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Opened 3 weeks ago
Closed 3 weeks ago
#19482 closed defect (limitation)
MemoryError saving session with maps
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
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
Change History (2)
comment:1 by , 3 weeks ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving session with maps |
comment:2 by , 3 weeks ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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The error means ChimeraX ran out of memory trying to save a session file (.cxs). You were using the option to "include maps" in the session file. Your density maps are 512 by 512 by 512 float32 so take 0.5 Gbytes each, not too big, but embedding them all in the session file is probably the main reason it ran out of memory. I suggest not using the "include maps" option. In that case ChimeraX just saves the path to the density map file in the session, so the session can still open the maps.
I also suggest updating to the current ChimeraX. You are using an old ChimeraX 1.6 version that I believe had a serious memory leak on Windows that may also be contributing to the out of memory error you got.