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#19482 new defect

ChimeraX bug report submission

Reported by:	jiao.li@…	Owned by:
Priority:	normal	Milestone:
Component:	Unassigned	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:
Project:

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "F:\\\mouse liver\\\comparison.cxs"

Opened cryosparc_P32_J1682_006_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.83, shown at level 0.0531, step 1, values float32  
Opened cryosparc_P32_J1676_volume_map.mrc as #6, grid size 512,512,512, pixel
0.83, shown at level 0.0154, step 1, values float32  
Log from Thu Dec 4 17:34:48 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "F:\\\mouse liver\\\comparison.cxs"

Opened cryosparc_P32_J1682_006_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.83, shown at level 0.0531, step 1, values float32  
Opened cryosparc_P32_J1676_volume_map.mrc as #6, grid size 512,512,512, pixel
0.83, shown at level 0.0154, step 1, values float32  
Log from Wed Dec 3 09:45:11 2025 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:/liver_normal/Normal_20251225 dataset/ATP
> synthase/cryosparc_P32_J1682_006_volume_mask_refine.mrc"

Opened cryosparc_P32_J1682_006_volume_mask_refine.mrc as #1, grid size
512,512,512, pixel 0.83, shown at level 1, step 2, values float32  

> volume #1 level 0.8779

> volume #1 level 0.9264

> open "D:/liver_normal/Normal_20251225 dataset/ATP
> synthase/cryosparc_P32_J1682_006_volume_map.mrc"

Opened cryosparc_P32_J1682_006_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.83, shown at level 0.0245, step 2, values float32  

> hide #!1 models

> close #1

> volume #2 step 1

> volume #2 level 0.01714

> volume #2 level 0.01223

> volume #2 level 0.01468

> volume #2 level 0.01877

> set bgColor white

> select add #2

2 models selected  

> transparency sel 50

> select clear

> open "D:/liver_normal/ATP
> synthase_normal/normal_2024/cryosparc_P13_J274_class_05_00142_volume.mrc"

Opened cryosparc_P13_J274_class_05_00142_volume.mrc as #1, grid size
128,128,128, pixel 3.28, shown at level 0.357, step 1, values float32  

> hide #!2 models

> close #1

> show #!2 models

> open "D:/liver_jxgsg/ATPase/ATP synthase
> model/model/Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb"

Summary of feedback from opening D:/liver_jxgsg/ATPase/ATP synthase
model/model/Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb  
---  
warning | PDB SEQRES record for chain S is incomplete. Ignoring input sequence
records as basis for sequence.  
  
Chain information for Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb
#1  
---  
Chain | Description | UniProt  
8 | No description available | ATP8_BOVIN 1-66  
A | No description available | ATPA_MOUSE 1-553  
B C | No description available |  
D E F | No description available |  
G | No description available |  
H | No description available |  
I | No description available |  
K M N O Q R | No description available |  
L P | No description available |  
S | No description available |  
a | No description available |  
b | No description available |  
d | No description available |  
e | No description available | ATP5I_MOUSE 1-71  
f | No description available |  
g | No description available |  
h | No description available |  
j | No description available | ATP68_MOUSE 1-58  
k | No description available | ATPMK_MOUSE 1-58  
  

> select add #1

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-0.70327,0,1,0,-12.251,0,0,1,-39.716

> view matrix models #1,1,0,0,-34.268,0,1,0,-24.854,0,0,1,-37.495

> fitmap #1 inMap #2

Fit molecule Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb (#1) to
map cryosparc_P32_J1682_006_volume_map.mrc (#2) using 49754 atoms  
average map value = 0.05243, steps = 200  
shifted from previous position = 9.83  
rotated from previous position = 2.52 degrees  
atoms outside contour = 3855, contour level = 0.018772  
  
Position of Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb (#1)
relative to cryosparc_P32_J1682_006_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99907526 -0.04286362 0.00336534 -22.12020370  
0.04289170 0.99904124 -0.00876906 -42.29228709  
-0.00298624 0.00890530 0.99995589 -40.53650235  
Axis 0.20133046 0.07235159 0.97684763  
Axis point 899.53248022 -314.18435224 0.00000000  
Rotation angle (degrees) 2.51574403  
Shift along axis -47.11137139  
  

> hide sel atoms

> show sel cartoons

> select clear

> select add #2

2 models selected  

> color #2 #ffffff80 models

> select clear

[Repeated 1 time(s)]

> open "D:/liver_jxgsg/ATPase/ATP synthase model/bovine ATP synthase monomer
> state 2 (combined)_6ZQM.cif"

Summary of feedback from opening D:/liver_jxgsg/ATPase/ATP synthase
model/bovine ATP synthase monomer state 2 (combined)_6ZQM.cif  
---  
warnings | Atom H1 is not in the residue template for ALA /G:1  
Atom H1 is not in the residue template for VAL /I:1  
Atom H1 is not in the residue template for ASP /K:1  
Atom H1 is not in the residue template for ASP /L:1  
Atom H1 is not in the residue template for ASP /M:1  
4 messages similar to the above omitted  
Too many hydrogens missing from residue template(s) to warn about  
  
bovine ATP synthase monomer state 2 (combined)_6ZQM.cif title:  
bovine ATP synthase monomer state 2 (combined) [more info...]  
  
Chain information for bovine ATP synthase monomer state 2 (combined)_6ZQM.cif
#3  
---  
Chain | Description | UniProt  
8 | ATP synthase protein 8 | ATP8_BOVIN 1-66  
A B C | ATP synthase subunit alpha, mitochondrial | ATPA_BOVIN 1-510  
D E F | ATP synthase subunit beta, mitochondrial | ATPB_BOVIN -3-478  
G | ATP synthase subunit gamma, mitochondrial | ATPG_BOVIN 1-273  
H | ATP synthase subunit delta, mitochondrial | ATPD_BOVIN 1-146  
I | ATP synthase subunit epsilon, mitochondrial | ATP5E_BOVIN 1-50  
J | ATPase inhibitor, mitochondrial | ATIF1_BOVIN 1-60  
K L M N O P Q R | ATP synthase F(0) complex subunit C2, mitochondrial |
AT5G2_BOVIN 1-75  
S | ATP synthase subunit O, mitochondrial | ATPO_BOVIN 1-190  
a | ATP synthase subunit a | ATP6_BOVIN 1-226  
b | ATP synthase F(0) complex subunit B1, mitochondrial | AT5F1_BOVIN 1-214  
d | ATP synthase subunit d, mitochondrial | ATP5H_BOVIN 1-160  
e | ATP synthase subunit e, mitochondrial | ATP5I_BOVIN 1-70  
f | ATP synthase subunit f, mitochondrial | ATPK_BOVIN 1-87  
g | ATP synthase subunit g, mitochondrial | ATP5L_BOVIN 1-102  
h | ATP synthase-coupling factor 6, mitochondrial | ATP5J_BOVIN 1-76  
j | ATP synthase subunit ATP5MPL, mitochondrial | ATP68_BOVIN 1-60  
k | ATP synthase membrane subunit DAPIT, mitochondrial | ATPMD_BOVIN 1-57  
  
Non-standard residues in bovine ATP synthase monomer state 2
(combined)_6ZQM.cif #3  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
M3L — N-trimethyllysine  
MG — magnesium ion  
  

> select add #3

81155 atoms, 81778 bonds, 34 pseudobonds, 5188 residues, 3 models selected  

> view matrix models #3,1,0,0,13.1,0,1,0,28.012,0,0,1,-110.82

> view matrix models #3,1,0,0,-73.761,0,1,0,-34.364,0,0,1,-128.49

> view matrix models #3,1,0,0,-65.324,0,1,0,-45.901,0,0,1,-127.04

> hide #!2 models

> hide #1 models

> show #!2 models

> fitmap #3 inMap #2

Fit molecule bovine ATP synthase monomer state 2 (combined)_6ZQM.cif (#3) to
map cryosparc_P32_J1682_006_volume_map.mrc (#2) using 81155 atoms  
average map value = 0.03466, steps = 140  
shifted from previous position = 9.57  
rotated from previous position = 8.66 degrees  
atoms outside contour = 23647, contour level = 0.018772  
  
Position of bovine ATP synthase monomer state 2 (combined)_6ZQM.cif (#3)
relative to cryosparc_P32_J1682_006_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99018578 -0.13885118 0.01588958 -24.03243080  
0.13773647 0.98880455 0.05739537 -101.24571389  
-0.02368110 -0.05464350 0.99822507 -111.12523535  
Axis -0.37218461 0.13145081 0.91880319  
Axis point 592.79038866 -500.35886277 0.00000000  
Rotation angle (degrees) 8.65678321  
Shift along axis -106.46655077  
  

> hide sel atoms

> show sel cartoons

> select clear

> open "D:/liver_jxgsg/ATPase/ATP synthase model/bovine ATP synthase monomer
> state 1 (combined)_6ZPO.cif"

Summary of feedback from opening D:/liver_jxgsg/ATPase/ATP synthase
model/bovine ATP synthase monomer state 1 (combined)_6ZPO.cif  
---  
warnings | Atom H1 is not in the residue template for MET /8:1  
Atom H1 is not in the residue template for ALA /G:1  
Atom H1 is not in the residue template for VAL /I:1  
Atom H1 is not in the residue template for ASP /K:1  
Atom H1 is not in the residue template for ASP /L:1  
4 messages similar to the above omitted  
Too many hydrogens missing from residue template(s) to warn about  
  
bovine ATP synthase monomer state 1 (combined)_6ZPO.cif title:  
bovine ATP synthase monomer state 1 (combined) [more info...]  
  
