Measure center: Array argument has non-numeric values

[zg2234@…]

The following bug report has been submitted:
Platform:        macOS-15.4.1-x86_64-i386-64bit
ChimeraX Version: 1.10.dev202504260127 (2025-04-26 01:27:24 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.dev202504260127 (2025-04-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/ZhenGong/Desktop/ECD.cxs

Opened 4ay9 map 10 as #1, grid size 44,36,35, pixel 3.33, shown at level
0.0653, step 1, values float32  
Opened J1738_deepEMhancer.mrc as #4, grid size 256,256,256, pixel 1.06, shown
at level 0.175, step 1, values float32  
Opened 4ay9 map 10 resampled as #3, grid size 256,256,256, pixel 1.06, shown
at level 0.0653, step 1, values float32  
Log from Mon Apr 28 11:39:10 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/ZhenGong/Desktop/ECD.cxs format session

Opened 4ay9 map 10 as #1, grid size 44,36,35, pixel 3.33, shown at level
0.0653, step 1, values float32  
Log from Sun Apr 27 21:13:50 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9.dev202408210848 (2024-08-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4a9y

Summary of feedback from opening 4a9y fetched from pdb  
---  
notes | Fetching compressed mmCIF 4a9y from http://files.rcsb.org/download/4a9y.cif  
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/AQZ/AQZ.cif  
Fetching CCD AQZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/AQZ/AQZ.cif  
  
4a9y title:  
P38Α map kinase bound to CMPD 8 [more info...]  
  
Chain information for 4a9y #1  
---  
Chain | Description | UniProt  
A | MITOGEN-ACTIVATED PROTEIN KINASE 14 | MK14_HUMAN 2-360  
  
Non-standard residues in 4a9y #1  
---  
AQZ —
N-(3-{[7-methoxy-6-(2-pyrrolidin-1-ylethoxy)quinazolin-4-yl]amino}-4-methylphenyl)-2-morpholin-4-ylisonicotinamide  
  

> open 4ay9

Summary of feedback from opening 4ay9 fetched from pdb  
---  
notes | Fetching compressed mmCIF 4ay9 from http://files.rcsb.org/download/4ay9.cif  
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif  
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/TYS/TYS.cif  
Fetching CCD TYS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/TYS/TYS.cif  
  
4ay9 title:  
Structure of follicle-stimulating hormone in complex with the entire
ectodomain of its receptor [more info...]  
  
Chain information for 4ay9 #2  
---  
Chain | Description | UniProt  
A D G | GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE | Q96QJ4_HUMAN 1-92  
B E H | FOLLITROPIN SUBUNIT BETA | FSHB_HUMAN 1-111  
X Y Z | FOLLICLE-STIMULATING HORMONE RECEPTOR | FSHR_HUMAN 17-366  
  
Non-standard residues in 4ay9 #2  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
4ay9 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
  

> close #1

> ui mousemode right zoom

> hide cartoons

> hide atoms

> show cartoons

> delete /Y-Z

> delete /C-F

> delete /G-H

> ui mousemode right zoom

> save /Users/ZhenGong/Desktop/ECD.cxs

> molmap #2 10

Opened 4ay9 map 10 as #1, grid size 44,36,35, pixel 3.33, shown at level
0.0653, step 1, values float32  

> molmap #2 20

Opened 4ay9 map 20 as #1, grid size 31,27,27, pixel 6.67, shown at level
0.0327, step 1, values float32  

> molmap #2 7

Opened 4ay9 map 7 as #1, grid size 55,43,43, pixel 2.33, shown at level
0.0852, step 1, values float32  

> molmap #2 10

Opened 4ay9 map 10 as #1, grid size 44,36,35, pixel 3.33, shown at level
0.0653, step 1, values float32  

> save /Users/ZhenGong/Desktop/ECD.cxs

——— End of log from Sun Apr 27 21:13:50 2025 ———

opened ChimeraX session  

> vop pad #1 size 44,44,44

> volume pad #1 size 44,44,44

Expected a density maps specifier or a keyword  

> vop new size 44

Opened new as #3, grid size 44,44,44, pixel 1, shown at step 1, values float32  

> hide #!1 models

> hide #!2 models

> volume #3 level -0.5276

> close #3

> show #!1 models

> info usage vop

Expected a models specifier or a keyword  

> usage vop pad

vop [optional]  
— alias of "volume $*"  
optional: the rest of line  
volume [volumes] [style style] [change change] [show] [hide] [toggle] [close
close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume
encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness
a number] [transparency a number] [appearance appearance] [nameAppearance a
text string] [nameForget nameForget] [step map step] [region map region]
[expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3
floats] [voxelSize 1 or 3 floats] [planes planes
x|y|z[,<start>[,<end>[,<increment>[,<depth>]]]]] [dumpHeader true or false]
[pickable true or false] [calculateSurfaces true or false] [boxFaces true or
false] [orthoplanes orthoplanes] [tiltedSlab true or false] [imageMode
imageMode] [symmetry symmetry] [center center point] [centerIndex 1 or 3
floats] [axis an axis vector] [coordinateSystem a coordinate-system]
[dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a
number] [showPlane true or false] [voxelLimitForPlane a number] [initialColors
initialColors] [showOutlineBox true or false] [outlineBoxRgb a color]
[limitVoxelCount true or false] [voxelLimit a number] [colormapOnGpu true or
false] [colorMode colorMode] [colormapSize an integer] [colormapExtendLeft
true or false] [colormapExtendRight true or false] [blendOnGpu true or false]
[projectionMode projectionMode] [rayStep a number] [planeSpacing planeSpacing]
[fullRegionOnGpu true or false] [btCorrection true or false]
[minimalTextureMemory true or false] [maximumIntensityProjection true or
false] [linearInterpolation true or false] [dimTransparency true or false]
[dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
true or false] [twoSidedLighting true or false] [flipNormals true or false]
[subdivideSurface true or false] [subdivisionLevels an integer]
[surfaceSmoothing true or false] [smoothingIterations an integer]
[smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
[positionPlanes positionPlanes] [tiltedSlabAxis an axis vector]
[tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount
an integer] [backingColor backingColor]  
— set volume model parameters, display style and colors  
style: one of image, mesh, solid, or surface  
change: one of image or surface  
close: one of image or surface  
level: some numbers, repeatable  
rmsLevel: some numbers, repeatable  
sdLevel: some numbers, repeatable  
encloseVolume: some numbers  
fastEncloseVolume: some numbers  
color: a color, repeatable  
appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin,
Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
Bone  
nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin,
Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
Bone  
orthoplanes: one of off, xy, xyz, xz, or yz  
imageMode: one of box faces, full region, orthoplanes, or tilted slab  
initialColors: some colors  
colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
rgba12, rgba16, rgba4, or rgba8  
projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, auto, or rays  
planeSpacing: one of max, mean, or min or a number  
positionPlanes: 3-tuple of integers  
backingColor: a color or none  
Subcommands are:

