id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19252 Read MRC: could not broadcast input array chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description Replace this text with list of actions that caused this problem to occur Log: Startup Messages --- warning | QWindowsWindow::setGeometry: Unable to set geometry 3200x1586-1280+273 (frame: 3222x1642-1291+228) on QWidgetWindow/""MainWindowClassWindow"" on ""DELL S2722QC"". Resulting geometry: 3196x1577-1278+280 (frame: 3218x1633-1289+235) margins: 11, 45, 11, 11 minimum size: 63x49 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=117, y=130))) UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > C:/Users/Rutambhara/Downloads/cryosparc_P38_J701_034_volume_map_sharp.mrc Opened cryosparc_P38_J701_034_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.825, shown at level 0.0387, step 1, values float32 > ui mousemode right ""pick blobs"" > measure blob #!1.1 triangleNumber 491112 color #0000ccff outline true Surface cryosparc_P38_J701_034_volume_map_sharp.mrc #1.1 blob: volume = 15.537 area = 38.42 size = 5.3905 3.4927 2.5505 > measure blob #!1.1 triangleNumber 495684 color #69c181ff outline true Surface cryosparc_P38_J701_034_volume_map_sharp.mrc #1.1 blob: volume = 10.744 area = 34.963 size = 6.0039 3.5867 2.4457 > measure blob #!1.1 triangleNumber 490924 color #0fec5fff outline true Surface cryosparc_P38_J701_034_volume_map_sharp.mrc #1.1 blob: volume = 15.022 area = 47.214 size = 9.3601 3.844 2.431 > measure blob #!1.1 triangleNumber 491061 color #cb8848ff outline true Surface cryosparc_P38_J701_034_volume_map_sharp.mrc #1.1 blob: volume = 38.144 area = 105.84 size = 11.119 6.9767 4.767 > ui mousemode right translate > close #1 > open ""C:/Users/Rutambhara/Downloads/cryosparc_P38_J672_007_volume_map_sharp > (1).mrc"" Opened cryosparc_P38_J672_007_volume_map_sharp (1).mrc as #1, grid size 256,256,256, pixel 0.825, shown at level 0.0333, step 1, values float32 > volume #1 level 0.05036 > volume #1 level 0.03334 > surface dust #1 size 8.25 > open 8v6k fromDatabase pdb format mmcif 8v6k title: Apo-state cryo-EM structure of human TRPV3 in cNW30 nanodiscs [more info...] Chain information for 8v6k #2 --- Chain | Description | UniProt A B C D | Transient receptor potential cation channel subfamily V member 3 | TRPV3_HUMAN 1-791 Non-standard residues in 8v6k #2 --- NA — sodium ion POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > hide atoms > select add #2 46605 atoms, 46660 bonds, 13 pseudobonds, 2973 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.81285,0.58217,-0.018942,-38.427,0.58159,-0.8094,0.081421,117.03,0.032069,-0.0772,-0.9965,218.31 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.81285,0.58217,-0.018942,-36.562,0.58159,-0.8094,0.081421,118.83,0.032069,-0.0772,-0.9965,221.79 > fitmap #2 inMap #1 Fit molecule 8v6k (#2) to map cryosparc_P38_J672_007_volume_map_sharp (1).mrc (#1) using 46605 atoms average map value = 0.02803, steps = 196 shifted from previous position = 2.24 rotated from previous position = 10.4 degrees atoms outside contour = 34973, contour level = 0.033345 Position of 8v6k (#2) relative to cryosparc_P38_J672_007_volume_map_sharp (1).mrc (#1) coordinates: Matrix rotation and translation 0.70685059 0.70735436 0.00347323 -39.68136768 0.70733029 -0.70685664 0.00612867 105.06534495 0.00679021 -0.00187533 -0.99997519 217.48212578 Axis -0.92380986 -0.38284151 -0.00277746 Axis point 0.00000000 61.00991738 108.67941321 Rotation angle (degrees) 179.75179035 Shift along axis -4.16938353 > select clear > ui tool show ""Side View"" > view > volume #1 level 0.05461 > volume #1 level 0.05887 > ui mousemode right ""pick blobs"" > measure blob #!1.1 triangleNumber 77981 color #5bb29fff outline true Surface cryosparc_P38_J672_007_volume_map_sharp (1).mrc #1.1 blob: volume = 