Chain information for bovine ATP synthase monomer state 1 (combined)_6ZPO.cif
#4  
---  
Chain | Description | UniProt  
8 | ATP synthase protein 8 | ATP8_BOVIN 1-66  
A B C | ATP synthase subunit alpha, mitochondrial | ATPA_BOVIN 1-510  
D E F | ATP synthase subunit beta, mitochondrial | ATPB_BOVIN -3-478  
G | ATP synthase subunit gamma, mitochondrial | ATPG_BOVIN 1-273  
H | ATP synthase subunit delta, mitochondrial | ATPD_BOVIN 1-146  
I | ATP synthase subunit epsilon, mitochondrial | ATP5E_BOVIN 1-50  
J | ATPase inhibitor, mitochondrial | ATIF1_BOVIN 1-60  
K L M N O P Q R | ATP synthase F(0) complex subunit C1, mitochondrial |
AT5G1_BOVIN 1-75  
S | ATP synthase subunit O, mitochondrial | ATPO_BOVIN 1-190  
a | ATP synthase subunit a | ATP6_BOVIN 1-226  
b | ATP synthase F(0) complex subunit B1, mitochondrial | AT5F1_BOVIN 1-214  
d | ATP synthase subunit d, mitochondrial | ATP5H_BOVIN 1-160  
e | ATP synthase subunit e, mitochondrial | ATP5I_BOVIN 1-70  
f | ATP synthase subunit f, mitochondrial | ATPK_BOVIN 1-87  
g | ATP synthase subunit g, mitochondrial | ATP5L_BOVIN 1-102  
h | ATP synthase-coupling factor 6, mitochondrial | ATP5J_BOVIN 1-76  
j | ATP synthase subunit ATP5MPL, mitochondrial | ATP68_BOVIN 1-60  
k | ATP synthase membrane subunit DAPIT, mitochondrial | ATPMD_BOVIN 1-57  
  
Non-standard residues in bovine ATP synthase monomer state 1
(combined)_6ZPO.cif #4  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
M3L — N-trimethyllysine  
MG — magnesium ion  
  

> select add #4

81052 atoms, 81676 bonds, 32 pseudobonds, 5183 residues, 3 models selected  

> view matrix models #4,1,0,0,-0.4921,0,1,0,-49.912,0,0,1,-124.03

> view matrix models #4,1,0,0,-48.255,0,1,0,-69.148,0,0,1,-125.25

> view matrix models #4,1,0,0,-55.403,0,1,0,-67.29,0,0,1,-128.78

> view matrix models #4,1,0,0,-50.885,0,1,0,-60.776,0,0,1,-130.77

> hide #!3 models

> fitmap #4 inMap #2

Fit molecule bovine ATP synthase monomer state 1 (combined)_6ZPO.cif (#4) to
map cryosparc_P32_J1682_006_volume_map.mrc (#2) using 81052 atoms  
average map value = 0.03724, steps = 172  
shifted from previous position = 15.8  
rotated from previous position = 9.3 degrees  
atoms outside contour = 20971, contour level = 0.018772  
  
Position of bovine ATP synthase monomer state 1 (combined)_6ZPO.cif (#4)
relative to cryosparc_P32_J1682_006_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98787572 -0.15520318 0.00367895 -15.11632249  
0.15487726 0.98688170 0.04558011 -100.86098404  
-0.01070486 -0.04445770 0.99895391 -115.13355234  
Axis -0.27857522 0.04450322 0.95938278  
Axis point 590.42119305 -342.27850959 0.00000000  
Rotation angle (degrees) 9.30001795  
Shift along axis -110.73475310  
  

> open "D:/liver_jxgsg/ATPase/ATP synthase model/bovine ATP synthase monomer
> state 3 (combined)_6ZQN.cif"

Summary of feedback from opening D:/liver_jxgsg/ATPase/ATP synthase
model/bovine ATP synthase monomer state 3 (combined)_6ZQN.cif  
---  
warnings | Atom H1 is not in the residue template for ALA /G:1  
Atom H1 is not in the residue template for VAL /I:1  
Atom H1 is not in the residue template for ASP /K:1  
Atom H1 is not in the residue template for ASP /L:1  
Atom H1 is not in the residue template for ASP /M:1  
4 messages similar to the above omitted  
Too many hydrogens missing from residue template(s) to warn about  
  
bovine ATP synthase monomer state 3 (combined)_6ZQN.cif title:  
bovine ATP synthase monomer state 3 (combined) [more info...]  
  
Chain information for bovine ATP synthase monomer state 3 (combined)_6ZQN.cif
#5  
---  
Chain | Description | UniProt  
8 | ATP synthase protein 8 | ATP8_BOVIN 1-66  
A B C | ATP synthase subunit alpha, mitochondrial | ATPA_BOVIN 1-510  
D E F | ATP synthase subunit beta, mitochondrial | ATPB_BOVIN -3-478  
G | ATP synthase subunit gamma, mitochondrial | ATPG_BOVIN 1-273  
H | ATP synthase subunit delta, mitochondrial | ATPD_BOVIN 1-146  
I | ATP synthase subunit epsilon, mitochondrial | ATP5E_BOVIN 1-50  
J | ATPase inhibitor, mitochondrial | ATIF1_BOVIN 1-60  
K L M N O P Q R | ATP synthase F(0) complex subunit C2, mitochondrial |
AT5G2_BOVIN 1-75  
S | ATP synthase subunit O, mitochondrial | ATPO_BOVIN 1-190  
a | ATP synthase subunit a | ATP6_BOVIN 1-226  
b | ATP synthase F(0) complex subunit B1, mitochondrial | AT5F1_BOVIN 1-214  
d | ATP synthase subunit d, mitochondrial | ATP5H_BOVIN 1-160  
e | ATP synthase subunit e, mitochondrial | ATP5I_BOVIN 1-70  
f | ATP synthase subunit f, mitochondrial | ATPK_BOVIN 1-87  
g | ATP synthase subunit g, mitochondrial | ATP5L_BOVIN 1-102  
h | ATP synthase-coupling factor 6, mitochondrial | ATP5J_BOVIN 1-76  
j | ATP synthase subunit ATP5MPL, mitochondrial | ATP68_BOVIN 1-60  
k | ATP synthase membrane subunit DAPIT, mitochondrial | ATPMD_BOVIN 1-57  
  
Non-standard residues in bovine ATP synthase monomer state 3
(combined)_6ZQN.cif #5  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
M3L — N-trimethyllysine  
MG — magnesium ion  
  

> hide #!4 models

> select subtract #4

Nothing selected  

> select add #5

81277 atoms, 81902 bonds, 34 pseudobonds, 5198 residues, 3 models selected  

> view matrix models #5,1,0,0,-20.129,0,1,0,8.9222,0,0,1,-106.3

> view matrix models #5,1,0,0,-75.886,0,1,0,-9.831,0,0,1,-131.71

> view matrix models #5,1,0,0,-60.458,0,1,0,-52.595,0,0,1,-132.12

> fitmap #5 inMap #2

Fit molecule bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5) to
map cryosparc_P32_J1682_006_volume_map.mrc (#2) using 81277 atoms  
average map value = 0.0359, steps = 136  
shifted from previous position = 6.94  
rotated from previous position = 9.74 degrees  
atoms outside contour = 22366, contour level = 0.018772  
  
Position of bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5)
relative to cryosparc_P32_J1682_006_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98614722 -0.16563051 0.00895537 -14.42856544  
0.16524007 0.98566471 0.03407039 -99.23828918  
-0.01447009 -0.03211863 0.99937931 -116.90950438  
Axis -0.19568760 0.06925727 0.97821766  
Axis point 527.41873997 -271.12532091 0.00000000  
Rotation angle (degrees) 9.73660548  
Shift along axis -118.41242390  
  

> fitmap #5 inMap #2

Fit molecule bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5) to
map cryosparc_P32_J1682_006_volume_map.mrc (#2) using 81277 atoms  
average map value = 0.0359, steps = 24  
shifted from previous position = 0.00329  
rotated from previous position = 0.00409 degrees  
atoms outside contour = 22375, contour level = 0.018772  
  
Position of bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5)
relative to cryosparc_P32_J1682_006_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98614583 -0.16564240 0.00888783 -14.39937946  
0.16525383 0.98566171 0.03409046 -99.25063656  
-0.01440722 -0.03214942 0.99937923 -116.91718130  
Axis -0.19582290 0.06886640 0.97821818  
Axis point 527.74433007 -271.02657491 0.00000000  
Rotation angle (degrees) 9.73736259  
Shift along axis -118.38581876  
  

> select clear

> select add #5

81277 atoms, 81902 bonds, 34 pseudobonds, 5198 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> fitmap #5 inMap #2

Fit molecule bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5) to
map cryosparc_P32_J1682_006_volume_map.mrc (#2) using 81277 atoms  
average map value = 0.0359, steps = 40  
shifted from previous position = 0.0129  
rotated from previous position = 0.00625 degrees  
atoms outside contour = 22367, contour level = 0.018772  
  
Position of bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5)
relative to cryosparc_P32_J1682_006_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98614715 -0.16562885 0.00899311 -14.45146873  
0.16523727 0.98566535 0.03406543 -99.23196388  
-0.01450641 -0.03210753 0.99937914 -116.90149853  
Axis -0.19564147 0.06947675 0.97821132  
Axis point 527.22053598 -271.22755071 0.00000000  
Rotation angle (degrees) 9.73653661  
Shift along axis -118.42137719  
  

> fitmap #5 inMap #2

Fit molecule bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5) to
map cryosparc_P32_J1682_006_volume_map.mrc (#2) using 81277 atoms  
average map value = 0.0359, steps = 28  
shifted from previous position = 0.013  
rotated from previous position = 0.00629 degrees  
atoms outside contour = 22370, contour level = 0.018772  
  
Position of bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5)
relative to cryosparc_P32_J1682_006_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98615428 -0.16559187 0.00889243 -14.41597684  
0.16520323 0.98567030 0.03408746 -99.23748972  
-0.01440961 -0.03214644 0.99937929 -116.91769244  
Axis -0.19586290 0.06890736 0.97820729  
Axis point 527.79551566 -271.21376506 0.00000000  
Rotation angle (degrees) 9.73446694  
Shift along axis -118.38437797  
  

> hide #!5 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 atoms

> show #!4 cartoons

> select clear

> hide #!4 models

> show #1 models

> volume #2 level 0.03145

> volume #2 level 0.04003

> color #2 #aa55ff80 models

> color #2 #ffff0080 models

> color #2 #aaffff80 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!2 models

> matchmaker #4/B to #1/C pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain C
(#1) with bovine ATP synthase monomer state 1 (combined)_6ZPO.cif, chain B
(#4), sequence alignment score = 2162.6  
RMSD between 354 pruned atom pairs is 1.054 angstroms; (across all 477 pairs:
2.180)  
  

> select clear

> color #4 white

> color #4 #d1d1d1ff

> select add #1

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> color sel bychain

> select clear

> hide #!4 models

> show #!4 models

> matchmaker #4/G to #1/G pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain G
(#1) with bovine ATP synthase monomer state 1 (combined)_6ZPO.cif, chain G
(#4), sequence alignment score = 1166  
RMSD between 221 pruned atom pairs is 1.052 angstroms; (across all 272 pairs:
2.267)  
  

> color #1 #aa55ffff

> matchmaker #4/S to #1/S pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain S
(#1) with bovine ATP synthase monomer state 1 (combined)_6ZPO.cif, chain S
(#4), sequence alignment score = 715.9  
RMSD between 146 pruned atom pairs is 1.196 angstroms; (across all 188 pairs:
1.766)  
  

> matchmaker #4/b to #1/b pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain b
(#1) with bovine ATP synthase monomer state 1 (combined)_6ZPO.cif, chain b
(#4), sequence alignment score = 977.2  
RMSD between 60 pruned atom pairs is 1.401 angstroms; (across all 209 pairs:
5.439)  
  

> open "D:/liver_normal/Normal_20251225 dataset/ATP
> synthase/cryosparc_P32_J1676_volume_map.mrc"

Opened cryosparc_P32_J1676_volume_map.mrc as #6, grid size 512,512,512, pixel
0.83, shown at level 0.0196, step 2, values float32  