  * volume add
  * volume bin
  * volume boxes
  * volume channels
  * volume copy
  * volume cover
  * volume defaultvalues
  * volume erase
  * volume falloff
  * volume flatten
  * volume flip
  * volume fourier
  * volume gaussian
  * volume laplacian
  * volume localCorrelation
  * volume mask
  * volume maximum
  * volume median
  * volume minimum
  * volume morph
  * volume multiply
  * volume new
  * volume octant
  * volume ~octant
  * volume onesmask
  * volume permuteAxes
  * volume resample
  * volume ridges
  * volume scale
  * volume settings
  * volume sharpen
  * volume splitbyzone
  * volume subtract
  * volume threshold
  * volume tile
  * volume unbend
  * volume unroll
  * volume unzone
  * volume zone

  

> hide #!1 models

> show #!1 models

> select #1

2 models selected  

> select #2

4100 atoms, 4142 bonds, 1 pseudobond, 569 residues, 2 models selected  

> molmap sel 20 onGrid #mymap

Invalid "onGrid" argument: invalid density map specifier  

> molmap sel 20 onGrid #1

Opened 4ay9 map 20 as #3, grid size 44,36,35, pixel 3.33, shown at level
0.0323, step 1, values float32  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> open /Users/ZhenGong/Documents/Xray/Phenix/F74/J1738_deepEMhancer.mrc

Opened J1738_deepEMhancer.mrc as #4, grid size 256,256,256, pixel 1.06, shown
at level 8.2e-05, step 1, values float32  

> close #3

> volume #4 level 0.1755

> select subtract #2

Nothing selected  

> select add #4

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,19.739,0,1,0,4.8842,0,0,1,-113.69

> view matrix models #4,1,0,0,-47.325,0,1,0,-144.66,0,0,1,-124.61

> view matrix models #4,1,0,0,-115.63,0,1,0,-117.49,0,0,1,-130.23

> view matrix models #4,1,0,0,-121,0,1,0,-126.36,0,0,1,-134.11

> view matrix models #4,1,0,0,-121.61,0,1,0,-126.42,0,0,1,-133.56

> view matrix models #4,1,0,0,-125.54,0,1,0,-122.54,0,0,1,-137.61

> vop resample #1 ongrid #4

Opened 4ay9 map 10 resampled as #3, grid size 256,256,256, pixel 1.06, shown
at step 1, values float32  

> vop center #3

[Repeated 1 time(s)]

> save /Users/ZhenGong/Desktop/4ay9_10A.mrc models #4

> save /Users/ZhenGong/Desktop/ECD.cxs

——— End of log from Mon Apr 28 11:39:10 2025 ———

> view name session-start

opened ChimeraX session  

> hide #!3 models

> molmap #2 5

Opened 4ay9 map 5 as #5, grid size 69,53,52, pixel 1.67, shown at level
0.0995, step 1, values float32  

> show #!4 models

> molmap #2 5 onGrid #4

Opened 4ay9 map 5 as #5, grid size 256,256,256, pixel 1.06, shown at level
0.0987, step 1, values float32  

> hide #!4 models

> center #5

Unknown command: center #5  

> toolshed show

> view #5

> save /Users/ZhenGong/Desktop/ECD_complex_5A.mrc models #5

> save /Users/ZhenGong/Desktop/ECD.cxs

> hide #!5 models

> combine #2

> delete #6/A-B

> rename #6 4ay9_ECD

> molmap #6 5 onGrid #5

Opened 4ay9_ECD map 5 as #7, grid size 256,256,256, pixel 1.06, shown at level
0.0942, step 1, values float32  

> save /Users/ZhenGong/Desktop/ECD.cxs

No map chosen to save  

> save /Users/ZhenGong/Desktop/4ay9_ECD_5A.mrc models #7

> hide #!6 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> combine #2

> delete #8/R

> select #8

4100 atoms, 4142 bonds, 1 pseudobond, 569 residues, 3 models selected  

> delete #8/X

> rename #8 4ay9_hFSH

> molmap #8 5 onGrid #7

Opened 4ay9_hFSH map 5 as #9, grid size 256,256,256, pixel 1.06, shown at
level 0.0912, step 1, values float32  

> save /Users/ZhenGong/Desktop/4ay9_hFSH_5A.mrc models #9

> save /Users/ZhenGong/Desktop/ECD.cxs

> open 8neb

Fetching url http://files.rcsb.org/download/8neb.cif failed:  
HTTP Error 404: Not Found  

> open 8enb

Summary of feedback from opening 8enb fetched from pdb  
---  
note | Fetching compressed mmCIF 8enb from http://files.rcsb.org/download/8enb.cif  
  
8enb title:  
Crystal structure of LGR ligand alpha2/beta5 from C. elegans in crystal form 2
[more info...]  
  
Chain information for 8enb #10  
---  
Chain | Description | UniProt  
A C | Bursicon | A0T3A2_CAEEL 1-92  
B D | Cys_knot domain-containing protein | A7DT38_CAEEL 1-106  
  
8enb mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> hide #!9 models

> hide #!8 models

> delete #10/C-D

> close #10

> open /Users/ZhenGong/Documents/AlphaFold/Wei/hA2B5/hA2B5.pdb

Chain information for hA2B5.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> molmap #10 5 onGrid #9

Opened hA2B5.pdb map 5 as #11, grid size 256,256,256, pixel 1.06, shown at
level 0.097, step 1, values float32  

> view #10

> save /Users/ZhenGong/Desktop/ECD.cxs

> save /Users/ZhenGong/Desktop/hA2B5_5A.mrc models #11

> hide #10 models

> hide #!11 models

> open
> /Users/ZhenGong/Downloads/cryosparc_P2_J346_class_00_00122_volume_sharp.mrc

Opened cryosparc_P2_J346_class_00_00122_volume_sharp.mrc as #12, grid size
200,200,200, pixel 1.14, shown at level 0.0567, step 1, values float32  

> view #12

> volume #12 level 0.1283

> volume #12 level 0.1641

> show #!2 models

> ui mousemode right "translate selected models"

> view matrix models #8,1,0,0,-74.169,0,1,0,-51.33,0,0,1,-65.126

> view matrix models #8,1,0,0,-77.261,0,1,0,-62.989,0,0,1,-78.78

> select add #12

1596 atoms, 1611 bonds, 233 residues, 4 models selected  

> view matrix models
> #8,1,0,0,-178.27,0,1,0,-148.83,0,0,1,-201.2,#12,1,0,0,-101.01,0,1,0,-85.845,0,0,1,-122.42

> volume #12 color #b2ffff81

> view matrix models
> #8,1,0,0,-173.44,0,1,0,-165.29,0,0,1,-193.57,#12,1,0,0,-96.177,0,1,0,-102.3,0,0,1,-114.79

> fitmap #2 inMap #12

Fit molecule 4ay9 (#2) to map
cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) using 4100 atoms  
average map value = 0.2383, steps = 84  
shifted from previous position = 6.95  
rotated from previous position = 1.51 degrees  
atoms outside contour = 1604, contour level = 0.16415  
  
Position of 4ay9 (#2) relative to
cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.99974818 0.00481500 0.02191777 102.61289223  
-0.00512003 0.99989053 0.01388221 100.60400404  
-0.02184853 -0.01399094 0.99966339 117.04283034  
Axis -0.52759164 0.82842202 -0.18805323  
Axis point 5492.76226159 0.00000000 -4791.79812976  
Rotation angle (degrees) 1.51367030  
Shift along axis 7.19458600  
  

> select subtract #12

1596 atoms, 1611 bonds, 233 residues, 1 model selected  

> save /Users/ZhenGong/Desktop/ECD.cxs

> ui mousemode right zoom

> hide #!12 models

> open
> /Users/ZhenGong/Downloads/cryosparc_P2_J346_class_03_00122_volume_sharp.mrc

Opened cryosparc_P2_J346_class_03_00122_volume_sharp.mrc as #13, grid size
200,200,200, pixel 1.14, shown at level 0.0555, step 1, values float32  

> view #12

No displayed objects specified.  