93.331 area = 185.65 size = 16.565 6.2267 5.1365 > measure blob #!1.1 triangleNumber 72720 color #549cb7ff outline true Surface cryosparc_P38_J672_007_volume_map_sharp (1).mrc #1.1 blob: volume = 27282 area = 43754 size = 112.75 72.01 70.128 > measure blob #!1.1 triangleNumber 72720 color #09ff02ff outline true Surface cryosparc_P38_J672_007_volume_map_sharp (1).mrc #1.1 blob: volume = 27282 area = 43754 size = 112.75 72.01 70.128 > measure blob #!1.1 triangleNumber 72720 color #ee115aff outline true Surface cryosparc_P38_J672_007_volume_map_sharp (1).mrc #1.1 blob: volume = 27282 area = 43754 size = 112.75 72.01 70.128 > volume #1 level 0.0376 > volume #1 level 0.05461 > volume #1 level 0.06099 > measure blob #!1.1 triangleNumber 56981 color #a511c2ff outline true Surface cryosparc_P38_J672_007_volume_map_sharp (1).mrc #1.1 blob: volume = 89.634 area = 181.43 size = 16.47 6.142 5.0801 > measure blob #!1.1 triangleNumber 28505 color #e76b10ff outline true Surface cryosparc_P38_J672_007_volume_map_sharp (1).mrc #1.1 blob: volume = 26164 area = 42075 size = 110.84 70.69 69.869 > measure blob #!1.1 triangleNumber 28505 color #d08e28ff outline true Surface cryosparc_P38_J672_007_volume_map_sharp (1).mrc #1.1 blob: volume = 26164 area = 42075 size = 110.84 70.69 69.869 > measure blob #!1.1 triangleNumber 28505 color #59e838ff outline true Surface cryosparc_P38_J672_007_volume_map_sharp (1).mrc #1.1 blob: volume = 26164 area = 42075 size = 110.84 70.69 69.869 > measure blob #!1.1 triangleNumber 28505 color #60b29cff outline true Surface cryosparc_P38_J672_007_volume_map_sharp (1).mrc #1.1 blob: volume = 26164 area = 42075 size = 110.84 70.69 69.869 > measure blob #!1.1 triangleNumber 61649 color #821fd9ff outline true Surface cryosparc_P38_J672_007_volume_map_sharp (1).mrc #1.1 blob: volume = 89.634 area = 181.43 size = 16.47 6.142 5.0801 > close #1 > open 42994 fromDatabase emdb format ccp4 Opened emdb 42994 as #1, grid size 256,256,256, pixel 0.8, shown at level 0.0083, step 1, values float32, fit PDB 8v6k > hide #!2 models > measure blob #!1.1 triangleNumber 210346 color #b07291ff outline true Surface emdb 42994 #1.1 blob: volume = 54857 area = 90536 size = 122.31 122.31 101.13 > ui mousemode right translate > volume #1 level 0.005719 > volume #1 level 0.0126 > volume #1 level 0.007784 QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: ""data"" > open ""C:/Users/Rutambhara/Downloads/cryosparc_P38_J602_005_volume_map_sharp > (1).mrc"" Opened cryosparc_P38_J602_005_volume_map_sharp (1).mrc as #3, grid size 256,256,256, pixel 0.825, shown at level 0.0625, step 1, values float32 > color #3 #b5b57eff models > select add #3 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.72666,0.687,0.00067621,-43.76,0.68695,-0.72659,-0.012587,111.23,-0.008156,0.009611,-0.99992,229.24 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.72666,0.687,0.00067621,-45.334,0.68695,-0.72659,-0.012587,107.75,-0.008156,0.009611,-0.99992,219.69 > fitmap #3 inMap #1 Fit map cryosparc_P38_J602_005_volume_map_sharp (1).mrc in map emdb 42994 using 167671 points correlation = 0.7679, correlation about mean = 0.3651, overlap = 244.5 steps = 72, shift = 2.59, angle = 1.65 degrees Position of cryosparc_P38_J602_005_volume_map_sharp (1).mrc (#3) relative to emdb 42994 (#1) coordinates: Matrix rotation and translation 0.70864620 0.70556400 0.00000232 -46.94094371 0.70556400 -0.70864620 -0.00000306 102.72597381 -0.00000052 0.00000381 -1.00000000 217.85810830 Axis 0.92429318 0.38168327 -0.00001567 Axis point 0.00000000 61.05480765 108.92876126 Rotation angle (degrees) 179.99978691 Shift along axis -4.18182202 > select clear > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > volume #1 level 0.006274 > hide #!1 models > show #!1 models > surface dust #1 size 8 > surface dust #3 size 8.25 > ui mousemode