Opened 7 months ago

Closed 7 months ago

#17389 closed defect (fixed)

MatchMaker: bad pairing arg produces traceback

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Comparison Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/mahamayabiswal/EMC-G09 chimera session 15th april 7_20 pm.cxs"
> format session

Opened cryosparc_P1_J610_006_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 0.92, shown at level 0.0733, step 2, values float32  
Log from Tue Apr 15 19:20:57 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/mahamayabiswal/Library/CloudStorage/OneDrive-
> Stanford/Pleiner/Pleiner lab/Structure/cryo EM str for Nnaobody-EMC
> complex/April 2025/15TH APRIL 2025 vol translucent.cxs"

Opened cryosparc_P1_J610_006_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 0.92, shown at level 0.0733, step 2, values float32  
Log from Tue Apr 15 16:28:58 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\mahamaya\OneDrive - Stanford\Pleiner\Pleiner
> lab\Structure\cryo EM str for Nnaobody-EMC complex\April 2025\15TH APRIL
> 2025.cxs" format session

Opened cryosparc_P1_J610_006_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 0.92, shown at level 0.0882, step 2, values float32  
Log from Tue Apr 15 15:47:29 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\mahamaya\OneDrive - Stanford\Pleiner\Pleiner
> lab\Structure\cryo EM str for Nnaobody-EMC complex\April
> 2025\cryosparc_P1_J610_006_volume_map_sharp.mrc" format mrc

Opened cryosparc_P1_J610_006_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 0.92, shown at level 0.0314, step 2, values float32  

> volume #1 level 0.06428

> volume #1 level 0.06877

> volume #1 level 0.08822

> open "C:/Users/mahamaya/OneDrive - Stanford/Pleiner/Pleiner
> lab/Structure/PDB/8s9s.cif"

Summary of feedback from opening C:/Users/mahamaya/OneDrive -
Stanford/Pleiner/Pleiner lab/Structure/PDB/8s9s.cif  
---  
warning | Atom C19 has no neighbors to form bonds with according to residue template for PCW /1:1002  
notes | Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif  
Fetching CCD PCW from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/PCW/PCW.cif  
  
8s9s.cif title:  
Structure of the human ER membrane protein complex (EMC) in GDN [more info...]  
  
Chain information for 8s9s.cif #2  
---  
Chain | Description | UniProt  
1 | ER membrane protein complex subunit 1 | EMC1_HUMAN 1-993  
10 | ER membrane protein complex subunit 10 | EMC10_HUMAN 1-262  
2 | ER membrane protein complex subunit 2 | EMC2_HUMAN 1-297  
3 | ER membrane protein complex subunit 3 | EMC3_HUMAN 1-261  
4 | ER membrane protein complex subunit 4 | EMC4_HUMAN 1-183  
5 | Membrane magnesium transporter 1 | MMGT1_HUMAN 1-131  
6 | ER membrane protein complex subunit 6 | EMC6_HUMAN 1-110  
7 | ER membrane protein complex subunit 7 | EMC7_HUMAN 1-242  
8 | ER membrane protein complex subunit 8 | EMC8_HUMAN 1-210  
  
Non-standard residues in 8s9s.cif #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)  
PCW — 1,2-dioleoyl-Sn-glycero-3-phosphocholine
((Z,Z)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxo-9-octadecenyl)oxy]-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium-4-oxide)  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 17706 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> ui mousemode right "translate selected models"

> select add #2

18012 atoms, 18413 bonds, 8 pseudobonds, 2275 residues, 2 models selected  

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,38.359,0,1,0,93.234,0,0,1,52.733

> view matrix models #2,1,0,0,71.822,0,1,0,84.767,0,0,1,60.327

> view matrix models #1,1,0,0,-2.0774,0,1,0,7.7212,0,0,1,-1.3246

> view matrix models #2,1,0,0,69.711,0,1,0,85.176,0,0,1,62.13

> view matrix models #1,1,0,0,-1.9297,0,1,0,13.715,0,0,1,0.39662

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.95129,-0.30737,0.023797,123.44,0.30816,0.95029,-0.044535,50.508,-0.0089247,0.049699,0.99872,55.748

> ui tool show "Fit in Map"

> select add #1

18012 atoms, 18413 bonds, 8 pseudobonds, 2275 residues, 4 models selected  

> select subtract #2

2 models selected  

> select subtract #1

Nothing selected  

> save "C:/Users/mahamaya/OneDrive - Stanford/Pleiner/Pleiner
> lab/Structure/cryo EM str for Nnaobody-EMC complex/April 2025/15TH APRIL
> 2025.cxs"