> view #13

> volume #13 level 0.1232

> volume #13 color #b2b2ff85

> ui mousemode right "translate selected models"

> view matrix models #8,1,0,0,-197.97,0,1,0,-198.66,0,0,1,-222.2

> view matrix models #8,1,0,0,-202.21,0,1,0,-201.1,0,0,1,-225.8

> select add #13

1596 atoms, 1611 bonds, 233 residues, 3 models selected  

> view matrix models
> #8,1,0,0,-298.23,0,1,0,-310.68,0,0,1,-329.3,#13,1,0,0,-96.02,0,1,0,-109.57,0,0,1,-103.51

> view matrix models
> #8,1,0,0,-292.84,0,1,0,-304.62,0,0,1,-338.93,#13,1,0,0,-90.624,0,1,0,-103.51,0,0,1,-113.13

> hide #!13 models

> show #!13 models

> select add #13

1596 atoms, 1611 bonds, 233 residues, 4 models selected  

> select subtract #13

1596 atoms, 1611 bonds, 233 residues, 1 model selected  

> show #!12 models

> hide #!13 models

> hide #!12 models

> show #!13 models

> fitmap #2 inMap #13

Fit molecule 4ay9 (#2) to map
cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) using 4100 atoms  
average map value = 0.1985, steps = 72  
shifted from previous position = 7.7  
rotated from previous position = 0.337 degrees  
atoms outside contour = 1983, contour level = 0.12318  
  
Position of 4ay9 (#2) relative to
cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) coordinates:  
Matrix rotation and translation  
0.99982384 0.00723047 0.01732050 103.87432226  
-0.00742308 0.99991104 0.01108226 99.12190251  
-0.01723883 -0.01120888 0.99978857 117.47480336  
Axis -0.51059242 0.79160300 -0.33564874  
Axis point 6609.57652282 0.00000000 -5517.18586549  
Rotation angle (degrees) 1.25079193  
Shift along axis -14.00251472  
  

> ui mousemode right zoom

> save /Users/ZhenGong/Desktop/ECD.cxs

> hide #!13 models

> show #!12 models

> hide #!12 models

> open
> /Users/ZhenGong/Downloads/cryosparc_P2_J346_class_04_00122_volume_sharp.mrc

Opened cryosparc_P2_J346_class_04_00122_volume_sharp.mrc as #14, grid size
200,200,200, pixel 1.14, shown at level 0.0585, step 1, values float32  

> hide #!2 models

> select add #14

1596 atoms, 1611 bonds, 233 residues, 3 models selected  

> view #4

No displayed objects specified.  

> view #14

> volume #14 level 0.1727

> volume #14 color #ffb2ff8a

> show #!2 models

> ui mousemode right "translate selected models"

> view matrix models
> #8,1,0,0,-363.61,0,1,0,-389.51,0,0,1,-448.23,#14,1,0,0,-70.767,0,1,0,-84.89,0,0,1,-109.31

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.29473,0.52925,0.79563,-657.36,0.54139,0.59361,-0.59542,-170.92,-0.78742,0.60624,-0.11158,124.4,#14,0.29473,0.52925,0.79563,-140.17,0.54139,0.59361,-0.59542,-33.359,-0.78742,0.60624,-0.11158,40.67

> view matrix models
> #8,0.03312,0.98496,-0.16958,-300.47,-0.97957,-0.001683,-0.20109,502.18,-0.19835,0.17278,0.96478,-423.16,#14,0.03312,0.98496,-0.16958,-48.209,-0.97957,-0.001683,-0.20109,146.66,-0.19835,0.17278,0.96478,-101.62

> view matrix models
> #8,0.23082,0.30128,0.92518,-597.64,0.40787,0.83332,-0.37313,-315.85,-0.88338,0.46348,0.069463,138.91,#14,0.23082,0.30128,0.92518,-124.7,0.40787,0.83332,-0.37313,-69.032,-0.88338,0.46348,0.069463,44.948

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.23082,0.30128,0.92518,-598.67,0.40787,0.83332,-0.37313,-329.77,-0.88338,0.46348,0.069463,143.91,#14,0.23082,0.30128,0.92518,-125.73,0.40787,0.83332,-0.37313,-82.952,-0.88338,0.46348,0.069463,49.951

> view matrix models
> #8,0.23082,0.30128,0.92518,-601.14,0.40787,0.83332,-0.37313,-328.77,-0.88338,0.46348,0.069463,143.5,#14,0.23082,0.30128,0.92518,-128.21,0.40787,0.83332,-0.37313,-81.947,-0.88338,0.46348,0.069463,49.535

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.31025,0.38609,0.86872,-641.91,0.3703,0.79256,-0.48449,-246.61,-0.87557,0.472,0.10293,121.72,#14,0.31025,0.38609,0.86872,-139.02,0.3703,0.79256,-0.48449,-60.955,-0.87557,0.472,0.10293,43.984

> view matrix models
> #8,0.26202,0.904,0.33782,-592.8,-0.092454,0.37196,-0.92363,309.26,-0.96062,0.21078,0.18104,226.78,#14,0.26202,0.904,0.33782,-126.2,-0.092454,0.37196,-0.92363,82.443,-0.96062,0.21078,0.18104,71.038

> view matrix models
> #8,0.22369,0.95123,0.21243,-539.82,-0.28013,0.2715,-0.92077,424.08,-0.93354,0.14646,0.3272,175.85,#14,0.22369,0.95123,0.21243,-112.55,-0.28013,0.2715,-0.92077,112.67,-0.93354,0.14646,0.3272,57.982

> view matrix models
> #8,0.21458,0.94715,0.23847,-546.31,-0.26187,0.29101,-0.92018,408.55,-0.94095,0.135,0.31047,191.07,#14,0.21458,0.94715,0.23847,-114.14,-0.26187,0.29101,-0.92018,108.63,-0.94095,0.135,0.31047,61.874

> view matrix models
> #8,0.22055,0.94002,0.26022,-555.67,-0.22581,0.30875,-0.92395,388.58,-0.94887,0.14502,0.28037,203.82,#14,0.22055,0.94002,0.26022,-116.54,-0.22581,0.30875,-0.92395,103.35,-0.94887,0.14502,0.28037,65.148

> view matrix models
> #8,0.22162,0.93269,0.28456,-564.14,-0.18902,0.32737,-0.9258,367.09,-0.95664,0.15139,0.24884,218.63,#14,0.22162,0.93269,0.28456,-118.69,-0.18902,0.32737,-0.9258,97.685,-0.95664,0.15139,0.24884,68.942

> view matrix models
> #8,0.16823,0.9003,0.40144,-582.56,-0.17645,0.42817,-0.8863,303.09,-0.96983,0.078263,0.23089,261.84,#14,0.16823,0.9003,0.40144,-122.99,-0.17645,0.42817,-0.8863,81.455,-0.96983,0.078263,0.23089,79.93