right ""pick blobs"" > measure blob #!3.1 triangleNumber 48649 color #50e64cff outline true Surface cryosparc_P38_J602_005_volume_map_sharp (1).mrc #3.1 blob: volume = 369.92 area = 776.19 size = 22.661 18.717 18.717 > measure blob #!3.1 triangleNumber 45242 color #b228b2ff outline true Surface cryosparc_P38_J602_005_volume_map_sharp (1).mrc #3.1 blob: volume = 369.92 area = 776.19 size = 22.661 18.717 18.717 > ui mousemode right translate > close #1-3 > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/WT-Apo.mrc"" Opened WT-Apo.mrc as #1, grid size 400,400,400, pixel 0.73, shown at level 0.07, step 2, values float32 > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/consensus.mrc"" Opened consensus.mrc as #2, grid size 256,256,256, pixel 0.825, shown at level 0.0625, step 1, values float32 > volume #1 level 0.1197 > color #2 #adad79ff models > select add #1 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.81218,0.57253,0.11213,165.44,0.57472,0.81821,-0.014961,-55.275,-0.10031,0.05229,-0.99358,281.71 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.81218,0.57253,0.11213,127.49,0.57472,0.81821,-0.014961,-87.142,-0.10031,0.05229,-0.99358,259.28 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.81298,0.57464,0.094116,129.78,0.57469,0.81785,-0.02925,-85.115,-0.093781,0.030308,-0.99513,261.75 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.81298,0.57464,0.094116,125.96,0.57469,0.81785,-0.02925,-88.092,-0.093781,0.030308,-0.99513,262.04 > view matrix models > #1,-0.81298,0.57464,0.094116,131.08,0.57469,0.81785,-0.02925,-90.459,-0.093781,0.030308,-0.99513,261.94 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.81211,0.57559,0.095735,130.59,0.57214,0.81773,-0.063015,-85.417,-0.11456,0.0035988,-0.99341,268.63 > view matrix models > #1,-0.75164,-0.6393,0.1623,289.87,-0.62875,0.76883,0.11654,72.212,-0.19929,-0.01445,-0.97983,281.75 > fitmap #2 inMap #1 Fit map consensus.mrc in map WT-Apo.mrc using 167671 points correlation = 0.7884, correlation about mean = 0.4764, overlap = 6236 steps = 172, shift = 5, angle = 11.5 degrees Position of consensus.mrc (#2) relative to WT-Apo.mrc (#1) coordinates: Matrix rotation and translation -0.76741897 -0.64114595 -0.00002178 294.66731907 -0.64114595 0.76741897 -0.00000330 132.58597694 0.00001884 0.00001143 -1.00000000 250.82029871 Axis 0.34100326 -0.94006211 -0.00001362 Axis point 171.37969921 0.00000000 125.41092926 Rotation angle (degrees) 179.99876221 Shift along axis -24.15995145 > select clear > ui mousemode right ""pick blobs"" > measure blob #!2.1 triangleNumber 45346 color #7c76bdff outline true Surface consensus.mrc #2.1 blob: volume = 369.92 area = 776.19 size = 22.661 18.717 18.717 > ui mousemode right translate > volume #1 level 0.1622 > volume #2 level 0.09387 > volume #1 level 0.1019 > volume #2 level 0.07505 > surface dust #1 size 7.3 > surface dust #2 size 8.25 > volume #2 level 0.07348 > ui mousemode right ""pick blobs"" > measure blob #!2.1 triangleNumber 86703 color #9b77a4ff outline true Surface consensus.mrc #2.1 blob: volume = 164.21 area = 386.6 size = 17.569 17.569 7.5117 > ui mousemode right translate > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/hTPV3-WT-Apo-15.5.25.pdb"" Chain information for hTPV3-WT-Apo-15.5.25.pdb #3 --- Chain | Description A B C D | No description available Computing secondary structure > select add #3 22782 atoms, 22932 bonds, 2874 residues, 1 model selected > hide sel atoms > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.1744,0.97809,0.11372,-27.824,0.97091,-0.19006,0.14562,6.7531,0.16405,0.085018,-0.98278,187.74 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.1744,0.97809,0.11372,-22.763,0.97091,-0.19006,0.14562,11.427,0.16405,0.085018,-0.98278,194.49 > view matrix models > #3,0.1744,0.97809,0.11372,-18.945,0.97091,-0.19006,0.14562,13.56,0.16405,0.085018,-0.98278,195.04 