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Opened 14 months ago
Closed 14 months ago
#15827 closed defect (not a bug)
Volume Viewer menu
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Volume Viewer does not show a full menu of actions when I launch ChimeraX 1.8. This makes it complicated to save files among other things. I attach an image of the Volume Viewer. Please advice on how I can resolve this bug.
Also I am running Widoiws 11 not Windows 10 as indicated and my PC is fully uptodate.
Thank you for your attn to this matter.
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\Users\Jurgen\Desktop\cryoEM_ALDOA_hFBP2_Transfer\Transfer\Chimera
> session_Complex_hFBP2+hALDOA_3 expts.cxs" format session
Opened no_DMSO_P223_J215_sharp.mrc as #1, grid size 256,256,256, pixel 1.07,
shown at level 0.5, step 1, values float32
Opened cryosparc_P352_J79_007_WT_volume_map.mrc as #3, grid size 384,384,384,
pixel 0.682, shown at level 0.077, step 1, values float32
Opened cryosparc_P25_J143_009_volume_map_sharp.mrc as #5, grid size
176,176,176, pixel 1.36, shown at step 1, values float32
Opened cryosparc_P25_J144_009_volume_map_sharp.mrc as #6, grid size
176,176,176, pixel 1.36, shown at step 1, values float32
Opened cryosparc_P25_J145_010_volume_map_sharp.mrc as #7, grid size
176,176,176, pixel 1.36, shown at step 1, values float32
Log from Mon Aug 26 22:00:46 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 5 time(s)]
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY2:" "The operation
completed successfully."
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 1 time(s)]
> open "C:/Users/Jurgen/My Files/CHUM_Inst_du_Cancer/Compounds/Cryo-
> EM/NoDMSO/no_DMSO_P223_J215_sharp.mrc"
Opened no_DMSO_P223_J215_sharp.mrc as #1, grid size 256,256,256, pixel 1.07,
shown at level 0.6, step 1, values float32
> open "C:/Users/Jurgen/My Files/CHUM_Inst_du_Cancer/Compounds/Cryo-
> EM/RealSpaceRefine_2/Refined_aldolaseA_noDMSO_cyc_2_real_space_refined.pdb"
Chain information for Refined_aldolaseA_noDMSO_cyc_2_real_space_refined.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
156 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/Jurgen/My Files/CHUM_Inst_du_Cancer/Darek
> Rakus/FBP2/Maps/WT/cryosparc_P352_J79_007_WT_volume_map.mrc"
Opened cryosparc_P352_J79_007_WT_volume_map.mrc as #3, grid size 384,384,384,
pixel 0.682, shown at level 0.0481, step 2, values float32
> open "C:/Users/Jurgen/My Files/CHUM_Inst_du_Cancer/Darek
> Rakus/FBP2/MR+Refine/RealSpaceRefine_51/4_ALDOA_real_space_refined_051.pdb"
Chain information for 4_ALDOA_real_space_refined_051.pdb #4
---
Chain | Description
A B C D | No description available
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/cryosparc_P25_J143_009_volume_map_sharp.mrc
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/cryosparc_P25_J144_009_volume_map_sharp.mrc
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/cryosparc_P25_J145_010_volume_map_sharp.mrc
Opened cryosparc_P25_J143_009_volume_map_sharp.mrc as #5.1, grid size
176,176,176, pixel 1.36, shown at level 0.0494, step 1, values float32
Opened cryosparc_P25_J144_009_volume_map_sharp.mrc as #5.2, grid size
176,176,176, pixel 1.36, shown at level 0.0917, step 1, values float32
Opened cryosparc_P25_J145_010_volume_map_sharp.mrc as #5.3, grid size
176,176,176, pixel 1.36, shown at level 0.0703, step 1, values float32
> close #5
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/cryosparc_P25_J143_009_volume_map_sharp.mrc
Opened cryosparc_P25_J143_009_volume_map_sharp.mrc as #5, grid size
176,176,176, pixel 1.36, shown at level 0.0494, step 1, values float32
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/cryosparc_P25_J144_009_volume_map_sharp.mrc