> fitmap #2 inMap #14

Fit molecule 4ay9 (#2) to map
cryosparc_P2_J346_class_04_00122_volume_sharp.mrc (#14) using 4100 atoms  
average map value = 0.1594, steps = 244  
shifted from previous position = 7.53  
rotated from previous position = 41.6 degrees  
atoms outside contour = 2733, contour level = 0.17271  
  
Position of 4ay9 (#2) relative to
cryosparc_P2_J346_class_04_00122_volume_sharp.mrc (#14) coordinates:  
Matrix rotation and translation  
0.19274257 0.43478583 -0.87966561 103.04460535  
0.57988377 0.67271390 0.45955503 84.78455024  
0.79157130 -0.59867963 -0.12246464 108.51232456  
Axis -0.53354093 -0.84260450 0.07315550  
Axis point -36.42614255 0.00000000 78.70707277  
Rotation angle (degrees) 97.38315762  
Shift along axis -118.48008459  
  

> hide #!14 models

> show #!13 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!13 models

> save /Users/ZhenGong/Desktop/ECD.cxs

> hide #!14 models

> show #!13 models

> fitmap #2 inMap #13

Fit molecule 4ay9 (#2) to map
cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) using 4100 atoms  
average map value = 0.1985, steps = 164  
shifted from previous position = 7.54  
rotated from previous position = 41.6 degrees  
atoms outside contour = 1983, contour level = 0.12318  
  
Position of 4ay9 (#2) relative to
cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) coordinates:  
Matrix rotation and translation  
0.99981506 0.00752044 0.01769989 103.86426667  
-0.00771132 0.99991258 0.01074060 99.12079799  
-0.01761756 -0.01087511 0.99978565 117.46972529  
Axis -0.48993081 0.80048759 -0.34523532  
Axis point 6497.22223353 0.00000000 -5465.37210870  
Rotation angle (degrees) 1.26404518  
Shift along axis -12.09603394  
  

> hide #!13 models

> show #!12 models

> fitmap #2 inMap #12

Fit molecule 4ay9 (#2) to map
cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) using 4100 atoms  
average map value = 0.2383, steps = 76  
shifted from previous position = 7.7  
rotated from previous position = 0.349 degrees  
atoms outside contour = 1603, contour level = 0.16415  
  
Position of 4ay9 (#2) relative to
cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.99973869 0.00506581 0.02229116 102.60786136  
-0.00537772 0.99988816 0.01395504 100.60598318  
-0.02221797 -0.01407126 0.99965412 117.04727616  
Axis -0.52263837 0.83001243 -0.19475243  
Axis point 5403.47171036 0.00000000 -4705.77970571  
Rotation angle (degrees) 1.53641727  
Shift along axis 7.08216925  
  

> view name 1

> view list

Named views: 1, session-start  

> view 1

> turn x 90

> turn x -90

> turn x 90

> view 1

> turn x 90

> turn x -90

> turn y 90

> save /Users/ZhenGong/Desktop/ECD.cxs

> view 1

> hide #!12 models

> show #!14 models

> hide #!14 models

> show #!13 models

> fitmap #2 inMap #13

Fit molecule 4ay9 (#2) to map
cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) using 4100 atoms  
average map value = 0.1985, steps = 72  
shifted from previous position = 7.71  
rotated from previous position = 0.351 degrees  
atoms outside contour = 1983, contour level = 0.12318  
  
Position of 4ay9 (#2) relative to
cryosparc_P2_J346_class_03_00122_volume_sharp.mrc (#13) coordinates:  
Matrix rotation and translation  
0.99982220 0.00727842 0.01739495 103.87288257  
-0.00746975 0.99991204 0.01095957 99.11815390  
-0.01731365 -0.01108755 0.99978863 117.47409245  
Axis -0.50469823 0.79454245 -0.33761219  
Axis point 6592.44871797 0.00000000 -5517.25306246  
Rotation angle (degrees) 1.25154726  
Shift along axis -13.33156469  
  

> volume #13 level 0.09416

> volume #13 level 0.1111

> hide #!13 models

> hide #!2 models

> open
> /Users/ZhenGong/Downloads/cryosparc_P2_J346_class_01_00122_volume_sharp.mrc

Opened cryosparc_P2_J346_class_01_00122_volume_sharp.mrc as #15, grid size
200,200,200, pixel 1.14, shown at level 0.164, step 1, values float32  

> view #15

> volume #15 level 0.107

> volume #15 level 0.1191

> volume #15 level 0.2191

> close #15

> open
> /Users/ZhenGong/Downloads/cryosparc_P2_J346_class_02_00122_volume_sharp.mrc

Opened cryosparc_P2_J346_class_02_00122_volume_sharp.mrc as #15, grid size
200,200,200, pixel 1.14, shown at level 0.112, step 1, values float32  

> volume #15 level 0.07776

> close #15

> open /Users/ZhenGong/Downloads/cryosparc_P2_J349_002_volume_map_sharp.mrc

Opened cryosparc_P2_J349_002_volume_map_sharp.mrc as #15, grid size
100,100,100, pixel 2.28, shown at level 0.206, step 1, values float32  

> volume #15 level 1.347

> close #15

> open
> /Users/ZhenGong/Downloads/cryosparc_P2_J362_class_00_00102_volume_sharp.mrc

Opened cryosparc_P2_J362_class_00_00102_volume_sharp.mrc as #15, grid size
200,200,200, pixel 1.14, shown at level 0.0583, step 1, values float32  

> volume #15 level 0.172

> volume #15 color #99bfe580

> show #!2 models

> ui mousemode right zoom

> show #!12 models

> hide #!15 models

> open
> /Users/ZhenGong/Downloads/cryosparc_P2_J362_class_01_00102_volume_sharp.mrc

Opened cryosparc_P2_J362_class_01_00102_volume_sharp.mrc as #16, grid size
200,200,200, pixel 1.14, shown at level 0.0568, step 1, values float32  

> volume #16 level 0.1553

> volume #16 level 0.1295

> open
> /Users/ZhenGong/Downloads/cryosparc_P2_J362_class_02_00102_volume_sharp.mrc

Opened cryosparc_P2_J362_class_02_00102_volume_sharp.mrc as #17, grid size
200,200,200, pixel 1.14, shown at level 0.0594, step 1, values float32  

> volume #17 level 0.2871

> hide #!12 models

> show #!14 models

> hide #!2 models

> close #15-17

> hide #!14 models

> open /Users/ZhenGong/Downloads/cryosparc_P2_J364_001_volume_map_sharp.mrc

Opened cryosparc_P2_J364_001_volume_map_sharp.mrc as #15, grid size
200,200,200, pixel 1.14, shown at level 0.0616, step 1, values float32  

> volume #15 level 0.1897

> volume #15 color #ffffb281

> hide #!15 models

> show #!15 models

> show #!12 models

> show #!2 models

> fitmap #2 inMap #12

Fit molecule 4ay9 (#2) to map
cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) using 4100 atoms  
average map value = 0.2383, steps = 76  
shifted from previous position = 7.69  
rotated from previous position = 0.334 degrees  
atoms outside contour = 1604, contour level = 0.16415  
  