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.77132,0.63572,0.030552,121.92,0.63537,0.76633,0.095111,-44.569,0.03705,0.092773,-0.995,208.57 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.77132,0.63572,0.030552,114.47,0.63537,0.76633,0.095111,-47.816,0.03705,0.092773,-0.995,207.54 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.69248,0.72052,0.036389,97.085,0.71967,0.68638,0.10468,-49.292,0.050445,0.098675,-0.99384,205.44 > view matrix models > #3,-0.70996,0.70337,0.035063,100.77,0.70264,0.7041,0.10271,-49.15,0.047558,0.097559,-0.99409,205.87 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.70996,0.70337,0.035063,106.17,0.70264,0.7041,0.10271,-47.294,0.047558,0.097559,-0.99409,207.78 > fitmap #3 inMap #1 Fit molecule hTPV3-WT-Apo-15.5.25.pdb (#3) to map WT-Apo.mrc (#1) using 22782 atoms average map value = 0.3113, steps = 128 shifted from previous position = 3.1 rotated from previous position = 7.39 degrees atoms outside contour = 5674, contour level = 0.10194 Position of hTPV3-WT-Apo-15.5.25.pdb (#3) relative to WT-Apo.mrc (#1) coordinates: Matrix rotation and translation 0.08697060 -0.99621088 -0.00000745 239.01937687 0.99621085 0.08697060 -0.00023863 35.01796570 0.00023837 0.00001333 0.99999997 32.89141235 Axis 0.00012646 -0.00012338 0.99999998 Axis point 100.40125564 147.90635103 0.00000000 Rotation angle (degrees) 85.01064924 Shift along axis 32.91731715 > select clear > save ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/model wrt consensus.pdb"" > relModel #3 > save ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/model wrt consensus.pdb"" > relModel #2 > close #3#1-2 > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/consensus.mrc"" Opened consensus.mrc as #1, grid size 256,256,256, pixel 0.825, shown at level 0.0625, step 1, values float32 > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/model wrt consensus.pdb"" Chain information for model wrt consensus.pdb #2 --- Chain | Description A B C D | No description available > hide atoms > select add #2 22782 atoms, 22932 bonds, 2874 residues, 1 model selected > view matrix models #2,1,0,0,-2.9157,0,1,0,0.38073,0,0,1,-7.4045 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.98504,-0.0022341,0.17232,-21.421,0.0046275,0.9999,-0.013489,1.4977,-0.17228,0.014084,0.98495,10.862 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.98504,-0.0022341,0.17232,-22.883,0.0046275,0.9999,-0.013489,18.032,-0.17228,0.014084,0.98495,13.775 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.94633,0.013159,0.32293,-38.036,-0.076889,0.97965,0.1854,4.9818,-0.31392,-0.20028,0.92808,55.271 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.94633,0.013159,0.32293,-44.369,-0.076889,0.97965,0.1854,-4.1385,-0.31392,-0.20028,0.92808,53.764 > view matrix models > #2,0.94633,0.013159,0.32293,-43.976,-0.076889,0.97965,0.1854,-3.5306,-0.31392,-0.20028,0.92808,54.075 > view matrix models > #2,0.94633,0.013159,0.32293,-42.309,-0.076889,0.97965,0.1854,-0.52612,-0.31392,-0.20028,0.92808,57.575 > view matrix models > #2,0.94633,0.013159,0.32293,-35.349,-0.076889,0.97965,0.1854,-7.4833,-0.31392,-0.20028,0.92808,55.669 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.92535,-0.081754,0.37019,-29.811,-0.005237,0.97362,0.22811,-19.351,-0.37908,-0.21302,0.90051,66.849 > view matrix models > #2,0.97326,-0.066804,0.2198,-18.487,-0.019923,0.92863,0.37047,-30.341,-0.22886,-0.36494,0.90247,65.366 > fitmap #2 inMap #1 Fit molecule model wrt consensus.pdb (#2) to map consensus.mrc (#1) using 22782 atoms average map value = 0.01727, steps = 80 shifted from previous position = 2.29 rotated from previous position = 4.51 degrees atoms outside contour = 18774, contour level = 0.062499 Position of model wrt consensus.pdb (#2) relative to consensus.mrc (#1) coordinates: Matrix rotation