Opened cryosparc_P25_J144_009_volume_map_sharp.mrc as #6, grid size
176,176,176, pixel 1.36, shown at level 0.0917, step 1, values float32
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/cryosparc_P25_J145_010_volume_map_sharp.mrc
Opened cryosparc_P25_J145_010_volume_map_sharp.mrc as #7, grid size
176,176,176, pixel 1.36, shown at level 0.0703, step 1, values float32
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/RMATet_dim_AB.pdb
Chain information for RMATet_dim_AB.pdb #8
---
Chain | Description
A B | No description available
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/RMATet_dim_AC.pdb
Chain information for RMATet_dim_AC.pdb #9
---
Chain | Description
A C | No description available
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/RMATet_dim_AD.pdb
Chain information for RMATet_dim_AD.pdb #10
---
Chain | Description
A D | No description available
> open C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/RMATet.pdb
Chain information for RMATet.pdb #11
---
Chain | Description
A B C D | No description available
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/hFBP2_tet_5et5.pdb
Summary of feedback from opening
C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/hFBP2_tet_5et5.pdb
---
warnings | Ignored bad PDB record found on line 2
hFBP2 Tetramer 1
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
6934 messages similar to the above omitted
Ignored bad PDB record found on line 17984
notes | Combining 2 symmetry atoms into HOH /A:418 O
Combining 2 symmetry atoms into HOH /C:418 O
Chain information for hFBP2_tet_5et5.pdb #12
---
Chain | Description
A B C D | No description available
56 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open
> C:\Users\Jurgen\Desktop\cryoEM_ALDOA_hFBP2_Transfer\Transfer\cryosparc_P25_J143_009_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P25_J143_009_volume_map_sharp.mrc as #13, grid size
176,176,176, pixel 1.36, shown at level 0.0494, step 1, values float32
> open "C:\Users\Jurgen\My Files\CHUM_Inst_du_Cancer\Compounds\Cryo-
> EM\NoDMSO\no_DMSO_P223_J215_sharp.mrc" format mrc
Opened no_DMSO_P223_J215_sharp.mrc as #14, grid size 256,256,256, pixel 1.07,
shown at level 0.6, step 1, values float32
> ui mousemode right select
> open
> C:\Users\Jurgen\Desktop\cryoEM_ALDOA_hFBP2_Transfer\Transfer\hFBP2_tet_5et5.pdb
> format pdb
Summary of feedback from opening
C:\Users\Jurgen\Desktop\cryoEM_ALDOA_hFBP2_Transfer\Transfer\hFBP2_tet_5et5.pdb
---
warnings | Ignored bad PDB record found on line 2
hFBP2 Tetramer 1
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
6934 messages similar to the above omitted
Ignored bad PDB record found on line 17984
notes | Combining 2 symmetry atoms into HOH /A:418 O
Combining 2 symmetry atoms into HOH /C:418 O
Chain information for hFBP2_tet_5et5.pdb #15
---
Chain | Description
A B C D | No description available
56 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> volume #3 level 0.07703
> ui tool show "Volume Viewer"
> ui windowfill toggle
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> select #1
2 models selected
> select subtract #1
Nothing selected
> select add #1
2 models selected
> ui tool show "Hide Dust"
> surface dust #1 size 10
> surface dust #1 size 9.98
> surface dust #1 size 10 metric "volume rank"
> surface dust #1 size 6 metric "volume rank"
> surface dust #1 size 1 metric "volume rank"
[Repeated 1 time(s)]
> surface dust #1 size 6 metric "size rank"
> surface dust #1 size 1 metric "size rank"
[Repeated 1 time(s)]
> volume #1 level 0.855
> volume #1 level 4.636
> volume #1 level -0.3456
> volume #1 level 0.1397
> volume #1 level 3.231
> volume #1 level 5.683
> volume #1 level 7.088
Drag select of 14 no_DMSO_P223_J215_sharp.mrc