——— End of log from Tue Apr 15 15:47:29 2025 ———

opened ChimeraX session  

> color #1 lightgray

> volume #1 smoothing true iterations 2 factor 0.3

Expected keyword "smoothingFactor" or "smoothingIterations"  

> volume #1 transparency 50

> volume #1 transparency 0

> volume #1 style surface

> volume #1 style mesh

> volume #1 level 0.1047

> volume #1 style surface

> volume #1 level 0.08522

> set bgColor white

> volume #1 transparency 0

[Repeated 1 time(s)]

> volume #1 transparency 30

> volume #1 transparency 50

> set bgColor black

> volume #1 transparency 0

> transparency 60 #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> volume #1 transparency 0.6

> set bgColor white

> set bgColor BLACK

Invalid "bgColor" argument: Invalid color name or specifier  

> set bgColor black

> volume #1 transparency 0.7

> volume #1 transparency 0.5

> volume #1 transparency 0.8

> volume #1 transparency 0.2

> volume #1 transparency 0.7

> volume #1 transparency 0.6

> volume #1 level 0.07326

> save "C:/Users/mahamaya/OneDrive - Stanford/Pleiner/Pleiner
> lab/Structure/cryo EM str for Nnaobody-EMC complex/April 2025/15TH APRIL
> 2025 vol translucent.cxs"

——— End of log from Tue Apr 15 16:28:58 2025 ———

opened ChimeraX session  

> open "/Users/mahamayabiswal/Library/CloudStorage/OneDrive-
> Stanford/Pleiner/Pleiner lab/Structure/Nanobody AF
> structures/fold_2025_04_15_16_31_nanobody_g09_only/fold_2025_04_15_16_31_nanobody_g09_only_model_1.cif"

Chain information for fold_2025_04_15_16_31_nanobody_g09_only_model_1.cif #3  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> select add #2

18012 atoms, 18413 bonds, 8 pseudobonds, 2275 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select add #3

887 atoms, 905 bonds, 115 residues, 1 model selected  

> ui mousemode right "move picked models"

> view matrix models #3,1,0,0,299.34,0,1,0,268.88,0,0,1,296.12

> ui mousemode right "move picked models"

> view matrix models #3,1,0,0,268.62,0,1,0,264.64,0,0,1,312.84

> view matrix models #3,1,0,0,279.28,0,1,0,280.12,0,0,1,300.84

> view matrix models #3,1,0,0,274.55,0,1,0,276.52,0,0,1,304.45

> view matrix models #1,1,0,0,-7.1357,0,1,0,7.9893,0,0,1,-1.8941

> undo

[Repeated 1 time(s)]

> view matrix models #3,1,0,0,278.89,0,1,0,281.29,0,0,1,306.36

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.017279,0.35505,0.93469,277.98,-0.89292,0.4261,-0.14535,283.7,-0.44988,-0.83209,0.32439,309.53

> view matrix models
> #3,0.15767,0.38701,0.9085,277.78,-0.92737,0.37414,0.0015727,283.57,-0.33929,-0.84276,0.41789,309.24

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,-5.708,0,1,0,13.602,0,0,1,-2.6753

> undo

> view matrix models
> #3,0.15767,0.38701,0.9085,263.7,-0.92737,0.37414,0.0015727,281.52,-0.33929,-0.84276,0.41789,301.66

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,-2.2664,0,1,0,14.37,0,0,1,1.315

> undo

> view matrix models
> #3,0.15767,0.38701,0.9085,261.6,-0.92737,0.37414,0.0015727,284.75,-0.33929,-0.84276,0.41789,306.56

> ui mousemode right "move picked models"

> view matrix models
> #3,0.15767,0.38701,0.9085,260.29,-0.92737,0.37414,0.0015727,285.79,-0.33929,-0.84276,0.41789,308.23

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.24538,0.081647,0.96598,260.58,-0.87912,0.4387,0.18624,285.29,-0.40858,-0.89491,0.17943,308.83

> view matrix models
> #3,0.31202,0.27935,0.90808,260.26,-0.94667,0.17227,0.27229,285.67,-0.080369,-0.94461,0.3182,308.23

> view matrix models
> #3,0.35599,0.11986,0.92677,260.43,-0.9141,0.25069,0.3187,285.42,-0.19413,-0.96062,0.19881,308.62