Position of 4ay9 (#2) relative to
cryosparc_P2_J346_class_00_00122_volume_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.99975159 0.00467759 0.02179171 102.62473300  
-0.00497948 0.99989210 0.01382002 100.61260709  
-0.02172471 -0.01392509 0.99966701 117.06077010  
Axis -0.52843236 0.82881218 -0.18392829  
Axis point 5527.00296467 0.00000000 -4831.31561060  
Rotation angle (degrees) 1.50431772  
Shift along axis 7.62793659  
  

> select add #15

1596 atoms, 1611 bonds, 233 residues, 5 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.16823,0.9003,0.40144,-715.84,-0.17645,0.42817,-0.8863,237.92,-0.96983,0.078263,0.23089,115.17,#14,0.16823,0.9003,0.40144,-256.27,-0.17645,0.42817,-0.8863,16.282,-0.96983,0.078263,0.23089,-66.735,#15,1,0,0,-133.28,0,1,0,-65.173,0,0,1,-146.67

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #8,0.32637,0.35025,-0.87796,63.168,-0.8984,-0.17382,-0.40331,581.59,-0.29387,0.92039,0.25794,-555.47,#14,0.32637,0.35025,-0.87796,-32.131,-0.8984,-0.17382,-0.40331,128.86,-0.29387,0.92039,0.25794,-273.74,#15,0.017786,0.87052,-0.49182,-61.541,-0.46953,0.44155,0.76457,-25.967,0.88274,0.21733,0.41659,-216.18

> view matrix models
> #8,-0.51885,-0.58937,-0.61922,719.56,-0.85224,0.41335,0.32067,-49.69,0.066964,0.69411,-0.71675,-138.53,#14,-0.51885,-0.58937,-0.61922,178.22,-0.85224,0.41335,0.32067,-64.659,0.066964,0.69411,-0.71675,-150.41,#15,-0.86648,0.38802,0.3141,14.937,0.35751,0.043151,0.93291,-98.771,0.34844,0.92064,-0.17611,-168.47

> view matrix models
> #8,-0.32055,-0.57609,0.75191,88.069,-0.01003,0.79581,0.60546,-626.37,-0.94718,0.18654,-0.26088,252.23,#14,-0.32055,-0.57609,0.75191,73.552,-0.01003,0.79581,0.60546,-181.68,-0.94718,0.18654,-0.26088,-56.734,#15,-0.27074,-0.85652,0.4394,74.9,0.95784,-0.19411,0.2118,-64.995,-0.096124,0.47822,0.87296,-177.29

> view matrix models
> #8,-0.064846,0.42349,0.90358,-594.05,-0.2186,0.87746,-0.42694,-183,-0.97366,-0.22521,0.035677,361.7,#14,-0.064846,0.42349,0.90358,-177.79,-0.2186,0.87746,-0.42694,-124.42,-0.97366,-0.22521,0.035677,20.068,#15,0.7331,-0.60807,0.30466,-62.447,0.58181,0.79267,0.1821,-131.99,-0.35223,0.043755,0.93489,-101.54

> view matrix models
> #8,-0.078833,0.39593,0.91489,-579.56,-0.31022,0.86244,-0.39996,-158.6,-0.94739,-0.31535,0.054836,394.95,#14,-0.078833,0.39593,0.91489,-171.95,-0.31022,0.86244,-0.39996,-122.29,-0.94739,-0.31535,0.054836,40.047,#15,0.71047,-0.62744,0.31868,-58.937,0.56371,0.77849,0.27601,-138.43,-0.42127,-0.016455,0.90679,-82.904

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.078833,0.39593,0.91489,-554.94,-0.31022,0.86244,-0.39996,-127.3,-0.94739,-0.31535,0.054836,421.48,#14,-0.078833,0.39593,0.91489,-147.34,-0.31022,0.86244,-0.39996,-90.99,-0.94739,-0.31535,0.054836,66.571,#15,0.71047,-0.62744,0.31868,-34.323,0.56371,0.77849,0.27601,-107.13,-0.42127,-0.016455,0.90679,-56.38

> view matrix models
> #8,-0.078833,0.39593,0.91489,-557,-0.31022,0.86244,-0.39996,-108.53,-0.94739,-0.31535,0.054836,436.76,#14,-0.078833,0.39593,0.91489,-149.4,-0.31022,0.86244,-0.39996,-72.216,-0.94739,-0.31535,0.054836,81.854,#15,0.71047,-0.62744,0.31868,-36.384,0.56371,0.77849,0.27601,-88.359,-0.42127,-0.016455,0.90679,-41.096

> view matrix models
> #8,-0.078833,0.39593,0.91489,-531.8,-0.31022,0.86244,-0.39996,-117.78,-0.94739,-0.31535,0.054836,430.13,#14,-0.078833,0.39593,0.91489,-124.2,-0.31022,0.86244,-0.39996,-81.468,-0.94739,-0.31535,0.054836,75.227,#15,0.71047,-0.62744,0.31868,-11.184,0.56371,0.77849,0.27601,-97.612,-0.42127,-0.016455,0.90679,-47.724

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.20314,-0.97914,-0.0030863,630.97,0.75023,-0.15767,0.64211,-309.42,-0.6292,0.12812,0.76661,-199.23,#14,-0.20314,-0.97914,-0.0030863,272.17,0.75023,-0.15767,0.64211,79.872,-0.6292,0.12812,0.76661,-84.626,#15,-0.91694,-0.38066,0.11967,180.84,0.24202,-0.76899,-0.59167,219.57,0.31725,-0.51357,0.79725,-67.498

> view matrix models
> #8,0.91187,-0.31884,0.25851,-168.6,-0.077046,0.48564,0.87075,-506.3,-0.40318,-0.81393,0.41828,388.85,#14,0.91187,-0.31884,0.25851,88.919,-0.077046,0.48564,0.87075,-85.805,-0.40318,-0.81393,0.41828,164.61,#15,-0.029877,-0.52654,-0.84962,196.04,0.77382,-0.55022,0.31378,29.105,-0.6327,-0.64808,0.42389,105.71

> view matrix models
> #8,0.83603,-0.52249,0.16749,2.2315,-0.099248,0.15622,0.98272,-366.78,-0.53963,-0.83821,0.078745,582.71,#14,0.83603,-0.52249,0.16749,144.66,-0.099248,0.15622,0.98272,-15.182,-0.53963,-0.83821,0.078745,196.04,#15,-0.26252,-0.51968,-0.81303,219.69,0.51845,-0.78659,0.33538,85.847,-0.81381,-0.33347,0.47593,85.076

> view matrix models
> #8,0.5928,-0.62649,-0.50606,408.96,-0.26033,-0.74371,0.61573,321.66,-0.76211,-0.23326,-0.60397,601.71,#14,0.5928,-0.62649,-0.50606,220.2,-0.26033,-0.74371,0.61573,227.57,-0.76211,-0.23326,-0.60397,102.78,#15,-0.66746,0.07568,-0.74079,191.15,-0.46618,-0.81822,0.33644,209.99,-0.58067,0.5699,0.58141,-61.529

> view matrix models
> #8,0.81647,-0.51438,0.26228,-35.399,-0.35291,-0.085043,0.93178,-138.93,-0.45699,-0.85333,-0.25097,702.14,#14,0.81647,-0.51438,0.26228,135.9,-0.35291,-0.085043,0.93178,47.629,-0.45699,-0.85333,-0.25097,223.32,#15,-0.22046,-0.59678,-0.77153,219.06,0.23812,-0.79999,0.55074,98.057,-0.94588,-0.062303,0.31847,86.602