> select add #6

2 models selected  

> transparency sel 50

> hide #!4 models

> select clear

> volume #6 step 1

> volume #6 level 0.01229

> volume #6 level 0.03113

> volume #6 level 0.007405

> fitmap #1 inMap #6

Fit molecule Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb (#1) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 49754 atoms  
average map value = 0.03708, steps = 60  
shifted from previous position = 0.706  
rotated from previous position = 0.453 degrees  
atoms outside contour = 3933, contour level = 0.0074048  
  
Position of Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb (#1)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99900640 -0.04423184 0.00545470 -22.30248270  
0.04423935 0.99902016 -0.00126451 -44.62338305  
-0.00539342 0.00150457 0.99998432 -37.40494868  
Axis 0.03105155 0.12164738 0.99208755  
Axis point 878.87654739 -493.61232755 0.00000000  
Rotation angle (degrees) 2.55557419  
Shift along axis -43.22982831  
  

> fitmap #1 inMap #6

Fit molecule Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb (#1) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 49754 atoms  
average map value = 0.03708, steps = 28  
shifted from previous position = 0.0175  
rotated from previous position = 0.00231 degrees  
atoms outside contour = 3934, contour level = 0.0074048  
  
Position of Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb (#1)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99900610 -0.04423541 0.00548170 -22.31392882  
0.04424312 0.99901996 -0.00129429 -44.60060903  
-0.00541907 0.00153553 0.99998414 -37.41089457  
Axis 0.03172719 0.12221636 0.99199624  
Axis point 877.62755137 -493.11988858 0.00000000  
Rotation angle (degrees) 2.55602197  
Shift along axis -43.27034927  
  

> select clear

> volume #6 level 0.05172

> select #1/F:465

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

63 atoms, 62 bonds, 7 residues, 1 model selected  

> select up

4503 atoms, 4561 bonds, 469 residues, 1 model selected  

> select up

4539 atoms, 4595 bonds, 475 residues, 1 model selected  

> select up

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> select down

4539 atoms, 4595 bonds, 475 residues, 1 model selected  

> save "D:/liver_normal/Normal_20251225 dataset/ATP synthase/subunit A.pdb"
> selectedOnly true relModel #6

> open "D:/liver_normal/Normal_20251225 dataset/ATP synthase/subunit A.pdb"

Summary of feedback from opening D:/liver_normal/Normal_20251225 dataset/ATP
synthase/subunit A.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR 8 6
PHE 8 21 1 16  
Start residue of secondary structure not found: HELIX 2 2 ILE 8 22 SER 8 30 1
9  
Start residue of secondary structure not found: HELIX 3 3 LYS A 175 ILE A 184
1 10  
Start residue of secondary structure not found: HELIX 4 4 GLN A 186 ARG A 188
1 3  
Start residue of secondary structure not found: HELIX 5 5 ARG A 210 ARG A 219
1 10  
332 messages similar to the above omitted  
  
Chain information for subunit A.pdb #7  
---  
Chain | Description  
F | No description available  
  

> hide #1 models

> select add #1

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> select subtract #1

Nothing selected  

> fitmap #7 inMap #6

Fit molecule subunit A.pdb (#7) to map cryosparc_P32_J1676_volume_map.mrc (#6)
using 4539 atoms  
average map value = 0.04416, steps = 80  
shifted from previous position = 1.99  
rotated from previous position = 4.51 degrees  
atoms outside contour = 2911, contour level = 0.051722  
  
Position of subunit A.pdb (#7) relative to cryosparc_P32_J1676_volume_map.mrc
(#6) coordinates:  
Matrix rotation and translation  
0.99816997 -0.01137469 0.05939124 -13.12038475  
0.01434864 0.99865164 -0.04989000 9.59113023  
-0.05874367 0.05065088 0.99698730 5.16796167  
Axis 0.63938968 0.75127889 0.16358746  
Axis point 77.65024875 0.00000000 219.66819310  
Rotation angle (degrees) 4.50939374  
Shift along axis -0.33801126  
  

> fitmap #7 inMap #6

Fit molecule subunit A.pdb (#7) to map cryosparc_P32_J1676_volume_map.mrc (#6)
using 4539 atoms  
average map value = 0.04416, steps = 28  
shifted from previous position = 0.0187  
rotated from previous position = 0.0232 degrees  
atoms outside contour = 2916, contour level = 0.051722  
  
Position of subunit A.pdb (#7) relative to cryosparc_P32_J1676_volume_map.mrc
(#6) coordinates:  
Matrix rotation and translation  
0.99814746 -0.01144103 0.05975578 -13.20889327  
0.01442378 0.99865878 -0.04972526 9.53443617  
-0.05910672 0.05049505 0.99697374 5.29742537  
Axis 0.63586919 0.75414851 0.16410484  
Axis point 79.30851570 0.00000000 219.89493111  
Rotation angle (degrees) 4.51992434  
Shift along axis -0.33941432  
  

> fitmap #7 inMap #6

Fit molecule subunit A.pdb (#7) to map cryosparc_P32_J1676_volume_map.mrc (#6)
using 4539 atoms  
average map value = 0.04416, steps = 48  
shifted from previous position = 0.000293  
rotated from previous position = 0.00628 degrees  
atoms outside contour = 2916, contour level = 0.051722  
  
Position of subunit A.pdb (#7) relative to cryosparc_P32_J1676_volume_map.mrc
(#6) coordinates:  
Matrix rotation and translation  
0.99815256 -0.01141467 0.05967556 -13.19613556  
0.01439757 0.99865560 -0.04979664 9.55961098  
-0.05902692 0.05056383 0.99697499 5.26102164  
Axis 0.63692025 0.75332458 0.16381291  
Axis point 78.80638784 0.00000000 219.92539923  
Rotation angle (degrees) 4.51877373  
Shift along axis -0.34157281  
  

> volume #6 level 0.03148

> volume #6 level 0.01683

> fitmap #7 inMap #6

Fit molecule subunit A.pdb (#7) to map cryosparc_P32_J1676_volume_map.mrc (#6)
using 4539 atoms  
average map value = 0.04416, steps = 44  
shifted from previous position = 0.00429  
rotated from previous position = 0.00522 degrees  
atoms outside contour = 390, contour level = 0.016827  
  
Position of subunit A.pdb (#7) relative to cryosparc_P32_J1676_volume_map.mrc
(#6) coordinates:  
Matrix rotation and translation  
0.99815745 -0.01139571 0.05959731 -13.17850563  
0.01437720 0.99865372 -0.04984019 9.57387352  
-0.05894911 0.05060520 0.99697749 5.23162186  
Axis 0.63774178 0.75266777 0.16363575  
Axis point 78.42447514 0.00000000 219.88589314  
Rotation angle (degrees) 4.51676679  
Shift along axis -0.34245722  
  

> fitmap #7 inMap #6

Fit molecule subunit A.pdb (#7) to map cryosparc_P32_J1676_volume_map.mrc (#6)
using 4539 atoms  
average map value = 0.04416, steps = 44  
shifted from previous position = 0.00826  
rotated from previous position = 0.00842 degrees  
atoms outside contour = 390, contour level = 0.016827  
  
Position of subunit A.pdb (#7) relative to cryosparc_P32_J1676_volume_map.mrc
(#6) coordinates:  
Matrix rotation and translation  
0.99816609 -0.01138788 0.05945403 -13.14040431  
0.01436396 0.99865233 -0.04987193 9.59121669  
-0.05880597 0.05063446 0.99698446 5.18777330  
Axis 0.63885898 0.75170811 0.16368908  
Axis point 77.88163651 0.00000000 219.81095353  
Rotation angle (degrees) 4.51159571  
Shift along axis -0.33588810  
  

> show #1 models

> hide #!6 models

> hide #7 models

> hide #1 models

> show #!6 models

> show #!2 models

> volume #6 level 0.02136

> volume #2 level 0.05026

> fitmap #2 inMap #6

Fit map cryosparc_P32_J1682_006_volume_map.mrc in map
cryosparc_P32_J1676_volume_map.mrc using 429383 points  
correlation = 0.9375, correlation about mean = 0.3247, overlap = 1421  
steps = 68, shift = 0.316, angle = 0.362 degrees  
  
Position of cryosparc_P32_J1682_006_volume_map.mrc (#2) relative to
cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99999849 0.00161121 0.00065575 -0.60409034  
-0.00161517 0.99998021 0.00608083 -1.03556982  
-0.00064593 -0.00608188 0.99998130 1.75054259  
Axis -0.96144028 0.10289551 -0.25503940  
Axis point 0.00000000 288.46640973 171.70992163  
Rotation angle (degrees) 0.36241262  
Shift along axis 0.02778398  
  

> fitmap #2 inMap #6

Fit map cryosparc_P32_J1682_006_volume_map.mrc in map
cryosparc_P32_J1676_volume_map.mrc using 429383 points  
correlation = 0.9375, correlation about mean = 0.3247, overlap = 1421  
steps = 44, shift = 0.00473, angle = 0.00297 degrees  
  
Position of cryosparc_P32_J1682_006_volume_map.mrc (#2) relative to
cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99999847 0.00160102 0.00070368 -0.61531419  
-0.00160528 0.99998012 0.00609768 -1.04518444  
-0.00069390 -0.00609880 0.99998116 1.76663323  
Axis -0.96125385 0.11014894 -0.25270189  
Axis point 0.00000000 290.37458305 172.89404064  
Rotation angle (degrees) 0.36348944  
Shift along axis 0.02991562  
  

> volume #6 level 0.03183

> volume #2 level 0.06866

> lighting full

[Repeated 1 time(s)]

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> color #6 #ffff7f80 models

> color #6 #aaffff80 models

> select add #2

2 models selected  

> transparency sel 0

> select clear

> hide #!6 models

> volume #2 level 0.05312

> color #2 #ffaaffff models

> show #!6 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> volume #6 level 0.01752

> hide #!3 models

> show #!4 models

> fitmap #4 inMap #6

Fit molecule bovine ATP synthase monomer state 1 (combined)_6ZPO.cif (#4) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 81052 atoms  
average map value = 0.03468, steps = 112  
shifted from previous position = 6.88  
rotated from previous position = 7.3 degrees  
atoms outside contour = 19145, contour level = 0.017524  
  
Position of bovine ATP synthase monomer state 1 (combined)_6ZPO.cif (#4)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98851412 -0.15109760 0.00305684 -16.63855869  
0.15077749 0.98739414 0.04815548 -101.20617530  
-0.01029449 -0.04714147 0.99883517 -115.03343689  
Axis -0.30077197 0.04213886 0.95276468  
Axis point 609.60705760 -373.15282528 0.00000000  
Rotation angle (degrees) 9.11523371  
Shift along axis -108.86009705  
  