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.35599,0.11986,0.92677,263.27,-0.9141,0.25069,0.3187,281.84,-0.19413,-0.96062,0.19881,303.95

> undo

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,-0.16322,0,1,0,13.626,0,0,1,-0.82384

> undo

> view matrix models
> #3,0.35599,0.11986,0.92677,260.29,-0.9141,0.25069,0.3187,285.28,-0.19413,-0.96062,0.19881,308.59

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 8s9s.cif (#2) to map cryosparc_P1_J610_006_volume_map_sharp.mrc
(#1) using 18012 atoms  
average map value = 0.1164, steps = 116  
shifted from previous position = 6.26  
rotated from previous position = 4.75 degrees  
atoms outside contour = 5499, contour level = 0.073257  
  
Position of 8s9s.cif (#2) relative to
cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97152642 -0.23233361 0.04644897 103.45442952  
0.23381914 0.97183102 -0.02954775 37.82469195  
-0.03827561 0.03956708 0.99848356 64.60585994  
Axis 0.14434882 0.17695036 0.97357690  
Axis point -49.74898996 398.86532523 0.00000000  
Rotation angle (degrees) 13.85125567  
Shift along axis 84.52539111  
  

> view matrix models #1,1,0,0,-0.90935,0,1,0,9.0579,0,0,1,3.3734

> fitmap #3 #1

Missing required "in_map" argument  

> fitmap #3 inMap MapID #1

Invalid "inMap" argument: invalid density map specifier  

> fitmap #3 inMap #1

Fit molecule fold_2025_04_15_16_31_nanobody_g09_only_model_1.cif (#3) to map
cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) using 887 atoms  
average map value = 0.1095, steps = 104  
shifted from previous position = 6.34  
rotated from previous position = 21.9 degrees  
atoms outside contour = 285, contour level = 0.073257  
  
Position of fold_2025_04_15_16_31_nanobody_g09_only_model_1.cif (#3) relative
to cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.50815510 0.33125550 0.79501458 255.76251337  
-0.85099994 0.05101927 0.52268167 273.68060561  
0.13258011 -0.94216072 0.30782412 302.77774913  
Axis -0.73404610 0.33195205 -0.59243916  
Axis point 0.00000000 283.31814798 -184.67368067  
Rotation angle (degrees) 93.81302634  
Shift along axis -276.27003242  
  

> select subtract #3

Nothing selected  

> select add #2

18012 atoms, 18413 bonds, 8 pseudobonds, 2275 residues, 2 models selected  

> fitmap #2 inMap #1

Fit molecule 8s9s.cif (#2) to map cryosparc_P1_J610_006_volume_map_sharp.mrc
(#1) using 18012 atoms  
average map value = 0.1164, steps = 76  
shifted from previous position = 5.6  
rotated from previous position = 0.0546 degrees  
atoms outside contour = 5503, contour level = 0.073257  
  
Position of 8s9s.cif (#2) relative to
cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97173432 -0.23144481 0.04653711 103.23950927  
0.23294517 0.97203164 -0.02985018 38.00535353  
-0.03832687 0.03984703 0.99847046 64.57015250  
Axis 0.14605521 0.17783819 0.97316055  
Axis point -50.62487842 398.81339173 0.00000000  
Rotation angle (degrees) 13.80385834  
Shift along axis 84.67459621  
  

> save "/Users/mahamayabiswal/EMC-G09 chimera session 15th april 7_20 pm.cxs"

——— End of log from Tue Apr 15 19:20:57 2025 ———

opened ChimeraX session  

> select add #3

18899 atoms, 19318 bonds, 8 pseudobonds, 2390 residues, 3 models selected  

> select subtract #2

887 atoms, 905 bonds, 115 residues, 1 model selected  

> close #3

> open "/Users/mahamayabiswal/Library/CloudStorage/OneDrive-
> Stanford/Pleiner/Pleiner lab/Structure/Nanobody AF
> structures/fold_2025_04_15_16_31_nanobody_g09_only/fold_2025_04_15_16_31_nanobody_g09_only_model_0.cif"

Chain information for fold_2025_04_15_16_31_nanobody_g09_only_model_0.cif #3  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> ui mousemode right "move picked models"

> select add #3

887 atoms, 905 bonds, 115 residues, 1 model selected  

> view matrix models #3,1,0,0,309.18,0,1,0,258.25,0,0,1,263.9

> view matrix models #3,1,0,0,307.81,0,1,0,245.01,0,0,1,299.49

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.11652,0.97182,-0.20489,312.16,-0.434,0.23538,0.86962,244.51,0.89335,-0.012403,0.44919,297.16