> view matrix models
> #8,0.74405,0.1043,0.65993,-513.91,-0.65702,0.29354,0.69438,-156.05,-0.12129,-0.95024,0.28693,432.9,#14,0.74405,0.1043,0.65993,-40.581,-0.65702,0.29354,0.69438,-23.689,-0.12129,-0.95024,0.28693,205.17,#15,0.48399,-0.67153,-0.56107,118.49,0.4325,-0.37381,0.82049,-5.6294,-0.76072,-0.63977,0.10951,154.97

> view matrix models
> #8,0.55988,-0.66475,0.49461,27.181,0.22084,0.69507,0.68418,-632.17,-0.7986,-0.27382,0.53596,164.86,#14,0.55988,-0.66475,0.49461,156.28,0.22084,0.69507,0.68418,-123.88,-0.7986,-0.27382,0.53596,29.241,#15,-0.30573,-0.8218,-0.48081,224.05,0.93759,-0.34775,-0.0018113,19.903,-0.16571,-0.45136,0.87682,-24.459

> view matrix models
> #8,-0.88228,-0.46104,0.095024,511.71,0.11831,-0.021802,0.99274,-339.11,-0.45562,0.88711,0.073782,-378.03,#14,-0.88228,-0.46104,0.095024,145.11,0.11831,-0.021802,0.99274,25.365,-0.45562,0.88711,0.073782,-216.21,#15,-0.52535,-0.12594,0.84152,23.498,0.3988,-0.91008,0.11276,139.53,0.75164,0.39484,0.52833,-198.16

> view matrix models
> #8,-0.73675,-0.26693,0.62124,145.9,-0.074213,0.94515,0.31809,-529.12,-0.67208,0.18825,-0.71615,391.98,#14,-0.73675,-0.26693,0.62124,59.397,-0.074213,0.94515,0.31809,-155.13,-0.67208,0.18825,-0.71615,9.7887,#15,-0.11486,-0.5349,0.83707,21.933,0.96613,0.13586,0.21939,-64.912,-0.23108,0.83392,0.50118,-126.62

> view matrix models
> #8,0.64841,0.52666,0.54973,-669.48,-0.22268,0.82172,-0.52458,-70.427,-0.728,0.21773,0.65009,-170.41,#14,0.64841,0.52666,0.54973,-132.86,-0.22268,0.82172,-0.52458,-63.122,-0.728,0.21773,0.65009,-96.936,#15,0.80391,-0.37614,-0.4607,33.476,0.49175,0.85607,0.15916,-85.094,0.33452,-0.3545,0.87317,-96.71

> view matrix models
> #8,0.41635,0.83806,0.35256,-688.19,-0.82853,0.19004,0.5267,20.51,0.37441,-0.5114,0.77349,-154.12,#14,0.41635,0.83806,0.35256,-191.49,-0.82853,0.19004,0.5267,14.288,0.37441,-0.5114,0.77349,61.897,#15,0.96608,-0.027108,-0.2568,-49.935,0.24316,-0.23925,0.94002,-11.454,-0.086921,-0.97058,-0.22454,148.21

> view matrix models
> #8,0.8959,-0.43716,-0.07905,39.585,0.11649,0.059464,0.99141,-382.18,-0.4287,-0.89742,0.1042,571.28,#14,0.8959,-0.43716,-0.07905,141.98,0.11649,0.059464,0.99141,6.0604,-0.4287,-0.89742,0.1042,207.69,#15,-0.2746,-0.2752,-0.92134,204.27,0.47113,-0.87379,0.12058,125.54,-0.83823,-0.40095,0.36959,107.71

> view matrix models
> #8,0.87573,-0.48214,-0.025457,47.966,0.090966,0.11298,0.98942,-402.83,-0.47416,-0.86878,0.1428,553.38,#14,0.87573,-0.48214,-0.025457,148.92,0.090966,0.11298,0.98942,-6.4331,-0.47416,-0.86878,0.1428,198.28,#15,-0.29697,-0.3384,-0.89291,211.33,0.51422,-0.8446,0.14907,113.69,-0.8046,-0.41489,0.42483,99.163

> view matrix models
> #8,0.87526,-0.48277,-0.029145,49.972,0.028738,-0.0082424,0.99955,-322.54,-0.4828,-0.87571,0.0066597,615.83,#14,0.87526,-0.48277,-0.029145,149.34,0.028738,-0.0082424,0.99955,22.14,-0.4828,-0.87571,0.0066597,209.95,#15,-0.2991,-0.33532,-0.89336,211.28,0.39868,-0.89451,0.20227,127.87,-0.86695,-0.29566,0.40123,95.339

> view matrix models
> #8,0.97989,0.074004,-0.18533,-219.5,0.17687,0.10803,0.97829,-421.19,0.092418,-0.99139,0.092763,471.48,#14,0.97989,0.074004,-0.18533,27.176,0.17687,0.10803,0.97829,-4.9246,0.092418,-0.99139,0.092763,227.99,#15,0.15707,0.023043,-0.98732,123.53,0.51973,-0.85202,0.062798,123.38,-0.83976,-0.52301,-0.1458,178.97

> view matrix models
> #8,0.50574,-0.63651,-0.58231,471.82,0.53927,-0.29361,0.78929,-233.21,-0.67337,-0.7132,0.19476,506.88,#14,0.50574,-0.63651,-0.58231,228.67,0.53927,-0.29361,0.78929,102.78,-0.67337,-0.7132,0.19476,158.45,#15,-0.72174,0.15434,-0.67474,181.26,0.14323,-0.92042,-0.36374,224.44,-0.67719,-0.35917,0.6422,53.093

> view matrix models
> #8,0.80185,-0.59727,-0.017691,129.4,0.16843,0.19752,0.96572,-462.14,-0.5733,-0.77734,0.25898,485.4,#14,0.80185,-0.59727,-0.017691,176.27,0.16843,0.19752,0.96572,-25.335,-0.5733,-0.77734,0.25898,168.5,#15,-0.40993,-0.38154,-0.82848,223.16,0.59384,-0.80107,0.075081,106.95,-0.69232,-0.46121,0.55496,76.565

> hide #!15 models

> open /Users/ZhenGong/Downloads/cryosparc_P2_J366_001_volume_map_sharp.mrc

Opened cryosparc_P2_J366_001_volume_map_sharp.mrc as #16, grid size
200,200,200, pixel 1.14, shown at level 0.0514, step 1, values float32  

> volume #16 level 0.2307

> select add #16

1596 atoms, 1611 bonds, 233 residues, 8 models selected  

> select subtract #15

1596 atoms, 1611 bonds, 233 residues, 6 models selected  

> select subtract #14

1596 atoms, 1611 bonds, 233 residues, 4 models selected  

> view matrix models
> #8,0.2216,0.90268,0.36886,-499.25,-0.49441,-0.22204,0.84039,-35.103,0.84051,-0.36859,0.39709,-164.44,#16,-0.36799,0.57184,-0.7332,168.53,-0.27869,0.68445,0.67369,-9.7395,0.88708,0.45224,-0.092505,-25.325