and translation 0.98312267 -0.10234291 0.15164350 -9.58561678 0.03984762 0.92877821 0.36848773 -35.07530361 -0.17855528 -0.35622601 0.91718103 57.21995837 Axis -0.89582906 0.40816345 0.17576375 Axis point 0.00000000 129.43215260 124.99777944 Rotation angle (degrees) 23.85937970 Shift along axis 4.32781143 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.98312,-0.10234,0.15164,-6.0485,0.039848,0.92878,0.36849,-37.24,-0.17856,-0.35623,0.91718,62.998 > fitmap #2 inMap #1 Fit molecule model wrt consensus.pdb (#2) to map consensus.mrc (#1) using 22782 atoms average map value = 0.08501, steps = 112 shifted from previous position = 3.77 rotated from previous position = 6.44 degrees atoms outside contour = 11016, contour level = 0.062499 Position of model wrt consensus.pdb (#2) relative to consensus.mrc (#1) coordinates: Matrix rotation and translation 0.99139346 -0.00523609 0.13081128 -17.92958989 -0.03567712 0.95057469 0.30843946 -22.99829693 -0.12596091 -0.31045183 0.94220672 49.84009698 Axis -0.92270653 0.38282228 -0.04538460 Axis point 0.00000000 141.96028980 104.11003682 Rotation angle (degrees) 19.59487786 Shift along axis 5.47751604 > select clear > save ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/model wrt consensus.pdb"" > relModel #1 > close #2 > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/model wrt consensus.pdb"" Chain information for model wrt consensus.pdb #2 --- Chain | Description A B C D | No description available > close #2 > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/WT-Apo.mrc"" Opened WT-Apo.mrc as #2, grid size 400,400,400, pixel 0.73, shown at level 0.07, step 2, values float32 > volume #2 level 0.1197 > select add #2 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.89507,-0.41077,0.17353,51.339,-0.4449,-0.84891,0.28532,295.4,0.030115,-0.33259,-0.94259,311.81 > view matrix models > #2,0.89443,-0.44504,-0.04399,86.406,-0.43891,-0.89244,0.10445,325.8,-0.085744,-0.074118,-0.99356,298.02 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.89443,-0.44504,-0.04399,45.116,-0.43891,-0.89244,0.10445,292.36,-0.085744,-0.074118,-0.99356,272.58 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.697,0.66749,0.26201,-130.58,0.67938,-0.73161,0.056551,112.31,0.22943,0.13859,-0.96341,191.4 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.697,0.66749,0.26201,-120.57,0.67938,-0.73161,0.056551,109.89,0.22943,0.13859,-0.96341,192.13 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.72714,0.67962,0.096833,-103.98,0.66593,-0.73257,0.14099,100.36,0.16676,-0.038037,-0.98526,230.06 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.72714,0.67962,0.096833,-109.32,0.66593,-0.73257,0.14099,103.05,0.16676,-0.038037,-0.98526,230.7 > fitmap #2 inMap #1 Fit map WT-Apo.mrc in map consensus.mrc using 36464 points correlation = 0.7976, correlation about mean = 0.5772, overlap = 1124 steps = 280, shift = 7.38, angle = 10.2 degrees Position of WT-Apo.mrc (#2) relative to consensus.mrc (#1) coordinates: Matrix rotation and translation 0.76740141 0.64116697 0.00000424 -99.93870706 0.64116697 -0.76740141 0.00000191 124.01997585 0.00000448 0.00000126 -1.00000000 250.81331572 Axis -0.94001428 -0.34113500 -0.00025146 Axis point 0.00000000 80.14409227 125.42001186 Rotation angle (degrees) 179.99998027 Shift along axis 51.57318849 > select clear > save ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/wrt consensus.mrc"" models #2 > close #2 > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/wrt consensus.mrc"" Opened wrt consensus.mrc as #2, grid size 400,400,400, pixel 0.73, shown at level 0.07, step 2, values float32 > close #2 > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/wrt consensus.mrc"" Opened wrt consensus.mrc as #2, grid size 400,400,400, pixel 0.73, shown at level 0.07, step 2, values float32 > volume #2 level 