> fitmap #4 inMap #6

Fit molecule bovine ATP synthase monomer state 1 (combined)_6ZPO.cif (#4) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 81052 atoms  
average map value = 0.03468, steps = 28  
shifted from previous position = 0.00656  
rotated from previous position = 0.00456 degrees  
atoms outside contour = 19145, contour level = 0.017524  
  
Position of bovine ATP synthase monomer state 1 (combined)_6ZPO.cif (#4)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98851567 -0.15108796 0.00303316 -16.63076749  
0.15076976 0.98739899 0.04808026 -101.17318247  
-0.01025929 -0.04707078 0.99883887 -115.06480092  
Axis -0.30037108 0.04196139 0.95289898  
Axis point 609.57130377 -372.89683799 0.00000000  
Rotation angle (degrees) 9.11340915  
Shift along axis -108.89509633  
  

> select clear

> hide #!4 models

> show #!3 models

> fitmap #3 inMap #6

Fit molecule bovine ATP synthase monomer state 2 (combined)_6ZQM.cif (#3) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 81155 atoms  
average map value = 0.03329, steps = 68  
shifted from previous position = 1.86  
rotated from previous position = 1.27 degrees  
atoms outside contour = 21181, contour level = 0.017524  
  
Position of bovine ATP synthase monomer state 2 (combined)_6ZQM.cif (#3)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98734448 -0.15711919 0.02155064 -21.60213011  
0.15598174 0.98664167 0.04698833 -101.65591771  
-0.02864553 -0.04303217 0.99866294 -111.54205657  
Axis -0.27309609 0.15228061 0.94985743  
Axis point 506.46281130 -379.09068507 0.00000000  
Rotation angle (degrees) 9.48646986  
Shift along axis -115.52981929  
  

> fitmap #3 inMap #6

Fit molecule bovine ATP synthase monomer state 2 (combined)_6ZQM.cif (#3) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 81155 atoms  
average map value = 0.03329, steps = 44  
shifted from previous position = 0.00747  
rotated from previous position = 0.00487 degrees  
atoms outside contour = 21178, contour level = 0.017524  
  
Position of bovine ATP synthase monomer state 2 (combined)_6ZQM.cif (#3)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98734265 -0.15711928 0.02163398 -21.63485378  
0.15597777 0.98664150 0.04700511 -101.66699718  
-0.02873039 -0.04303573 0.99866035 -111.51679603  
Axis -0.27313498 0.15277816 0.94976635  
Axis point 506.14977770 -379.32252844 0.00000000  
Rotation angle (degrees) 9.48726955  
Shift along axis -115.53816102  
  

> fitmap #3 inMap #6

Fit molecule bovine ATP synthase monomer state 2 (combined)_6ZQM.cif (#3) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 81155 atoms  
average map value = 0.03329, steps = 44  
shifted from previous position = 0.00343  
rotated from previous position = 0.00144 degrees  
atoms outside contour = 21179, contour level = 0.017524  
  
Position of bovine ATP synthase monomer state 2 (combined)_6ZQM.cif (#3)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98734039 -0.15713594 0.02161585 -21.62454838  
0.15599504 0.98663852 0.04701040 -101.66985941  
-0.02871405 -0.04304331 0.99866049 -111.51769590  
Axis -0.27314879 0.15265945 0.94978147  
Axis point 506.20734528 -379.22736215 0.00000000  
Rotation angle (degrees) 9.48815455  
Shift along axis -115.53158595  
  

> hide #!3 models

> show #!5 models

> fitmap #5 inMap #6

Fit molecule bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 81277 atoms  
average map value = 0.03354, steps = 64  
shifted from previous position = 1.1  
rotated from previous position = 0.532 degrees  
atoms outside contour = 20890, contour level = 0.017524  
  
Position of bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98470685 -0.17398927 0.00895340 -11.96826286  
0.17353768 0.98409926 0.03785913 -102.51092402  
-0.01539812 -0.03572639 0.99924297 -116.75528992  
Axis -0.20666275 0.06839053 0.97601908  
Axis point 520.62347771 -255.29322061 0.00000000  
Rotation angle (degrees) 10.25520064  
Shift along axis -118.49277319  
  

> fitmap #5 inMap #6

Fit molecule bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 81277 atoms  
average map value = 0.03354, steps = 24  
shifted from previous position = 0.0111  
rotated from previous position = 0.00434 degrees  
atoms outside contour = 20897, contour level = 0.017524  
  
Position of bovine ATP synthase monomer state 3 (combined)_6ZQN.cif (#5)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98471001 -0.17396790 0.00902006 -12.00735608  
0.17351351 0.98410243 0.03788750 -102.51985037  
-0.01546787 -0.03574310 0.99924130 -116.72749162  
Axis -0.20680432 0.06877858 0.97596182  
Axis point 520.45862282 -255.61794391 0.00000000  
Rotation angle (degrees) 10.25445057  
Shift along axis -118.48957248  
  

> select clear

[Repeated 1 time(s)]

> hide #!6 models

> show #!4 models

> hide #!5 models

> show #!6 models

> fitmap #4 inMap #6

Fit molecule bovine ATP synthase monomer state 1 (combined)_6ZPO.cif (#4) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 81052 atoms  
average map value = 0.03468, steps = 28  
shifted from previous position = 0.0058  
rotated from previous position = 0.00264 degrees  
atoms outside contour = 19145, contour level = 0.017524  
  
Position of bovine ATP synthase monomer state 1 (combined)_6ZPO.cif (#4)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98851417 -0.15109739 0.00305057 -16.63688170  
0.15077792 0.98739572 0.04812173 -101.19377581  
-0.01028319 -0.04710905 0.99883682 -115.04572508  
Axis -0.30058252 0.04208614 0.95282680  
Axis point 609.57018870 -373.03587971 0.00000000  
Rotation angle (degrees) 9.11464101  
Shift along axis -108.87674888  
  

> volume #6 level 0.01159

> volume #6 level 0.004962

> volume #6 level 0.01543

> fitmap #4 inMap #6

Fit molecule bovine ATP synthase monomer state 1 (combined)_6ZPO.cif (#4) to
map cryosparc_P32_J1676_volume_map.mrc (#6) using 81052 atoms  
average map value = 0.03468, steps = 36  
shifted from previous position = 0.00269  
rotated from previous position = 0.00144 degrees  
atoms outside contour = 16546, contour level = 0.015431  
  
Position of bovine ATP synthase monomer state 1 (combined)_6ZPO.cif (#4)
relative to cryosparc_P32_J1676_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98851440 -0.15109581 0.00305478 -16.63917976  
0.15077590 0.98739483 0.04814643 -101.20419796  
-0.01029100 -0.04713285 0.99883562 -115.03609356  
Axis -0.30072453 0.04212252 0.95278038  
Axis point 609.61465828 -373.13299720 0.00000000  
Rotation angle (degrees) 9.11497910  
Shift along axis -108.86329970  
  

> save "D:/liver_normal/Normal_20251225 dataset/comparison.cxs" includeMaps
> true

——— End of log from Wed Dec 3 09:45:11 2025 ———

opened ChimeraX session  

> show #1 models

> hide #!6 models

> show #!2 models

> hide #!4 models

> show #!4 models

> show #!3 models

> show #!5 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> select add #1

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> color sel bychain

> select clear

> select add #1

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> show sel surfaces

> select clear

> open "F:/mouse liver/normal 1/Mus_normal_Atp_synthase-coot-1004.pdb"

Summary of feedback from opening F:/mouse liver/normal
1/Mus_normal_Atp_synthase-coot-1004.pdb  
---  
warning | PDB SEQRES record for chain S is incomplete. Ignoring input sequence
records as basis for sequence.  
  
Chain information for Mus_normal_Atp_synthase-coot-1004.pdb #8  
---  
Chain | Description | UniProt  
8 | No description available | ATP8_BOVIN 1-66  
A | No description available | ATPA_MOUSE 1-553  
B C | No description available |  
D E F | No description available |  
G | No description available |  
H | No description available |  
I | No description available |  
K M N O Q R | No description available |  
L P | No description available |  
S | No description available |  
a | No description available |  
b | No description available |  
d | No description available |  
e | No description available | ATP5I_MOUSE 1-71  
f | No description available |  
g | No description available |  
h | No description available |  
j | No description available | ATP68_MOUSE 1-58  
k | No description available | ATPMK_MOUSE 1-58  
  

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> hide sel atoms

> show sel surfaces

> select clear

> matchmaker #8/A to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain A
(#1) with Mus_normal_Atp_synthase-coot-1004.pdb, chain A (#8), sequence
alignment score = 2283.5  
RMSD between 483 pruned atom pairs is 1.003 angstroms; (across all 503 pairs:
1.107)  
  

> color #8 white

> color #8 #d6d6d6ff

> color #8 #bebebeff

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> select add #1

99500 atoms, 100785 bonds, 10472 residues, 30 models selected  

> hide sel surfaces

> show sel cartoons

[Repeated 1 time(s)]

> select clear

> select #1/A,B,C

13565 atoms, 13713 bonds, 1512 residues, 1 model selected  

> color (#!1 & sel) red

> select clear

> select #1/D,E,F

13631 atoms, 13801 bonds, 1420 residues, 1 model selected  

> color (#!1 & sel) yellow

> select clear

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!1 models

> hide #!8 models

> show #!8 models

> show #!1 models

> hide #!3 models

> matchmaker #8/S to #1/S pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain S
(#1) with Mus_normal_Atp_synthase-coot-1004.pdb, chain S (#8), sequence
alignment score = 883.1  
RMSD between 169 pruned atom pairs is 1.216 angstroms; (across all 188 pairs:
1.389)  
  

> save "F:/mouse liver/comparison.cxs" includeMaps true

——— End of log from Thu Dec 4 17:34:48 2025 ———

opened ChimeraX session  

> hide #!1 models

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> color sel bychain

> select clear

> show #!1 models

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> color #1 white

> select add #1

99500 atoms, 100785 bonds, 10472 residues, 30 models selected  

> color (#!1,8 & sel) light gray

> select clear

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> color sel bychain

> select clear

> matchmaker #8/S to #1/S pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain S
(#1) with Mus_normal_Atp_synthase-coot-1004.pdb, chain S (#8), sequence
alignment score = 883.1  
RMSD between 169 pruned atom pairs is 1.216 angstroms; (across all 188 pairs:
1.389)  
  

> select clear

> select add #1

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> select add #8

99500 atoms, 100785 bonds, 10472 residues, 30 models selected  

> show sel surfaces

> hide sel surfaces

> select clear

> select #8/A,B,C

13565 atoms, 13713 bonds, 1512 residues, 1 model selected  

> color (#!8 & sel) yellow

> select clear

> select #8/D,E,F

13623 atoms, 13792 bonds, 1420 residues, 1 model selected  

> color (#!8 & sel) red

> select clear

> lighting soft

> graphics silhouettes true

> save "F:/mouse liver/normal+ADP compare to APAP.png" width 2010 height 1213
> supersample 4 transparentBackground true