> view matrix models
> #3,0.40361,-0.17111,0.89879,308.51,0.6752,-0.60721,-0.41881,241.39,0.61742,0.77589,-0.12955,299.71

> ui mousemode right "move picked models"

> view matrix models
> #3,0.40361,-0.17111,0.89879,265.33,0.6752,-0.60721,-0.41881,253.54,0.61742,0.77589,-0.12955,332.65

> view matrix models
> #3,0.40361,-0.17111,0.89879,272.11,0.6752,-0.60721,-0.41881,277.77,0.61742,0.77589,-0.12955,305.06

> view matrix models
> #3,0.40361,-0.17111,0.89879,259.22,0.6752,-0.60721,-0.41881,285.56,0.61742,0.77589,-0.12955,308.36

> view matrix models #1,1,0,0,0.41773,0,1,0,10.417,0,0,1,7.0869

> fitmap #3 inMap #1

Fit molecule fold_2025_04_15_16_31_nanobody_g09_only_model_0.cif (#3) to map
cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) using 887 atoms  
average map value = 0.1129, steps = 68  
shifted from previous position = 2.64  
rotated from previous position = 14.6 degrees  
atoms outside contour = 211, contour level = 0.073257  
  
Position of fold_2025_04_15_16_31_nanobody_g09_only_model_0.cif (#3) relative
to cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.43088031 -0.40558774 0.80612700 256.97778977  
0.58445498 -0.55520976 -0.59173854 274.07807244  
0.68757147 0.72611343 -0.00218117 299.40839719  
Axis 0.79745808 0.07174027 0.59909427  
Axis point 0.00000000 106.45891590 134.40318714  
Rotation angle (degrees) 124.28122439  
Shift along axis 403.96530639  
  

> fitmap #2 inMap #1

Fit molecule 8s9s.cif (#2) to map cryosparc_P1_J610_006_volume_map_sharp.mrc
(#1) using 18012 atoms  
average map value = 0.1164, steps = 84  
shifted from previous position = 4.16  
rotated from previous position = 0.0124 degrees  
atoms outside contour = 5502, contour level = 0.073257  
  
Position of 8s9s.cif (#2) relative to
cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97173478 -0.23147017 0.04640120 103.27812756  
0.23295871 0.97203352 -0.02968287 37.95914857  
-0.03823283 0.03965344 0.99848178 64.57537558  
Axis 0.14531584 0.17737697 0.97335539  
Axis point -50.60160025 399.25352359 0.00000000  
Rotation angle (degrees) 13.80221936  
Shift along axis 84.59581623  
  

> save "/Users/mahamayabiswal/Library/CloudStorage/OneDrive-
> Stanford/Pleiner/Pleiner lab/Structure/cryo EM str for Nnaobody-EMC
> complex/G09-EMC.cxs"

> open "/Users/mahamayabiswal/Library/CloudStorage/OneDrive-
> Stanford/Pleiner/Pleiner lab/Structure/Nanobody AF
> structures/fold_2025_04_15_17_33_e2_nanobody_only/fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif"

Chain information for fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif #4  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> select subtract #3

Nothing selected  

> select add #4

873 atoms, 890 bonds, 114 residues, 1 model selected  

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,218.91,0,1,0,302.97,0,0,1,129.6

> ui mousemode right "move picked models"

> view matrix models #4,1,0,0,221.28,0,1,0,292.55,0,0,1,137.12

> view matrix models #1,1,0,0,0.32155,0,1,0,10.475,0,0,1,6.8896

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.62183,0.1443,-0.76975,220.82,-0.55283,0.77706,-0.30093,292.07,0.55471,0.61266,0.56297,137.43

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,1.0264,0,1,0,9.8833,0,0,1,8.1352

> view matrix models
> #4,0.62183,0.1443,-0.76975,226.13,-0.55283,0.77706,-0.30093,285.82,0.55471,0.61266,0.56297,145.5

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.87679,0.37919,0.29573,226.2,0.32843,-0.022996,-0.94425,287.37,-0.35125,0.92503,-0.1447,144.32

> ui mousemode right "move picked models"

> view matrix models
> #4,0.87679,0.37919,0.29573,238.95,0.32843,-0.022996,-0.94425,298.02,-0.35125,0.92503,-0.1447,143.12

> view matrix models
> #4,0.87679,0.37919,0.29573,239.85,0.32843,-0.022996,-0.94425,294.12,-0.35125,0.92503,-0.1447,144.39