0.1232 > select add #2 2 models selected > view matrix models #2,1,0,0,-41.461,0,1,0,-30.457,0,0,1,-21.495 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.18084,0.97763,0.10741,-79.392,0.98093,-0.1872,0.05233,-7.5712,0.071267,0.095899,-0.99284,228.84 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.18084,0.97763,0.10741,-82.86,0.98093,-0.1872,0.05233,-10.023,0.071267,0.095899,-0.99284,228.44 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.68932,0.71641,0.10768,82.194,0.70539,0.6976,-0.12561,-74.397,-0.1651,-0.010631,-0.98622,277.56 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.68932,0.71641,0.10768,87.157,0.70539,0.6976,-0.12561,-81.507,-0.1651,-0.010631,-0.98622,279.23 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.66364,0.72058,0.20084,69.958,0.70681,0.69195,-0.14705,-77.935,-0.24493,0.044371,-0.96852,280.41 > fitmap #2 inMap #1 Fit map wrt consensus.mrc in map consensus.mrc using 35421 points correlation = 0.1788, correlation about mean = 0.04247, overlap = 164.4 steps = 92, shift = 1.87, angle = 2.47 degrees Position of wrt consensus.mrc (#2) relative to consensus.mrc (#1) coordinates: Matrix rotation and translation -0.63314516 0.74124531 0.22289595 59.44276992 0.72876514 0.66790059 -0.15103037 -78.23149256 -0.26082289 0.06681465 -0.96307177 277.24340543 Axis 0.41051998 0.91154826 -0.02351836 Axis point 67.78697809 0.00000000 131.58277601 Rotation angle (degrees) 164.61354738 Shift along axis -53.42964652 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.63315,0.74125,0.2229,66.599,0.72877,0.6679,-0.15103,-77.518,-0.26082,0.066815,-0.96307,284.43 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.65896,0.75163,-0.028677,103.53,0.74603,0.64823,-0.15241,-76.977,-0.09597,-0.12183,-0.9879,291.33 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.65896,0.75163,-0.028677,97.636,0.74603,0.64823,-0.15241,-77.688,-0.09597,-0.12183,-0.9879,284.21 > view matrix models > #2,-0.65896,0.75163,-0.028677,94.019,0.74603,0.64823,-0.15241,-79.972,-0.09597,-0.12183,-0.9879,284.66 > fitmap #2 inMap #1 Fit map wrt consensus.mrc in map consensus.mrc using 35421 points correlation = 0.7995, correlation about mean = 0.5732, overlap = 1121 steps = 136, shift = 4.81, angle = 9.01 degrees Position of wrt consensus.mrc (#2) relative to consensus.mrc (#1) coordinates: Matrix rotation and translation -0.64132968 0.76726543 -0.00000053 87.22347172 0.76726543 0.64132968 -0.00000046 -99.94219855 -0.00000001 -0.00000070 -1.00000000 250.83298447 Axis -0.42242587 -0.90639672 -0.00116566 Axis point 66.90072912 0.00000000 125.48076587 Rotation angle (degrees) 179.99998353 Shift along axis 53.44944319 > select clear > vop resample #2 onGrid #1 Opened wrt consensus.mrc resampled as #3, grid size 256,256,256, pixel 0.825, shown at step 1, values float32 > save ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/wrt consensus.mrc"" models #3 > hide #!3 models > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/wrt consensus.mrc"" Opened wrt consensus.mrc as #4, grid size 400,400,400, pixel 0.73, shown at level 0.07, step 2, values float32 > close #4 > show #!3 models > close #3 > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot > test/cryosparc_P38_J702_034_volume_map_sharp.mrc"" Opened cryosparc_P38_J702_034_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 0.825, shown at level 0.0451, step 1, values float32 > close #3 > open > C:/Users/Rutambhara/Downloads/cryosparc_P38_J715_map_aligned_0_map_sharp.mrc Opened cryosparc_P38_J715_map_aligned_0_map_sharp.mrc as #3, grid size 256,256,256, pixel 0.825, shown at level 0.0426, step 1, values float32 > open ""C:/Users/Rutambhara/Downloads/cryosparc_P38_J657_005_volume_map_sharp > (1).mrc"" Opened cryosparc_P38_J657_005_volume_map_sharp (1).mrc as #4, grid size 256,256,256, pixel 0.825, shown at level 0.0466, step 