> ui tool show Distances

> show #!1,8 atoms

> select clear

> select #8/S:76@CB

1 atom, 1 residue, 1 model selected  

> select clear

> ui tool show "Side View"

> select clear

> lighting depthCue true depthCueStart 0.1 depthCueEnd 1.0

> lighting depthCue true depthCueStart 0.8 depthCueEnd 1.0

> select clear

> select #8/S:76@CG

1 atom, 1 residue, 1 model selected  

> select add #8/M:73@CE2

2 atoms, 2 residues, 2 models selected  

> distance #8/S:76@CG #8/M:73@CE2

Distance between Mus_normal_Atp_synthase-coot-1004.pdb #8/S GLU 76 CG and /M
PHE 73 CE2: 202.5  

> select clear

> select add #1/S:76@OE2

1 atom, 1 residue, 1 model selected  

> select add #1/M:73@CD2

2 atoms, 2 residues, 2 models selected  

> distance #1/S:76@OE2 #1/M:73@CD2

Distance between Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb #1/S
GLU 76 OE2 and /M PHE 73 CD2: 211.4  

> select #8/S:128@CG

1 atom, 1 residue, 1 model selected  

> select add #8/k:50@CB

2 atoms, 2 residues, 2 models selected  

> distance #8/S:128@CG #8/k:50@CB

Distance between Mus_normal_Atp_synthase-coot-1004.pdb #8/S ASP 128 CG and /k
LYS 50 CB: 211.8  

> hide #!9 models

> hide #9.1 models

> hide #!1 models

> hide sel atoms

[Repeated 1 time(s)]

> select add #8

49746 atoms, 50388 bonds, 2 pseudobonds, 5236 residues, 4 models selected  

> select subtract #8

28 models selected  

> select add #8

49746 atoms, 50388 bonds, 2 pseudobonds, 5236 residues, 2 models selected  

> hide sel atoms

> show sel surfaces

> close #9

> select clear

> select #8/G,H,I,J,K,L,M,N,O,P,K,R,S,T,a,b,c,d,e,f,g,h,i,j,k

21484 atoms, 21792 bonds, 2191 residues, 1 model selected  

> transparency sel 50

> select clear

> select #8/G,H,I,J,K,L,M,N,O,P,K,R,S,T,a,b,c,d,e,f,g,h,i,j,k,8

21858 atoms, 22174 bonds, 2229 residues, 1 model selected  

> transparency sel 0

> transparency sel 50

> select clear

[Repeated 2 time(s)]

> save "F:/mouse liver/normal+ADP_surface.png" width 2010 height 1213
> supersample 4 transparentBackground true

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> hide sel surfaces

> select clear

> show #!1 models

> select add #1

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> morph #1,2 frames 40

Require at least 2 structures for morph  

> morph #8,1 frames 40

Computed 41 frame morph #9  

> coordset #9 1,41

> morph #1,8 frames 40

Computed 41 frame morph #10  

> coordset #10 1,41

> hide #9 models

> show #!8 models

> movie record

> movie encode F:\mouse liver\No substrate to +ADP.mp4

Expected ',' or a keyword  

> movie encode F:\mouse liver\No substrate to ADP added.mp4

Expected ',' or a keyword  

> movie encode F:\mouse liver\No-substrate-to-ADP-added.mp4

Expected ',' or a keyword  

> save "F:/mouse liver/normal+ADP_surface-test.png" width 1615 height 975
> supersample 3

> movie encode F:/mouse liver/No-substrate-to-ADP-added.mp4

Expected ',' or a keyword  

> movie encode "F:/mouse liver/No-substrate-to-ADP-added.mp4"

Movie saved to F:/mouse liver/No-substrate-to-ADP-added.mp4  
  

> movie record

> morph #1,8 frames 20

Computed 21 frame morph #11  

> coordset #11 1,21

> hide #10 models

> show #10 models

> show #9 models

> hide #9 models

> close #9

> close #10

> close #11

> movie encode "F:/mouse liver/No-substrate-to-ADP-added.mp4"

Movie saved to F:/mouse liver/No-substrate-to-ADP-added.mp4  
  

> show #!1 models

> show #!8 models

> movie record

> morph #1,8 frames 20

Computed 21 frame morph #9  

> coordset #9 1,21

> show #!8 models

> movie encode "F:/mouse liver/No-substrate-to-ADP-added.mp4"

Movie saved to F:/mouse liver/No-substrate-to-ADP-added.mp4  
  

> movie record

> hide #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

79676 atoms, 80733 bonds, 8374 residues, 2 models selected  

> hide sel & #!8 cartoons

> hide #9 models

> show #9 models

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> hide sel & #9#!8 atoms

> hide sel & #9#!8 cartoons

> movie encode "F:/mouse liver/No-substrate-to-ADP-added.mp4"

Movie saved to F:/mouse liver/No-substrate-to-ADP-added.mp4  
  

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> show sel & #9#!8 cartoons

> select clear

> movie record

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> hide sel & #9#!8 cartoons

[Repeated 1 time(s)]

> view

> movie encode "F:/mouse liver/No-substrate-to-ADP-added.mp4"

Movie saved to F:/mouse liver/No-substrate-to-ADP-added.mp4  
  

> close #9

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

79676 atoms, 80733 bonds, 8374 residues, 2 models selected  

> show sel & #!8 cartoons

> select clear

> show #!1 models

> morph #1,8 frames 40

Computed 41 frame morph #9  

> coordset #9 1,41

> show #!8 models

> movie record

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> hide sel & #9#!8 cartoons

> view

> movie encode "F:/mouse liver/No-substrate-to-ADP-added.mp4"

Movie saved to F:/mouse liver/No-substrate-to-ADP-added.mp4  
  

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> show sel & #9#!8 cartoons

> select clear

> movie record

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> hide sel & #9#!8 cartoons

> view

> movie encode "F:/mouse liver/No-substrate-to-ADP-added-2.mp4"

Movie saved to F:/mouse liver/No-substrate-to-ADP-added-2.mp4  
  

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> show sel & #9#!8 cartoons

> select clear

> movie record

> view name p1

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> hide sel & #9#!8 cartoons

> zone 0.75

Expected an atoms specifier or a keyword  

> Zone 0.75

Unknown command: Zone 0.75  

> Zone in 0.75

Unknown command: Zone in 0.75  

> zone in 0.75

Expected an atoms specifier or a keyword  

> movie encode "F:/mouse liver/No-substrate-to-ADP-added.mp4"

Movie saved to F:/mouse liver/No-substrate-to-ADP-added.mp4  
  

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> show sel & #9#!8 cartoons

> select clear

> movie record

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> hide sel & #9#!8 cartoons

> movie encode "F:/mouse liver/No-substrate-to-ADP-added.mp4"

Movie saved to F:/mouse liver/No-substrate-to-ADP-added.mp4  
  

> select #1/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #8/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

118687 atoms, 120288 bonds, 12527 residues, 3 models selected  

> show sel & #9#!8 cartoons

> select clear

> hide #9 models

> graphics silhouettes false

> graphics silhouettes true

> select clear

> lighting soft

[Repeated 1 time(s)]

> show #!3 models

> matchmaker #8/S to #3/S pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain S
(#3) with Mus_normal_Atp_synthase-coot-1004.pdb, chain S (#8), sequence
alignment score = 737.5  
RMSD between 149 pruned atom pairs is 1.081 angstroms; (across all 188 pairs:
1.684)  
  

> select #8/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,,a,b,c,d,e,f,g,h,i,j,k,8
> #9/A,B,C,D,E,F,S,a,b,c,d,e,f,g,h,i,j,k,8

Expected an objects specifier or a keyword  

> select #8/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,,a,b,c,d,e,f,g,h,i,j,k,8

Expected an objects specifier or a keyword  

> select #8/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,a,b,c,d,e,f,g,h,i,j,k,8

46528 atoms, 47134 bonds, 4898 residues, 1 model selected  

> hide sel cartoons

> select #3/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,a,b,c,d,e,f,g,h,i,j,k,8

75994 atoms, 76582 bonds, 34 pseudobonds, 4852 residues, 3 models selected  

> hide sel cartoons

> select #3/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

78151 atoms, 78757 bonds, 34 pseudobonds, 5000 residues, 3 models selected  

> hide sel cartoons

> select #8/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

47928 atoms, 48552 bonds, 5048 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> show #!4 models

> select add #4

128980 atoms, 130228 bonds, 32 pseudobonds, 10231 residues, 31 models selected  

> color #4 white

> select add #3

210135 atoms, 212006 bonds, 66 pseudobonds, 15419 residues, 34 models selected  

> select subtract #4

129083 atoms, 130330 bonds, 34 pseudobonds, 10236 residues, 31 models selected  

> color (#!3,8 & sel) dark gray

> select clear

> select add #4

81052 atoms, 81676 bonds, 32 pseudobonds, 5183 residues, 3 models selected  

> color (#!4 & sel) white

> select clear

> select add #3

81155 atoms, 81778 bonds, 34 pseudobonds, 5188 residues, 3 models selected  

> color (#!3 & sel) dark gray

> select clear

> show #!5 models

> select add #5

81277 atoms, 81902 bonds, 34 pseudobonds, 5198 residues, 3 models selected  

> color (#!5 & sel) dim gray

> select clear

> select add #5

81277 atoms, 81902 bonds, 34 pseudobonds, 5198 residues, 3 models selected  

> color (#!5 & sel) gray

> select clear

> select add #5

81277 atoms, 81902 bonds, 34 pseudobonds, 5198 residues, 3 models selected  

> transparency #8.1-28 0

> transparency #5 20

> select clear

> transparency #5 20 cartoons

> select clear

> select add #3

81155 atoms, 81778 bonds, 34 pseudobonds, 5188 residues, 3 models selected  

> select subtract #3

Nothing selected  

> select add #3

81155 atoms, 81778 bonds, 34 pseudobonds, 5188 residues, 3 models selected  

> show sel cartoons

> select clear

> transparency #8 0 cartoons

> select #8/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

47928 atoms, 48552 bonds, 5048 residues, 1 model selected  

> hide sel cartoons

> select #3/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

78151 atoms, 78757 bonds, 34 pseudobonds, 5000 residues, 3 models selected  

> hide sel cartoons

> select #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

78048 atoms, 78655 bonds, 32 pseudobonds, 4995 residues, 3 models selected  

> hide sel cartoons

> select #5/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

78288 atoms, 78896 bonds, 34 pseudobonds, 5011 residues, 3 models selected  

> hide sel cartoons

> select clear

> matchmaker #4/S to #3/S pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain S
(#3) with bovine ATP synthase monomer state 1 (combined)_6ZPO.cif, chain S
(#4), sequence alignment score = 905.9  
RMSD between 188 pruned atom pairs is 0.738 angstroms; (across all 188 pairs:
0.738)  
  

