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Opened 51 minutes ago
#19482 new defect
ChimeraX bug report submission
| Reported by: | 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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