> view matrix models
> #4,0.87679,0.37919,0.29573,240.66,0.32843,-0.022996,-0.94425,289.63,-0.35125,0.92503,-0.1447,143.43

> fitmap #4 inMap #1

Fit molecule fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif (#4) to map
cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) using 873 atoms  
average map value = 0.1039, steps = 228  
shifted from previous position = 11.3  
rotated from previous position = 70.7 degrees  
atoms outside contour = 231, contour level = 0.073257  
  
Position of fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif (#4) relative
to cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48309535 0.09077566 0.87084939 240.45018563  
0.31955353 0.90772360 -0.27188861 272.18473633  
-0.81517141 0.40963112 0.40950936 142.84816333  
Axis 0.37182857 0.91987168 0.12481831  
Axis point 146.77452353 0.00000000 -36.29977554  
Rotation angle (degrees) 66.41155918  
Shift along axis 357.61134524  
  

> fitmap #4 inMap #1

Fit molecule fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif (#4) to map
cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) using 873 atoms  
average map value = 0.1039, steps = 60  
shifted from previous position = 0.0154  
rotated from previous position = 0.0282 degrees  
atoms outside contour = 232, contour level = 0.073257  
  
Position of fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif (#4) relative
to cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48273098 0.09059936 0.87106978 240.46021712  
0.31985544 0.90768402 -0.27166563 272.19257743  
-0.81526885 0.40975782 0.40918850 142.83985026  
Axis 0.37171189 0.91988633 0.12505764  
Axis point 146.67959291 0.00000000 -36.33644278  
Rotation angle (degrees) 66.43421452  
Shift along axis 357.63136689  
  

> select subtract #4

Nothing selected  

> fitmap #4 inMap #1

Fit molecule fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif (#4) to map
cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) using 873 atoms  
average map value = 0.1039, steps = 48  
shifted from previous position = 0.00308  
rotated from previous position = 0.0116 degrees  
atoms outside contour = 232, contour level = 0.073257  
  
Position of fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif (#4) relative
to cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48281981 0.09061806 0.87101860 240.46181669  
0.31968537 0.90774973 -0.27164626 272.19493163  
-0.81528295 0.40960810 0.40931028 142.83895225  
Axis 0.37164409 0.91992660 0.12496289  
Axis point 146.73125438 0.00000000 -36.35945904  
Rotation angle (degrees) 66.42557790  
Shift along axis 357.61513881  
  

> select add #4

873 atoms, 890 bonds, 114 residues, 1 model selected  

> fitmap #4 inMap #1

Fit molecule fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif (#4) to map
cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) using 873 atoms  
average map value = 0.1039, steps = 48  
shifted from previous position = 0.0225  
rotated from previous position = 0.0404 degrees  
atoms outside contour = 231, contour level = 0.073257  
  
Position of fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif (#4) relative
to cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48334973 0.09087013 0.87069837 240.44838631  
0.31963537 0.90761300 -0.27216150 272.17944249  
-0.81498851 0.40985518 0.40964919 142.84706951  
Axis 0.37212485 0.91975165 0.12481987  
Axis point 146.74329194 0.00000000 -36.22957797  
Rotation angle (degrees) 66.40269302  
Shift along axis 357.64446254  
  

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,1.6231,0,1,0,10.395,0,0,1,7.7925

> view matrix models #1,1,0,0,1.2692,0,1,0,10.083,0,0,1,9.8417

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.66223,0.65243,-0.36849,239.91,-0.2448,-0.65318,-0.71654,282.38,-0.70818,-0.38431,0.59227,151.57

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,-0.71224,0,1,0,8.3766,0,0,1,12.513

> view matrix models #1,1,0,0,-5.1644,0,1,0,4.5362,0,0,1,19.839

> undo

[Repeated 1 time(s)]

> view matrix models
> #4,-0.66223,0.65243,-0.36849,236.13,-0.2448,-0.65318,-0.71654,283.6,-0.70818,-0.38431,0.59227,140.41

> view matrix models #1,1,0,0,2.0755,0,1,0,11.274,0,0,1,10.726

> undo

> view matrix models
> #4,-0.66223,0.65243,-0.36849,242.02,-0.2448,-0.65318,-0.71654,293.15,-0.70818,-0.38431,0.59227,144.35