> select add #1
4 models selected
> select subtract #1
2 models selected
> select clear
> select add #1
2 models selected
> select clear
> surface dust #1 size 1 metric "size rank"
> select add #1
2 models selected
> surface dust #1 size 1 metric "size rank"
> surface dust #1 size 6 metric "volume rank"
[Repeated 1 time(s)]
> surface dust #1 size 1 metric "volume rank"
[Repeated 1 time(s)]
> surface dust #1 size 10 metric "volume rank"
> surface dust #1 size 100 metric "volume rank"
[Repeated 1 time(s)]
> surface dust #1 size 1000 metric "volume rank"
> surface dust #1 size 6.44
> surface dust #1 size 1.68
[Repeated 1 time(s)]
> surface dust #1 size 661.76
[Repeated 1 time(s)]
> volume #1 level 2.439
> volume #1 step 2
> surface dust #1 size 661.76
> surface dust #1 size 662 metric "volume rank"
> surface dust #1 size 6 metric "volume rank"
> surface dust #1 size 306 metric "volume rank"
[Repeated 1 time(s)]
> volume #1 level 0.6673
> show #!1 models
> surface undust #1
> surface dust #1 size 306 metric "volume rank"
> surface dust #1 size 2 metric "volume rank"
> surface undust #1
> surface dust #1 size 2 metric "volume rank"
Drag select of 15 no_DMSO_P223_J215_sharp.mrc
> select subtract #1
2 models selected
> select add #1
4 models selected
> select clear
Drag select of 14 no_DMSO_P223_J215_sharp.mrc
> select clear
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> select add #1
2 models selected
> hide #1.1 models
> select subtract #1.1
1 model selected
> surface dust #1 size 2 metric "volume rank"
> show #1.1 models
> hide #!1 models
> select add #1
2 models selected
> select subtract #1
Nothing selected
> select add #1.1
1 model selected
> hide #!2 models
> hide #1.1 models
> show #!1 models
> show #1.1 models
> hide #!1 models
> volume #1 level 5
> show #!1 models
> volume #1 style image
> volume #1 style mesh
> volume #1 style surface
> volume #1 step 16
> volume #1 step 1
> volume #3 step 1
> volume #3 step 2
> volume #1 change image level -0.2023,0 level 0.6001,0.8 level 7.124,1
> volume #1 color #aaffff
> volume #1 color #000037
> volume #1 color #aaffff
> open "C:\Users\Jurgen\My Files\CHUM_Inst_du_Cancer\Darek
> Rakus\FBP2\Maps\WT\cryosparc_P352_J79_007_WT_volume_map.mrc" format mrc
Opened cryosparc_P352_J79_007_WT_volume_map.mrc as #16, grid size 384,384,384,
pixel 0.682, shown at level 0.0481, step 2, values float32
> hide #!14 models
> hide #14.1 models
> select clear
[Repeated 1 time(s)]
> select add #1
3 models selected
> select add #1.2
3 models selected
> select add #1.2
3 models selected
> show #1.2 models
> hide #!16 models
> select subtract #1.1
2 models selected
> select add #1
3 models selected
> select subtract #1.1
2 models selected
> select add #1
3 models selected
> hide #!1 models
> hide #1.1 models
> select subtract #1.1
2 models selected
> select add #1
3 models selected
> show #!1 models
> show #1.1 models
> hide #1.2 target m
> select add #1.2
3 models selected
> volume #1
> volume #1 level 3
[Repeated 1 time(s)]
> volume #1 level 0.6021
> select clear
> surface dust #1 size 3 metric "volume rank"
> surface dust #1 size 2 metric "volume rank"
> surface dust #1 size 1 metric "volume rank"
> select clear
> show #!16 models
> hide #!16 models
> select clear
[Repeated 1 time(s)]
> color #1 #aaaaffff models
> color #1 yellow models
> color #1 red models
> color #1 black models
> color #1 #010000ff models
> color #1 #010100ff models
> color #1 #010101ff models
> color #1 #010102ff models
> color #1 #0101ffff models
> color #1 #0102ffff models
> color #1 #01ffffff models
> color #1 #02ffffff models
> color #1 white models
> hide #1.2 target m
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> select add #1.2