> matchmaker #5/S to #3/S pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain S
(#3) with bovine ATP synthase monomer state 3 (combined)_6ZQN.cif, chain S
(#5), sequence alignment score = 894.5  
RMSD between 183 pruned atom pairs is 0.638 angstroms; (across all 187 pairs:
0.724)  
  

> matchmaker #5/S to #3/S pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain S
(#3) with bovine ATP synthase monomer state 3 (combined)_6ZQN.cif, chain S
(#5), sequence alignment score = 894.5  
RMSD between 183 pruned atom pairs is 0.638 angstroms; (across all 187 pairs:
0.724)  
  

> select clear

> show #!1 models

> hide #!1 models

> transparency #3 20 cartoons

> transparency #4 20 cartoons

> transparency #5 20 cartoons

> select clear

[Repeated 1 time(s)]

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> transparency #5 40 cartoons

> select clear

> select #8/S:53

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

25 atoms, 24 bonds, 3 residues, 2 models selected  

> select up

1818 atoms, 1836 bonds, 188 residues, 2 models selected  

> select down

25 atoms, 24 bonds, 3 residues, 2 models selected  

> select add #8/S:50

36 atoms, 34 bonds, 4 residues, 2 models selected  

> select up

53 atoms, 53 bonds, 6 residues, 2 models selected  

> select add #8/S:56

63 atoms, 62 bonds, 7 residues, 2 models selected  

> select up

147 atoms, 149 bonds, 15 residues, 2 models selected  

> graphics silhouettes true

> graphics selection silhouettes color red width 3

Expected a keyword  

> graphics selection color red width 3

> graphics selection black red width 3

Expected a keyword  

> graphics selection black width 3

Expected a keyword  

> graphics selection color black width 3

> graphics selection color red width 3

> save "F:/mouse liver/OSCP_normal_compare_state123.png" width 2010 height
> 1213 supersample 4 transparentBackground true

> select #5/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

78288 atoms, 78896 bonds, 34 pseudobonds, 5011 residues, 3 models selected  

> show sel cartoons

> select clear

> select #5/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

78288 atoms, 78896 bonds, 34 pseudobonds, 5011 residues, 3 models selected  

> select #3/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

78151 atoms, 78757 bonds, 34 pseudobonds, 5000 residues, 3 models selected  

> show sel cartoons

> select #3/G:18

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #4/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

78048 atoms, 78655 bonds, 32 pseudobonds, 4995 residues, 3 models selected  

> show sel cartoons

> select clear

> matchmaker #4/B to #3/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain A
(#3) with bovine ATP synthase monomer state 1 (combined)_6ZPO.cif, chain B
(#4), sequence alignment score = 2381  
RMSD between 434 pruned atom pairs is 0.650 angstroms; (across all 477 pairs:
1.060)  
  

> select #5/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

78288 atoms, 78896 bonds, 34 pseudobonds, 5011 residues, 3 models selected  

> show sel cartoons

[Repeated 1 time(s)]

> select clear

> matchmaker #5/C to #3/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain A
(#3) with bovine ATP synthase monomer state 3 (combined)_6ZQN.cif, chain C
(#5), sequence alignment score = 2288.6  
RMSD between 480 pruned atom pairs is 0.646 angstroms; (across all 483 pairs:
0.703)  
  

> select #8/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

47928 atoms, 48552 bonds, 5048 residues, 1 model selected  

> show sel cartoons

> select clear

> hide #!5 models

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> color sel bychain

> select clear

> matchmaker #8/C to #3/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain A
(#3) with Mus_normal_Atp_synthase-coot-1004.pdb, chain C (#8), sequence
alignment score = 2194.4  
RMSD between 422 pruned atom pairs is 0.928 angstroms; (across all 486 pairs:
1.981)  
  

> matchmaker #8/A,B,C

Missing required "to" argument  

> select #8/A,B,C

13565 atoms, 13713 bonds, 1512 residues, 1 model selected  

> color (#!8 & sel) yellow

> select #8/D,E,F

13623 atoms, 13792 bonds, 1420 residues, 1 model selected  

> color (#!8 & sel) red

> select clear

> select #8/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8

47928 atoms, 48552 bonds, 5048 residues, 1 model selected  

> select #8/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8,S

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> select #8/A,B,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8,S

44998 atoms, 45591 bonds, 4745 residues, 1 model selected  

> hide sel cartoons

> select #3/A,B,C, D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8,S

81155 atoms, 81778 bonds, 34 pseudobonds, 5188 residues, 3 models selected  

> select #3/B,C, D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8,S

73589 atoms, 74163 bonds, 28 pseudobonds, 4697 residues, 3 models selected  

> hide sel cartoons

> select #4/A,C, D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8,S

73613 atoms, 74191 bonds, 25 pseudobonds, 4701 residues, 3 models selected  

> hide sel cartoons

> select clear

> show #!5 models

> select #4/A,B, D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8,S

73307 atoms, 73884 bonds, 25 pseudobonds, 4680 residues, 3 models selected  

> hide sel cartoons

> select #4/C

7745 atoms, 7792 bonds, 7 pseudobonds, 503 residues, 3 models selected  

> show sel cartoons

> hide sel cartoons

> select #4/B

7439 atoms, 7485 bonds, 7 pseudobonds, 482 residues, 3 models selected  

> show sel cartoons

> select #5/A,B, D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,a,b,c,d,e,f,g,h,i,j,k,8,S

73742 atoms, 74319 bonds, 27 pseudobonds, 4710 residues, 3 models selected  

> hide sel cartoons

> select clear

> hide #!8 models

> show #!8 models

> select #8/C:418

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

102 atoms, 101 bonds, 11 residues, 2 models selected  

> select up

4701 atoms, 4752 bonds, 486 residues, 2 models selected  

> select down

102 atoms, 101 bonds, 11 residues, 2 models selected  

> select add #8/C:399

113 atoms, 111 bonds, 12 residues, 2 models selected  

> select up

225 atoms, 225 bonds, 23 residues, 2 models selected  

> select down

113 atoms, 111 bonds, 12 residues, 2 models selected  

> select add #8/C:411

123 atoms, 120 bonds, 13 residues, 2 models selected  

> select up

293 atoms, 295 bonds, 31 residues, 2 models selected  

> select subtract #8/C:392

283 atoms, 285 bonds, 30 residues, 2 models selected  

> select subtract #8/C:393

272 atoms, 274 bonds, 29 residues, 2 models selected  

> select subtract #8/C:394

262 atoms, 264 bonds, 28 residues, 2 models selected  

> select subtract #8/C:395

255 atoms, 257 bonds, 27 residues, 2 models selected  

> select add #8/C:395

262 atoms, 263 bonds, 28 residues, 2 models selected  

> select add #8/C:296

269 atoms, 269 bonds, 29 residues, 2 models selected  

> select add #8/C:295

277 atoms, 277 bonds, 30 residues, 2 models selected  

> select add #8/C:294

291 atoms, 291 bonds, 31 residues, 2 models selected  

> select add #8/C:293

298 atoms, 297 bonds, 32 residues, 2 models selected  

> select add #8/C:291

311 atoms, 309 bonds, 33 residues, 2 models selected  

> select add #8/C:292

322 atoms, 319 bonds, 34 residues, 2 models selected  

> select add #8/C:290

329 atoms, 325 bonds, 35 residues, 2 models selected  

> select add #8/C:289

337 atoms, 333 bonds, 36 residues, 2 models selected  

> select add #8/C:288

345 atoms, 341 bonds, 37 residues, 2 models selected  

> select add #8/C:287

358 atoms, 353 bonds, 38 residues, 2 models selected  

> select add #3/A:286

382 atoms, 376 bonds, 39 residues, 3 models selected  

> select subtract #3/A:286

358 atoms, 353 bonds, 38 residues, 2 models selected  

> select add #8/C:286

371 atoms, 365 bonds, 39 residues, 2 models selected  

> select add #8/C:285

381 atoms, 374 bonds, 40 residues, 2 models selected  

> save "F:/mouse liver/alpha_normal_compare_state123.png" width 2010 height
> 1213 supersample 4 transparentBackground true

> show #!1 models

> select #5/D

7207 atoms, 7262 bonds, 7 pseudobonds, 475 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select #5/F

7175 atoms, 7229 bonds, 7 pseudobonds, 473 residues, 2 models selected  

> show sel cartoons

> select #3/F

7175 atoms, 7229 bonds, 7 pseudobonds, 473 residues, 2 models selected  

> show sel cartoons

> select #3/E

7171 atoms, 7230 bonds, 468 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/D

7207 atoms, 7262 bonds, 6 pseudobonds, 475 residues, 2 models selected  

> show sel cartoons

> select clear

> select #4/D

7207 atoms, 7262 bonds, 6 pseudobonds, 475 residues, 2 models selected  

> show sel cartoons

> select #4/E

7171 atoms, 7230 bonds, 468 residues, 1 model selected  

> show sel cartoons

> select #4/D

7207 atoms, 7262 bonds, 6 pseudobonds, 475 residues, 2 models selected  

> hide sel cartoons

> hide #!1 models

> select #3/F

7175 atoms, 7229 bonds, 7 pseudobonds, 473 residues, 2 models selected  

> hide sel cartoons

> select clear

> select #8/F

4539 atoms, 4594 bonds, 475 residues, 1 model selected  

> show sel cartoons

> select clear

[Repeated 1 time(s)]

> lighting flat

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> save "F:/mouse liver/alpha+beta_normal_compare_state123.png" width 2010
> height 1213 supersample 4 transparentBackground true

> matchmaker #8/F to #3/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain D
(#3) with Mus_normal_Atp_synthase-coot-1004.pdb, chain F (#8), sequence
alignment score = 2035.9  
RMSD between 189 pruned atom pairs is 0.988 angstroms; (across all 467 pairs:
3.636)  
  

> matchmaker #4/E to #3/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain D
(#3) with bovine ATP synthase monomer state 1 (combined)_6ZPO.cif, chain E
(#4), sequence alignment score = 2235.1  
RMSD between 148 pruned atom pairs is 0.558 angstroms; (across all 467 pairs:
5.663)  
  

> matchmaker #5/F to #3/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain D
(#3) with bovine ATP synthase monomer state 3 (combined)_6ZQN.cif, chain F
(#5), sequence alignment score = 2184.7  
RMSD between 459 pruned atom pairs is 0.608 angstroms; (across all 467 pairs:
0.692)  
  

> select #4/E

7171 atoms, 7230 bonds, 468 residues, 1 model selected  

> hide sel surfaces

> show sel surfaces

> select clear

> hide #!3-5,8 surfaces

> select #8/F

4539 atoms, 4594 bonds, 475 residues, 1 model selected  

> show sel surfaces

> select clear

> hide #!3-5,8 surfaces

> select #8/C:493

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

165 atoms, 165 bonds, 17 residues, 2 models selected  

> select up

4701 atoms, 4752 bonds, 486 residues, 2 models selected  

> select up

4748 atoms, 4797 bonds, 491 residues, 2 models selected  

> save "F:/mouse liver/alpha+beta_normal_compare_state123_align beta.png"
> width 1615 height 975 supersample 3