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.2216,0.90268,0.36886,-656.15,-0.49441,-0.22204,0.84039,-95.86,0.84051,-0.36859,0.39709,-220.01,#16,-0.36799,0.57184,-0.7332,11.627,-0.27869,0.68445,0.67369,-70.497,0.88708,0.45224,-0.092505,-80.898

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.89831,0.43647,0.050287,-515.41,-0.2281,0.36549,0.90243,-446.31,0.3755,-0.82214,0.42789,90.647,#16,0.45873,0.28608,-0.84126,-34.208,-0.41716,0.90527,0.080373,-12.989,0.78456,0.31408,0.53462,-125.23

> show #!13 models

> hide #!12 models

> hide #!16 models

> open /Users/ZhenGong/Downloads/cryosparc_P2_J368_001_volume_map_sharp.mrc

Opened cryosparc_P2_J368_001_volume_map_sharp.mrc as #17, grid size
200,200,200, pixel 1.14, shown at level 0.0476, step 1, values float32  

> volume #17 level 0.2292

> select subtract #16

1596 atoms, 1611 bonds, 233 residues, 1 model selected  

> select add #17

1596 atoms, 1611 bonds, 233 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.89831,0.43647,0.050287,-659.79,-0.2281,0.36549,0.90243,-504.87,0.3755,-0.82214,0.42789,36.012,#17,1,0,0,-144.39,0,1,0,-58.559,0,0,1,-54.635

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.38302,-0.91918,-0.091629,265.68,0.49435,0.12017,0.86092,-692.76,-0.78033,-0.37505,0.50043,308.37,#17,-0.061727,-0.50601,0.86032,-69.955,0.53983,0.70808,0.4552,-139.77,-0.83951,0.49252,0.22945,74.702

> view matrix models
> #8,0.68726,-0.63692,0.34928,-238.4,-0.71711,-0.51822,0.46604,353.59,-0.11583,-0.57076,-0.8129,814.76,#17,0.35695,-0.074355,0.93116,-172.02,-0.84694,0.39474,0.35619,60.958,-0.39405,-0.91578,0.077925,195.87

> view matrix models
> #8,0.61874,-0.42854,0.65842,-470.87,0.0063428,-0.83536,-0.54966,727.34,0.78557,0.34427,-0.51415,-167.22,#17,0.40189,0.29642,0.86638,-209.97,-0.38655,-0.8028,0.45397,128.66,0.8301,-0.51735,-0.20805,48.583

> hide #!17 models

> show #!15 models

> hide #!13 models

> view matrix models
> #8,0.61874,-0.42854,0.65842,-470.87,0.0063428,-0.83536,-0.54966,727.34,0.78557,0.34427,-0.51415,-167.22,#17,0.40189,0.29642,0.86638,-209.97,-0.38655,-0.8028,0.45397,128.66,0.8301,-0.51735,-0.20805,48.583

> ui mousemode right "translate selected models"

> select add #15

1596 atoms, 1611 bonds, 233 residues, 5 models selected  

> select subtract #17

1596 atoms, 1611 bonds, 233 residues, 3 models selected  

> view matrix models
> #8,0.61874,-0.42854,0.65842,-473.3,0.0063428,-0.83536,-0.54966,660.58,0.78557,0.34427,-0.51415,-204.43,#15,-0.40993,-0.38154,-0.82848,220.72,0.59384,-0.80107,0.075081,40.19,-0.69232,-0.46121,0.55496,39.35

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.46041,-0.70209,0.54322,-233.83,0.21779,-0.5039,-0.83585,616.19,0.86057,0.50315,-0.079091,-556.03,#15,-0.10373,-0.51944,-0.84818,201.66,0.30959,-0.82728,0.46878,34.778,-0.94519,-0.21397,0.24663,75.078

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.46041,-0.70209,0.54322,-255.43,0.21779,-0.5039,-0.83585,623.12,0.86057,0.50315,-0.079091,-538.68,#15,-0.10373,-0.51944,-0.84818,180.05,0.30959,-0.82728,0.46878,41.708,-0.94519,-0.21397,0.24663,92.432

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.3963,-0.76797,0.50316,-178.96,0.13298,-0.49424,-0.8591,670.78,0.90844,0.40737,-0.093742,-515.66,#15,-0.0064043,-0.54223,-0.8402,169.95,0.3771,-0.7795,0.50018,24.36,-0.92615,-0.31364,0.20947,105.93

> view matrix models
> #8,0.64279,-0.60998,0.46341,-322.03,-0.68524,-0.18743,0.70378,-15.977,-0.34244,-0.76993,-0.53846,735.22,#15,-0.28077,-0.60145,-0.74795,200.36,0.47946,0.58719,-0.65216,-22.505,0.83143,-0.54172,0.12351,-72.89

> view matrix models
> #8,-0.27125,0.093691,0.95794,-474.66,-0.36878,-0.92942,-0.013523,547.04,0.88906,-0.35694,0.28666,-452.44,#15,-0.067304,0.63514,-0.76946,30.865,0.81528,-0.40956,-0.40937,27.152,-0.57515,-0.65488,-0.49025,180.13

> view matrix models
> #8,-0.54317,-0.83405,0.096537,502.06,0.76792,-0.447,0.45879,-413.68,-0.3395,0.32333,0.88329,-518.95,#15,0.87396,-0.19314,-0.44597,-22.324,-0.47004,-0.5691,-0.67467,232.48,-0.1235,0.79926,-0.58816,-35.76

> view matrix models
> #8,-0.36458,-0.92648,0.093331,459.44,0.74818,-0.23179,0.62169,-581.73,-0.55436,0.29648,0.77768,-351.34,#15,0.78462,-0.36457,-0.50146,14.919,-0.61379,-0.34272,-0.7112,227.41,0.087426,0.86581,-0.49267,-79.925

> hide #!2 models

> view matrix models
> #8,0.57819,0.26833,0.77052,-801.14,-0.76661,0.50194,0.40046,-53.245,-0.2793,-0.82222,0.49592,108.64,#15,-0.79407,0.16033,-0.5863,155.65,0.23177,0.97157,-0.048217,-103.91,0.5619,-0.17418,-0.80866,19.308

> view matrix models
> #8,-0.7143,0.67338,0.19063,-34.966,-0.58668,-0.72466,0.36149,343.36,0.38156,0.14637,0.91268,-788.73,#15,0.1449,0.9661,0.21366,-142.24,0.78369,0.019767,-0.62084,3.6802,-0.60402,0.2574,-0.75426,105.19

> view matrix models
> #8,-0.69143,0.71446,0.10711,-10.289,-0.69409,-0.61582,-0.37284,789.27,-0.20042,-0.33214,0.92169,-361.31,#15,0.12387,0.94439,0.30461,-147.11,0.98463,-0.15506,0.080352,-77.431,0.12312,0.28997,-0.94908,33.765

> select subtract #8

2 models selected  

> show #!1 models

> hide #!15 models

> hide #!1 models

> show #!2 models

> show #!12 models

> hide #!12 models

> hide #!2 models

> open 7vd8

Summary of feedback from opening 7vd8 fetched from pdb  
---  
notes | Fetching compressed mmCIF 7vd8 from http://files.rcsb.org/download/7vd8.cif  
Fetching CCD NA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif  
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif  
  
7vd8 title:  
1.96 A structure of human apoferritin obtained from Talos Arctica microscope
[more info...]  
  