> view matrix models #1,1,0,0,0.96419,0,1,0,9.4801,0,0,1,9.6331

> fitmap #4 inMap #1

Fit molecule fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif (#4) to map
cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) using 873 atoms  
average map value = 0.09564, steps = 124  
shifted from previous position = 7.8  
rotated from previous position = 42.8 degrees  
atoms outside contour = 273, contour level = 0.073257  
  
Position of fold_2025_04_15_17_33_e2_nanobody_only_model_0.cif (#4) relative
to cryosparc_P1_J610_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.84915964 0.52790681 -0.01556651 239.30599778  
-0.04697099 -0.10484675 -0.99337852 276.97485039  
-0.52604338 -0.84280577 0.11382794 139.03422542  
Axis 0.19219984 0.65160243 -0.73380754  
Axis point 165.08988894 170.27700231 0.00000000  
Rotation angle (degrees) 156.93912959  
Shift along axis 124.44769661  
  

> save "/Users/mahamayabiswal/Library/CloudStorage/OneDrive-
> Stanford/Pleiner/Pleiner lab/Structure/cryo EM str for Nnaobody-EMC
> complex/G09-EMC-E02 WITH CLASH_7_47 PM.cxs"

> open "/Users/mahamayabiswal/Library/CloudStorage/OneDrive-
> Stanford/Pleiner/Pleiner lab/Structure/PDB/8eoi (1).cif"

Summary of feedback from opening
/Users/mahamayabiswal/Library/CloudStorage/OneDrive-Stanford/Pleiner/Pleiner
lab/Structure/PDB/8eoi (1).cif  
---  
notes | Fetching CCD 9Z9 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/9Z9/9Z9.cif  
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif  
  
8eoi (1).cif title:  
Structure of a human EMC:human Cav1.2 channel complex in GDN detergent [more
info...]  
  
Chain information for 8eoi (1).cif #5  
---  
Chain | Description | UniProt  
A | ER membrane protein complex subunit 1 | EMC1_HUMAN 21-993  
B | ER membrane protein complex subunit 2 | EMC2_HUMAN 3-293  
C | ER membrane protein complex subunit 3 | EMC3_HUMAN 4-261  
D | ER membrane protein complex subunit 4 | EMC4_HUMAN 14-183  
E | ER membrane protein complex subunit 5 | EMC5_HUMAN 3-103  
F | ER membrane protein complex subunit 6 | EMC6_HUMAN 11-110  
G | ER membrane protein complex subunit 7 | EMC7_HUMAN 43-158  
H | ER membrane protein complex subunit 8 | EMC8_HUMAN 3-210  
I | ER membrane protein complex subunit 10 | EMC10_HUMAN 50-206  
J | Voltage-dependent L-type calcium channel subunit beta-3 | CACB3_RABIT 38-361  
K | Voltage-dependent L-type calcium channel subunit alpha-1C | CAC1C_HUMAN 109-1658  
  
Non-standard residues in 8eoi (1).cif #5  
---  
9Z9 —
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en  
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)  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 28584 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> fitmap #moving1 inMap #reference5

Missing or invalid "atomsOrMap" argument: invalid objects specifier  

> matchmaker #1 #5

Missing required "to" argument  

> matchmaker #2 #5

Missing required "to" argument  

> matchmaker #5 #reference2

Expected a keyword  

> matchmaker #5 #2

Missing required "to" argument  

> open some_model1.pdb # will get #1

'#' has no suffix  

> open some_model2.pdb # will get #2

'#' has no suffix  

> matchmaker #2 to #1

No 'to' model specified  

> select subtract #4

Nothing selected  

> matchmaker #5 to #2 pairing structure

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 767, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 415, in match  
raise ValueError("No such chain-pairing method")  
ValueError: No such chain-pairing method  
  
ValueError: No such chain-pairing method  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py", line 415, in match  
raise ValueError("No such chain-pairing method")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: MGND3LL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.61.3
      OS Loader Version: 11881.61.3

Software:

    System Software Overview:

      System Version: macOS 15.2 (24C101)
      Kernel Version: Darwin 24.2.0
      Time since boot: 12 days, 8 hours, 58 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    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: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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
    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: 1.2.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    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: 1.18.1
    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
    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: 1.41
    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: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    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
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by Eric Pettersen, 7 months ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → MatchMaker: bad pairing arg produces traceback

comment:2 by Eric Pettersen, 7 months ago

Resolution: → fixed
Status: accepted → closed

Changed 'pairing' and 'alg' keywords to EnumOf annotations for better error handling.

Fix: ​https://github.com/RBVI/ChimeraX/commit/03b79f5b88f0aec757fabe504a9bc12607da58f2

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