> select #8/C #3/A #4/B #5/C

27288 atoms, 27480 bonds, 20 pseudobonds, 1952 residues, 9 models selected  

> hide sel cartoons

> select clear

> graphics selection color black width 3

> select #8/F:403

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

144 atoms, 143 bonds, 14 residues, 2 models selected  

> select up

4503 atoms, 4561 bonds, 469 residues, 2 models selected  

> select up

4539 atoms, 4594 bonds, 475 residues, 2 models selected  

> graphics selection color green width 3

> select clear

> select #8/F:277

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

137 atoms, 139 bonds, 15 residues, 2 models selected  

> select up

4503 atoms, 4561 bonds, 469 residues, 2 models selected  

> select down

137 atoms, 139 bonds, 15 residues, 2 models selected  

> graphics selection color magenta width 3

> graphics selection color blue width 3

> select add #8/F:272

147 atoms, 148 bonds, 16 residues, 2 models selected  

> select up

164 atoms, 166 bonds, 18 residues, 2 models selected  

> select up

4503 atoms, 4561 bonds, 469 residues, 2 models selected  

> select down

164 atoms, 166 bonds, 18 residues, 2 models selected  

> select add #8/F:266

172 atoms, 173 bonds, 19 residues, 2 models selected  

> select up

283 atoms, 287 bonds, 30 residues, 2 models selected  

> select add #3/D:259

303 atoms, 307 bonds, 31 residues, 3 models selected  

> select subtract #8/F:259

290 atoms, 292 bonds, 30 residues, 3 models selected  

> select subtract #8/F:260

277 atoms, 279 bonds, 29 residues, 3 models selected  

> select subtract #8/F:258

267 atoms, 270 bonds, 28 residues, 3 models selected  

> select subtract #3/D:259

247 atoms, 250 bonds, 27 residues, 2 models selected  

> select subtract #8/F:261

234 atoms, 236 bonds, 26 residues, 2 models selected  

> select subtract #8/F:262

225 atoms, 227 bonds, 25 residues, 2 models selected  

> select add #8/F:288

235 atoms, 236 bonds, 26 residues, 2 models selected  

> select add #8/F:51

246 atoms, 246 bonds, 27 residues, 2 models selected  

> select up

611 atoms, 615 bonds, 64 residues, 2 models selected  

> select down

246 atoms, 246 bonds, 27 residues, 2 models selected  

> select add #8/F:52

258 atoms, 258 bonds, 28 residues, 2 models selected  

> select add #8/F:53

268 atoms, 267 bonds, 29 residues, 2 models selected  

> select add #8/F:54

275 atoms, 273 bonds, 30 residues, 2 models selected  

> select add #8/F:55

286 atoms, 283 bonds, 31 residues, 2 models selected  

> select add #8/F:56

294 atoms, 290 bonds, 32 residues, 2 models selected  

> select add #8/F:56-81

525 atoms, 522 bonds, 57 residues, 2 models selected  

> select add #8/F:7-81

930 atoms, 935 bonds, 101 residues, 2 models selected  

> hide #!8 models

> show #!8 models

> select add #8/F:403

939 atoms, 943 bonds, 102 residues, 2 models selected  

> select add #8/F:383-403

1134 atoms, 1138 bonds, 122 residues, 2 models selected  

> save "F:/mouse liver/beta_normal_compare_state123.png" width 2010 height
> 1213 supersample 4 transparentBackground true

> select #8/C #3/A #4/B #5/C

27288 atoms, 27480 bonds, 20 pseudobonds, 1952 residues, 9 models selected  

> select #8/F #3/D #4/E #5/F

26092 atoms, 26315 bonds, 13 pseudobonds, 1891 residues, 6 models selected  

> select #8/H,I,J

1696 atoms, 1713 bonds, 178 residues, 1 model selected  

> show sel cartoons

> select #8/GH,I

463 atoms, 468 bonds, 47 residues, 1 model selected  

> select #8/G,H,I

4356 atoms, 4398 bonds, 451 residues, 1 model selected  

> show sel cartoons

> select clear

> select #3/G,H,I

7021 atoms, 7064 bonds, 451 residues, 1 model selected  

> show sel cartoons

> select clear

> select #4/G,H,I

7021 atoms, 7064 bonds, 451 residues, 1 model selected  

> show sel cartoons

> select clear

> select #5/G,H,I

7004 atoms, 7047 bonds, 450 residues, 1 model selected  

> show sel cartoons

> select clear

> transparency #5 20 cartoons

> select clear

> matchmaker #5/G to #3/G pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain G
(#3) with bovine ATP synthase monomer state 3 (combined)_6ZQN.cif, chain G
(#5), sequence alignment score = 1322.5  
RMSD between 271 pruned atom pairs is 0.447 angstroms; (across all 272 pairs:
0.466)  
  

> matchmaker #4/G to #3/G pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain G
(#3) with bovine ATP synthase monomer state 1 (combined)_6ZPO.cif, chain G
(#4), sequence alignment score = 1339.9  
RMSD between 272 pruned atom pairs is 0.511 angstroms; (across all 272 pairs:
0.511)  
  

> matchmaker #8/G to #3/G pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain G
(#3) with Mus_normal_Atp_synthase-coot-1004.pdb, chain G (#8), sequence
alignment score = 1167.8  
RMSD between 237 pruned atom pairs is 0.844 angstroms; (across all 272 pairs:
1.807)  
  

> select #8/F #3/D #4/E #5/F

26092 atoms, 26315 bonds, 13 pseudobonds, 1891 residues, 6 models selected  

> show sel surfaces

> select clear

> select #4/E:475@HB2

1 atom, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 2 models selected  

> select up

209 atoms, 209 bonds, 14 residues, 2 models selected  

> select up

7132 atoms, 7189 bonds, 467 residues, 2 models selected  

> transparency sel 10 surfaces

> select clear

> lighting soft

> graphics silhouettes false

> lighting shadows true intensity 0.5

> graphics silhouettes true

> select clear

> lighting soft

> turn x 90

> select clear

> turn x -90

> turn x 90

> turn x -90

> save "F:/mouse liver/normal+ADP compare to state123.png" width 2010 height
> 1213 supersample 4 transparentBackground true

> turn x 90

> save "F:/mouse liver/normal+ADP compare to state123_x90.png" width 2010
> height 1213 supersample 4 transparentBackground true

> select #8/F #3/D #4/E #5/F

26092 atoms, 26315 bonds, 13 pseudobonds, 1891 residues, 6 models selected  

> hide sel cartoons

> hide sel surfaces

> select clear

> select #8/I

463 atoms, 468 bonds, 47 residues, 1 model selected  

> select #8/H

1233 atoms, 1245 bonds, 131 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel violet

> select clear

> select #8/G:273

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

18 atoms, 17 bonds, 2 residues, 2 models selected  

> select up

2660 atoms, 2685 bonds, 273 residues, 2 models selected  

> select down

18 atoms, 17 bonds, 2 residues, 2 models selected  

> graphics selection color red width 3

> select add #8/G:271

25 atoms, 23 bonds, 3 residues, 2 models selected  

> select add #8/G:270

32 atoms, 29 bonds, 4 residues, 2 models selected  

> select add #8/G:269

39 atoms, 35 bonds, 5 residues, 2 models selected  

> select add #8/G:268

46 atoms, 41 bonds, 6 residues, 2 models selected  

> select add #8/G:267

54 atoms, 48 bonds, 7 residues, 2 models selected  

> select add #8/G:266

64 atoms, 57 bonds, 8 residues, 2 models selected  

> select add #8/G:264

75 atoms, 67 bonds, 9 residues, 2 models selected  

> select add #8/G:265

85 atoms, 76 bonds, 10 residues, 2 models selected  

> select add #8/G:263

95 atoms, 85 bonds, 11 residues, 2 models selected  

> select add #8/G:262

105 atoms, 94 bonds, 12 residues, 2 models selected  

> select add #8/G:261

116 atoms, 104 bonds, 13 residues, 2 models selected  

> select add #8/G:260

127 atoms, 114 bonds, 14 residues, 2 models selected  

> select add #8/G:259

136 atoms, 122 bonds, 15 residues, 2 models selected  

> select add #8/I:31

147 atoms, 132 bonds, 16 residues, 2 models selected  

> select add #8/I:32

154 atoms, 138 bonds, 17 residues, 3 models selected  

> select add #8/I:34

161 atoms, 144 bonds, 18 residues, 3 models selected  

> select add #8/I:35

172 atoms, 154 bonds, 19 residues, 3 models selected  

> select add #3/I:34

182 atoms, 163 bonds, 20 residues, 4 models selected  

> select subtract #3/I:34

172 atoms, 154 bonds, 19 residues, 3 models selected  

> select add #3/I:34

182 atoms, 163 bonds, 20 residues, 4 models selected  

> select add #5/I:34

192 atoms, 172 bonds, 21 residues, 5 models selected  

> select subtract #5/I:34

182 atoms, 163 bonds, 20 residues, 4 models selected  

> select add #5/I:33

196 atoms, 176 bonds, 21 residues, 5 models selected  

> select subtract #5/I:33

182 atoms, 163 bonds, 20 residues, 4 models selected  

> select add #5/I:33

196 atoms, 176 bonds, 21 residues, 5 models selected  

> select subtract #5/I:33

182 atoms, 163 bonds, 20 residues, 4 models selected  

> select subtract #3/I:34

172 atoms, 154 bonds, 19 residues, 3 models selected  

> select add #5/I:33

186 atoms, 167 bonds, 20 residues, 4 models selected  

> select subtract #5/I:33

172 atoms, 154 bonds, 19 residues, 3 models selected  
Drag select of 28 residues  

> select #8/G:257

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select 8/G:257-272

Expected an objects specifier or a keyword  

> select #8/G:257-272

147 atoms, 146 bonds, 16 residues, 1 model selected  

> select #8/G:257-272 #/I:28-35

Expected a keyword  

> select #8/G:257-272 #8/I:28-35

226 atoms, 225 bonds, 24 residues, 1 model selected  

> save "F:/mouse liver/gamma_normal_compare_state123.png" width 2010 height
> 1213 supersample 4 transparentBackground true

> select #8/F #3/D #4/E #5/F

26092 atoms, 26315 bonds, 13 pseudobonds, 1891 residues, 6 models selected  

> show sel cartoons

> select clear

> select #8/F #3/D #4/E #5/F

26092 atoms, 26315 bonds, 13 pseudobonds, 1891 residues, 6 models selected  

> transparency sel 0 cartoons

> select clear

[Repeated 1 time(s)]

