Opened 5 days ago

Closed 4 days ago

#19252 closed defect (limitation)

Read MRC: could not broadcast input array

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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

Change History (2)

comment:1 by Eric Pettersen, 5 days ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Read MRC: could not broadcast input array

comment:2 by Tom Goddard, 4 days ago

Resolution: → limitation
Status: assigned → closed

The user opened a map "wrt consensus.mrc" then overwrote that file with another map, then tried showing the original map which attempted to read the data from the original map which now had a different size. One way to give a sensible error message were to have the code record the last modification time of the mrc file when it is opened and if later an error occurs it can see if the file has been modified and more recently and report that the file was overwritten. This is sufficiently rare an error that I don't think it is worth doing unless reported more times.

Note: See TracTickets for help on using tickets.