1, values float32 > hide #!1 models > hide #!3 models > surface dust #4 size 8.25 > ui mousemode right ""pick blobs"" > measure blob #!4.1 triangleNumber 589250 color #9aac6cff outline true Surface cryosparc_P38_J657_005_volume_map_sharp (1).mrc #4.1 blob: volume = 79508 area = 1.253e+05 size = 122.01 115.67 117.91 > volume #4 level 0.04436 > hide #!4 models > open ""D:/TRPV3/TRPV3 HCQ/RP14 PNCC/coot test/test-1.pdb"" Chain information for test-1.pdb #5 --- Chain | Description A B C D | No description available > select #5/A 5693 atoms, 5733 bonds, 716 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #5/B 5690 atoms, 5733 bonds, 713 residues, 1 model selected > select #5/D 5701 atoms, 5733 bonds, 724 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #5/B 5690 atoms, 5733 bonds, 713 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #5/C:907 52 atoms, 51 bonds, 1 residue, 1 model selected > hide sel atoms > select #5/C: 443-521 655 atoms, 676 bonds, 79 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #5/C: 903 52 atoms, 51 bonds, 1 residue, 1 model selected > hide sel cartoons > hide sel atoms > select #5/C: 904 52 atoms, 51 bonds, 1 residue, 1 model selected > hide sel atoms > select #5/C: 522-565 370 atoms, 383 bonds, 44 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #5/C: 909-910 2 atoms, 2 residues, 1 model selected > hide sel atoms > select #5/C: 666 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #5/C: 666 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!2 models Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\core\triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\map\volume.py"", line 4069, in _update_drawings v.update_drawings() File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\map\volume.py"", line 821, in update_drawings self._keep_displayed_data = self.displayed_matrices() ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\map\volume.py"", line 1771, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\map\volume.py"", line 1254, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\map\volume.py"", line 1278, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\map_data\griddata.py"", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\map_data\mrc\mrc_grid.py"", line 50, in read_matrix m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\map_data\mrc\mrc_format.py"", line 287, in read_matrix matrix = read_array(self.path, self.data_offset, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\map_data\readarray.py"", line 68, in read_array matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep] ~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: could not broadcast input array from shape (0,) into shape (200,) Error processing trigger ""graphics update"": ValueError: could not broadcast input array from shape (0,) into shape (200,) File ""C:\Program Files\ChimeraX 1.10.1\bin\Lib\site- packages\chimerax\map_data\readarray.py"", line 68, in read_array matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep] ~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 - Build 32.0.101.6881 OpenGL renderer: Intel(R) Arc(TM) A370M Graphics OpenGL vendor: Intel Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: windows Manufacturer: Dell Inc. Model: XPS 15 9530 OS: Microsoft Windows 11 Pro (Build 26100) Memory: 34,014,814,208 MaxProcessMemory: 137,438,953,344 CPU: 16 13th Gen Intel(R) Core(TM) i7-13620H OSLanguage: en-US Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2025.7.14 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.10 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.2.0 OpenMM-CUDA-12: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pywin32: 310 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 WMI: 1.5.1 }}} " defect closed normal Volume Data limitation all ChimeraX