #42.2 3650 atoms, 3640 bonds, 1 model selected > select #42.1 16541 atoms, 16541 bonds, 1 model selected > select #42.2 3650 atoms, 3640 bonds, 1 model selected > select #42.3 3377 atoms, 3372 bonds, 1 pseudobond, 2 models selected Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/model_panel/tool.py", line 69, in <lambda> for i in self.tree.selectedItems()]] or self.models, ses)) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/model_panel/tool.py", line 268, in close concise_model_spec(session, [m for m in models if isinstance(m, Model)])) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 2542, in run prev_annos = self._process_positional_arguments() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 2328, in _process_positional_arguments value, text = self._parse_arg(anno, text, session, False) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 2191, in _parse_arg value, replacement, rest = annotation.parse(text, session) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 1042, in parse models = aspec.evaluate(session).models File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 1000, in evaluate results = self._left_spec.evaluate(session, models, top=False) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 926, in evaluate return self.find_matches(session, models, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 929, in find_matches self._specifier.find_matches(session, models, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 405, in find_matches model_spec.find_matches(session, model_list, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 562, in find_matches self.my_parts.find_matches(session, model_list, self.sub_parts, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 420, in find_matches self._check(session, model_list, sub_parts, results, 0) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 440, in _check self._check(session, match_list, sub_parts, results, i + 1) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 437, in _check if mr.matches(mid): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 473, in matches if self.start != 'start' and self.start != '*' and mid < self.start: TypeError: '<' not supported between instances of 'int' and 'NoneType' TypeError: ' File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 473, in matches if self.start != 'start' and self.start != '*' and mid < self.start: See log for complete Python traceback. Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/model_panel/tool.py", line 69, in <lambda> for i in self.tree.selectedItems()]] or self.models, ses)) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/model_panel/tool.py", line 268, in close concise_model_spec(session, [m for m in models if isinstance(m, Model)])) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 2542, in run prev_annos = self._process_positional_arguments() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 2328, in _process_positional_arguments value, text = self._parse_arg(anno, text, session, False) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 2191, in _parse_arg value, replacement, rest = annotation.parse(text, session) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 1042, in parse models = aspec.evaluate(session).models File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 1000, in evaluate results = self._left_spec.evaluate(session, models, top=False) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 926, in evaluate return self.find_matches(session, models, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 929, in find_matches self._specifier.find_matches(session, models, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 405, in find_matches model_spec.find_matches(session, model_list, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 562, in find_matches self.my_parts.find_matches(session, model_list, self.sub_parts, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 420, in find_matches self._check(session, model_list, sub_parts, results, 0) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 440, in _check self._check(session, match_list, sub_parts, results, i + 1) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 437, in _check if mr.matches(mid): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 473, in matches if self.start != 'start' and self.start != '*' and mid < self.start: TypeError: '<' not supported between instances of 'int' and 'NoneType' TypeError: ' File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 473, in matches if self.start != 'start' and self.start != '*' and mid < self.start: See log for complete Python traceback. > save session /Users/jliu/Desktop/T7-Ian/maps/ATPase/Jun-ATPase.cxs Session file format is not finalized, and thus might not be restorable in other versions of ChimeraX. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. Error in saving session for "NamedView": Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 206, in take_snapshot self.remove_deleted_models() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/view.py", line 194, in remove_deleted_models if m.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Unable to save "NamedView". Session might not restore properly. > toolshed show "Model Panel" Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/model_panel/tool.py", line 69, in <lambda> for i in self.tree.selectedItems()]] or self.models, ses)) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/model_panel/tool.py", line 268, in close concise_model_spec(session, [m for m in models if isinstance(m, Model)])) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 2542, in run prev_annos = self._process_positional_arguments() File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 2328, in _process_positional_arguments value, text = self._parse_arg(anno, text, session, False) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 2191, in _parse_arg value, replacement, rest = annotation.parse(text, session) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py", line 1042, in parse models = aspec.evaluate(session).models File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 1000, in evaluate results = self._left_spec.evaluate(session, models, top=False) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 926, in evaluate return self.find_matches(session, models, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 929, in find_matches self._specifier.find_matches(session, models, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 405, in find_matches model_spec.find_matches(session, model_list, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 562, in find_matches self.my_parts.find_matches(session, model_list, self.sub_parts, results) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 420, in find_matches self._check(session, model_list, sub_parts, results, 0) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 440, in _check self._check(session, match_list, sub_parts, results, i + 1) File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 437, in _check if mr.matches(mid): File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 473, in matches if self.start != 'start' and self.start != '*' and mid < self.start: TypeError: '<' not supported between instances of 'int' and 'NoneType' TypeError: ' File "/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/atomspec.py", line 473, in matches if self.start != 'start' and self.start != '*' and mid < self.start: See log for complete Python traceback. OpenGL version: 4.1 INTEL-10.12.13 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc.
Change History (2)
comment:1 by , 7 years ago
| Component: | Unassigned → Command Line |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Atom spec parsing: '<' not supported between instances of 'int' and 'NoneType' |
comment:2 by , 7 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Probably fixed by 256c79188.
Atomspecs like #0-1 will generate the above traceback because the test for whether the start value was "if ast.number:" rather the the correct "if ast.number is not None".