> select #4/G:272

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

4300 atoms, 4326 bonds, 272 residues, 1 model selected  

> select down

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select add #4/G:271

29 atoms, 27 bonds, 2 residues, 1 model selected  

> select add #4/G:270

39 atoms, 36 bonds, 3 residues, 1 model selected  

> select #3/G:260-272

195 atoms, 194 bonds, 13 residues, 1 model selected  

> hbonds sel reveal true

89 hydrogen bonds found  

> hide sel atoms

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

[Repeated 1 time(s)]

> select #3/A:286@CA

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> hide sel cartoons

[Repeated 1 time(s)]

> hide sel atoms

> select #8/A:286@CB

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

40 atoms, 41 bonds, 5 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #3/G:260-272

195 atoms, 194 bonds, 9 pseudobonds, 13 residues, 2 models selected  

> select #3/G:260-272

195 atoms, 194 bonds, 9 pseudobonds, 13 residues, 2 models selected  

> show sel cartoons

> hbonds sel reveal true

89 hydrogen bonds found  

> select #3/A:286@CA

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 24 atom styles  

> select #8/A:286@CB

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> hide sel atoms

> select #4/G:267@CB

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

1148 atoms, 1152 bonds, 73 residues, 1 model selected  

> select down

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> select #5/G:267@HB3

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> select clear

> select #3/G:264@CB

1 atom, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

1148 atoms, 1152 bonds, 73 residues, 1 model selected  

> hide sel atoms

[Repeated 2 time(s)]

> select #3/C:292@O

1 atom, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

77 atoms, 77 bonds, 5 residues, 1 model selected  

> select up

6176 atoms, 6215 bonds, 402 residues, 1 model selected  

> select add #5/C:292@N

6177 atoms, 6215 bonds, 403 residues, 2 models selected  

> select up

6191 atoms, 6229 bonds, 403 residues, 2 models selected  

> select clear

> select #3/C:292@O

1 atom, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

77 atoms, 77 bonds, 5 residues, 1 model selected  

> style sel stick

Changed 77 atom styles  

> select #5/C:292@O

1 atom, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 15 atom styles  

> select clear

> hide #10 models

> select #8/F #3/D #4/E #5/F

26092 atoms, 26315 bonds, 13 pseudobonds, 1891 residues, 6 models selected  

> show sel surfaces

> select clear

> select #8/F #3/D #4/E #5/F

26092 atoms, 26315 bonds, 13 pseudobonds, 1891 residues, 6 models selected  

> hide sel surfaces

> select clear

> select #8/F #3/D #4/E #5/F

26092 atoms, 26315 bonds, 13 pseudobonds, 1891 residues, 6 models selected  

> hide sel cartoons

> show sel surfaces

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #4/G:267@CB

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select up

22 atoms, 20 bonds, 2 residues, 2 models selected  

> select up

2296 atoms, 2304 bonds, 146 residues, 2 models selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> hide sel atoms

> turn x 90

[Repeated 3 time(s)]

> select #8/F #3/D #4/E #5/F

26092 atoms, 26315 bonds, 13 pseudobonds, 1891 residues, 6 models selected  

> show sel cartoons

> transparency sel 20 cartoons

> transparency sel 0 cartoons

> transparency sel 20 surfaces

> select clear

> select #8/F #3/D #4/E #5/F

26092 atoms, 26315 bonds, 13 pseudobonds, 1891 residues, 6 models selected  

> transparency sel 50 surfaces

> transparency sel 40 surfaces

> transparency sel 30 surfaces

> select clear

> lighting depthCue true depthCueStart 0.5 depthCueEnd 0.7

> select clear

> save C:\Users\2023.12\Desktop\image20.png supersample 3

> select clear

> select add #5

81277 atoms, 81902 bonds, 34 pseudobonds, 5198 residues, 3 models selected  

> select subtract #5

1 model selected  

> select add #1

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select subtract #1

28 models selected  

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> show sel cartoons

> select clear

> hide #!3 models

> hide #!4 models

> hide #!5 models

> show #!1 models

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> select subtract #8

28 models selected  

> matchmaker #8/b to #1/b pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain b
(#1) with Mus_normal_Atp_synthase-coot-1004.pdb, chain b (#8), sequence
alignment score = 1031.4  
RMSD between 128 pruned atom pairs is 1.227 angstroms; (across all 209 pairs:
2.572)  
  

> hide #!8 models

> select add #1

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> select subtract #1

28 models selected  

> select ::name="ADP"

522 atoms, 550 bonds, 14 residues, 5 models selected  

> show sel & #!1 atoms

> style sel & #!1 stick

Changed 105 atom styles  

> select clear

> select ::name="ADP"

522 atoms, 550 bonds, 14 residues, 5 models selected  

> select #1/A,B,C

13565 atoms, 13713 bonds, 1512 residues, 1 model selected  

> color (#!1 & sel) yellow

> select clear

> select ::name="ADP"

522 atoms, 550 bonds, 14 residues, 5 models selected  

> color (#!1 & sel) magenta

> color sel & #!1 byhetero

> select clear

> select ::name="ATP"

683 atoms, 717 bonds, 17 residues, 6 models selected  

> show sel & #!1 atoms

> color (#!1 & sel) cyan

> color sel & #!1 byhetero

> hide #!1 models

> show #!3 models

> show #!8 models

> select add #3

81709 atoms, 82360 bonds, 50 pseudobonds, 5202 residues, 9 models selected  

> show sel & #!3,8 cartoons

> select clear

> matchmaker #8/S to #1/S pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain S
(#1) with Mus_normal_Atp_synthase-coot-1004.pdb, chain S (#8), sequence
alignment score = 883.1  
RMSD between 169 pruned atom pairs is 1.216 angstroms; (across all 188 pairs:
1.389)  
  

> matchmaker #8/S to #3/S pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker bovine ATP synthase monomer state 2 (combined)_6ZQM.cif, chain S
(#3) with Mus_normal_Atp_synthase-coot-1004.pdb, chain S (#8), sequence
alignment score = 737.5  
RMSD between 149 pruned atom pairs is 1.081 angstroms; (across all 188 pairs:
1.684)  
  

> select add #3

81155 atoms, 81778 bonds, 50 pseudobonds, 5188 residues, 4 models selected  

> hide #!3 models

> select subtract #3

1 model selected  

> show #!1 models

> matchmaker #8/A to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain A
(#1) with Mus_normal_Atp_synthase-coot-1004.pdb, chain A (#8), sequence
alignment score = 2283.5  
RMSD between 483 pruned atom pairs is 1.003 angstroms; (across all 503 pairs:
1.107)  
  

> select #1/B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,a,b,c,d,e,f,g,h,i,j

45063 atoms, 45639 bonds, 4632 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #8/B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,a,b,c,d,e,f,g,h,i,j

45055 atoms, 45630 bonds, 4632 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> matchmaker #8/A to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain A
(#1) with Mus_normal_Atp_synthase-coot-1004.pdb, chain A (#8), sequence
alignment score = 2283.5  
RMSD between 483 pruned atom pairs is 1.003 angstroms; (across all 503 pairs:
1.107)  
  

> select #1/G #8/G

5320 atoms, 5370 bonds, 546 residues, 2 models selected  

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> show sel cartoons

> matchmaker #8/G to #1/G pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb, chain G
(#1) with Mus_normal_Atp_synthase-coot-1004.pdb, chain G (#8), sequence
alignment score = 1192.1  
RMSD between 242 pruned atom pairs is 1.110 angstroms; (across all 273 pairs:
1.358)  
  

> select #8/F:143@CB

1 atom, 1 residue, 1 model selected  

> select up

10 atoms, 9 bonds, 1 residue, 2 models selected  

> select up

39 atoms, 38 bonds, 4 residues, 2 models selected  

> hide sel surfaces

> select #8/F:360@CG

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 8 bonds, 1 residue, 2 models selected  

> select #1/G:273

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

25 atoms, 24 bonds, 3 residues, 2 models selected  

> select up

2660 atoms, 2685 bonds, 273 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 2660 atom styles  

> select clear

[Repeated 1 time(s)]

> select #8/G:273

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

18 atoms, 17 bonds, 2 residues, 2 models selected  

> select up

2660 atoms, 2685 bonds, 273 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 2660 atom styles  

> select clear

> ui tool show Distances

> select clear

[Repeated 1 time(s)]

> select #1/G:272@CD1

1 atom, 1 residue, 1 model selected  

> select add #1/G:238@CG

1 atom, 1 bond, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> show sel atoms

[Repeated 1 time(s)]

> style sel sphere

Changed 1 atom style  

> select #1/G:272@CD1

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select #1/G:272@CD1

1 atom, 1 residue, 1 model selected  

> select add #1/G:238@CG

2 atoms, 2 residues, 2 models selected  

> distance #1/G:272@CD1 #1/G:238@CG

Distance between Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb #1/G
LEU 272 CD1 and ASN 238 CG: 58.0  

> select clear

[Repeated 2 time(s)]

> select #8/G:237@CG

1 atom, 1 residue, 1 model selected  

> show sel atoms

[Repeated 1 time(s)]

> select #8/G:271

7 atoms, 6 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 7 atom styles  

> select clear

> select #1/G:272@CD1

1 atom, 1 residue, 1 model selected  

> select add #8/G:271@CB

2 atoms, 2 residues, 3 models selected  

> distance #1/G:272@CD1 #8/G:271@CB

Distance between Mus_F1F0_model_del_SHEET-coot-1002_complete_del_CL.pdb #1/G
LEU 272 CD1 and Mus_normal_Atp_synthase-coot-1004.pdb #8/G ALA 271 CB: 8.2  

> select add #1

49755 atoms, 50397 bonds, 1 pseudobond, 5237 residues, 5 models selected  

> show sel cartoons

> select clear

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> show sel cartoons

> select clear

> select add #8

49746 atoms, 50388 bonds, 5236 residues, 1 model selected  

> hide #!11 models

> close #11

> show #10 models

> close #10

> hide sel atoms

> select add #1

99500 atoms, 100785 bonds, 10472 residues, 30 models selected  

> hide sel atoms

> hide sel surfaces

> select clear

> select add #1

49754 atoms, 50397 bonds, 5236 residues, 1 model selected  

> color (#!1 & sel) light gray

> select clear

> save "F:/mouse liver/normal liver+ADP compare with APAP.png" width 2010
> height 1213 supersample 4 transparentBackground true

> save "F:/mouse liver/normal liver+ADP compare with APAP.cxs" includeMaps
> true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 740, in write  
compressed = self._compressor.compress(data)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 740, in write  
compressed = self._compressor.compress(data)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 10 教育版 (Build 19045)
Memory: 34,088,153,088
MaxProcessMemory: 137,438,953,344
CPU: 28 Intel(R) Core(TM) i7-14700K
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    Send2Trash: 1.8.3
    SEQCROW: 1.8.18
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

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#19482 new defect

ChimeraX bug report submission

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