Chain information for 7vd8 #18  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain | FRIH_HUMAN 5-176  
  
Non-standard residues in 7vd8 #18  
---  
NA — sodium ion  
ZN — zinc ion  
  
1248 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> show #!2 models

> close #18

> open 8fm3

Summary of feedback from opening 8fm3 fetched from pdb  
---  
notes | Fetching compressed mmCIF 8fm3 from http://files.rcsb.org/download/8fm3.cif  
Fetching CCD Y26 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/Y26/Y26.cif  
  
8fm3 title:  
HIV-1 gp120 complex with CJF-III-288 [more info...]  
  
Chain information for 8fm3 #18  
---  
Chain | Description  
A B C D | Envelope glycoprotein gp120  
  
Non-standard residues in 8fm3 #18  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
Y26 — propyl
(2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate  
  
8fm3 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> hide #!2 models

> delete #18/B-D

> show #!2 models

> close #18

> open 9DU3

Summary of feedback from opening 9DU3 fetched from pdb  
---  
notes | Fetching compressed mmCIF 9du3 from http://files.rcsb.org/download/9du3.cif  
Fetching CCD A1BCX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/A1BCX/A1BCX.cif  
  
9du3 title:  
SARS-CoV-2 Mpro in complex with compound 1 [more info...]  
  
Chain information for 9du3 #18  
---  
Chain | Description | UniProt  
A | 3C-like proteinase nsp5 | R1AB_SARS2 1-306  
  
Non-standard residues in 9du3 #18  
---  
A1BCX —
N-[(2S)-3-cyclopropyl-1-({(2R)-1-hydroxy-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]-4-methoxy-1H-indole-2-carboxamide  
  
9du3 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> hide #!2 models

> color #18 #29ffafff

> show #!2 models

> hide #!2 models

> close #18

> open 15c8

Summary of feedback from opening 15c8 fetched from pdb  
---  
note | Fetching compressed mmCIF 15c8 from http://files.rcsb.org/download/15c8.cif  
  
15c8 title:  
Catalytic antibody 5C8, free fab [more info...]  
  
Chain information for 15c8 #18  
---  
Chain | Description | UniProt  
H | IGG 5C8 FAB (HEAVY CHAIN) | IGH1M_MOUSE 2-226  
L | IGG 5C8 FAB (LIGHT CHAIN) | KAC_MOUSE 2-212  
  

> show #!2 models

> hide #!2 models

> molmap #18 5 onGrid #11

Opened 15c8 map 5 as #19, grid size 256,256,256, pixel 1.06, shown at level
0.102, step 1, values float32  
No map chosen to save  

> save /Users/ZhenGong/Desktop/15C8_5A.mrc models #19

> close #19

> close #18

> open 16GS

Summary of feedback from opening 16GS fetched from pdb  
---  
notes | Fetching compressed mmCIF 16gs from http://files.rcsb.org/download/16gs.cif  
Fetching CCD MES from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/MES/MES.cif  
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif  
  
16gs title:  
Glutathione S-transferase P1-1 apo form 3 [more info...]  
  
Chain information for 16gs #18  
---  
Chain | Description | UniProt  
A B | GLUTATHIONE S-TRANSFERASE | GSTP1_HUMAN 1-209  
  
Non-standard residues in 16gs #18  
---  
MES — 2-(N-morpholino)-ethanesulfonic acid  
SO4 — sulfate ion  
  

> show #!13 models

> hide #!13 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> molmap #18 5 onGrid #11

Opened 16gs map 5 as #19, grid size 256,256,256, pixel 1.06, shown at level
0.113, step 1, values float32  

> save /Users/ZhenGong/Desktop/16GS_5A.mrc models #19

> view #18

> view #19

> hide #18 models

> save /Users/ZhenGong/Desktop/16GS_5A.mrc models #19

> open 15c8

15c8 title:  
Catalytic antibody 5C8, free fab [more info...]  
  
Chain information for 15c8 #20  
---  
Chain | Description | UniProt  
H | IGG 5C8 FAB (HEAVY CHAIN) | IGH1M_MOUSE 2-226  
L | IGG 5C8 FAB (LIGHT CHAIN) | KAC_MOUSE 2-212  
  

> view #20

> hide #!19 models

> molmap #20 5 onGrid #11

Opened 15c8 map 5 as #21, grid size 256,256,256, pixel 1.06, shown at level
0.102, step 1, values float32  

> hide #20 models

> view #21

> save /Users/ZhenGong/Desktop/15C8_5A.mrc models #21

> center #21

Unknown command: center #21  

> crosslinks

Missing or invalid "pbonds" argument: empty atom specifier  

> ui tool show "Map Coordinates"

> view #21

> save /Users/ZhenGong/Desktop/15C8_5A.mrc models #21

> ui mousemode right zoom

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!13 models

> hide #!13 models

> view #21

> hide #!19 models

> save /Users/ZhenGong/Desktop/15C8_5A.mrc models #21

> center

Unknown command: center  

> measure center #19

Center of mass grid index for 16GS_5A.mrc = (136.53, 127.02, 146.29)  
Center of mass xyz scene coordinates for 16GS_5A.mrc = (19.18, 12.10, 17.45)  

> measure center #21

Center of mass grid index for 15C8_5A.mrc = (173.43, 123.03, 179.26)  
Center of mass xyz scene coordinates for 15C8_5A.mrc = (58.30, 7.87, 52.40)  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 72, in measure_center  
areas = vertex_areas(surf.vertices, surf.triangles)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: Array argument has non-numeric values  
  
TypeError: Array argument has non-numeric values  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 72, in measure_center  
areas = vertex_areas(surf.vertices, surf.triangles)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> measure center #21

Center of mass grid index for 15C8_5A.mrc = (173.43, 123.03, 179.26)  
Center of mass xyz scene coordinates for 15C8_5A.mrc = (58.30, 7.87, 52.40)  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 72, in measure_center  
areas = vertex_areas(surf.vertices, surf.triangles)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: Array argument has non-numeric values  
  
TypeError: Array argument has non-numeric values  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 72, in measure_center  
areas = vertex_areas(surf.vertices, surf.triangles)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-23.0.26
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2075.101.2.0.0 (iBridge: 22.16.14248.0.0,0)
      OS Loader Version: 583~900

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 7 days, 20 hours, 5 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL2407WFPHC:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: GM50481P3ENS 
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: Analog VGA or Analog Over DVI-I


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.3
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.16
    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: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    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: 1.2.6
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202504260127
    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: 1.6.1
    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: 2.2.1
    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: 2.7.9
    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: 1.1.1
    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: 1.2.0
    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: 1.45.1
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.57.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    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: 8.1.6
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.14
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.7
    pluggy: 1.5.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    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: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    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: 2.2.0
    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
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    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.13.2
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[Eric Pettersen]

Reported by Zhen Gong

[Tom Goddard]

Fixed.

The "measure center #21" command on a map gave this error because the map had a clip cap surface introduced by the earlier "view #21" command that had vertex and triangle arrays equal to None (ie. nothing clipped). Not sure why the clip surface was not deleted since it had no intersection with the surface. But measure center tried to measure the center of that clip cap surface and did not handle vertices and triangles = None. I put in code so measure center handles empty surfaces.