1 model selected
> hide #1.2 target m
> show #1.2 models
> hide #1.2 models
> select add #1.1
2 models selected
> select subtract #1.1
1 model selected
> hide #1.1 models
> select add #1.2
1 model selected
> select add #1.2
1 model selected
> show #1.1 models
> select add #1.2
1 model selected
> show #1.2 models
> select add #1.2
1 model selected
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> select add #1.2
1 model selected
> select add #1
3 models selected
> select add #1
3 models selected
> select add #1
3 models selected
> select subtract #1.1
2 models selected
> select add #1.2
2 models selected
> select add #1
3 models selected
> hide #!1 models
> hide #1.1 models
> select add #1.2
3 models selected
> show #1.2 models
> select clear
> select #1
3 models selected
> select clear
> hide #1.2 models
> show #1.1 models
> show #!16 models
> select clear
Drag select of 16 cryosparc_P352_J79_007_WT_volume_map.mrc
> select clear
> volume #3 step 1
> volume #1
> volume #1 level 0.5494
> volume #16 level 2
> volume #16 level 0.5
> volume #16 level 0.05
> volume #1 level 0.2
> volume #1 level 0.25
> volume #1 level 0.5
> select add #16
2 models selected
> hide #!16 target m
> close #16
> show #!3 models
> ui mousemode right select
> volume show
> volume hide
> show #!1 models
> close #14
> show #!3 models
> save "C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/Chimera
> session_Complex_hFBP2+hALDOA_3 expts.cxs"
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 8 time(s)]
> show #!2 models
> hide #!2 models
> show #4 models
> show #!5 models
> select add #3
2 models selected
> surface dust #3 size 6.82
> surface dust #1 size 1 metric "volume rank"
[Repeated 1 time(s)]
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select subtract #3
Nothing selected
> hide #4 models
> show #4 models
> hide #!5 models
> show #!5 models
> select add #5
2 models selected
> surface dust #5 size 13.6
> select clear
> show #!6 models
> select add #6
2 models selected
> close #13
> close #15
> surface dust #6 size 13.6
> select subtract #6
Nothing selected
> show #!7 models
> select add #7
2 models selected
> select subtract #7
Nothing selected
> hide #!3 models
> hide #4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #12.1 models
> show #!12 models
> show #!7 models
> hide #!1 models
> hide #1.1 models
> select add #7
2 models selected
> surface dust #7 size 13.6
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> select clear
> select add #12
9194 atoms, 8792 bonds, 16 pseudobonds, 1658 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,41.897,0,1,0,132.81,0,0,1,127.31
> view matrix models #12,1,0,0,115.4,0,1,0,116.43,0,0,1,118.45
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.4642,-0.82312,0.32711,115.4,-0.20851,0.25737,0.94355,116.43,-0.86084,-0.5062,-0.052159,118.45
> view matrix models
> #12,0.45065,-0.8631,0.22799,115.4,-0.21445,0.14325,0.96617,116.43,-0.86656,-0.4843,-0.12054,118.45
> ui mousemode right select
> select clear
> select add #7.1
1 model selected
> transparency sel 50
> show #!12 target m
> transparency #7.1 70
> select clear
> transparency #7#!12 80
> volume #!7 style surface
[Repeated 1 time(s)]
> select add #7
2 models selected
> volume #7 color #ffbf9933
> volume #7 color #ffff9933
> volume #7 color #ffffff33
> select clear
> select add #7
2 models selected
> volume #7 color #feffff33
> volume #7 color #fefeff33
> volume #7 color #fefefe33
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select clear
> select add #7
2 models selected
> show #!7 target m
> hide #7.1 models
> show #7.1 models
> volume sel style surface
> volume sel show
> volume sel style image
> close #7.2
> show #7.1 models
> select clear
> select add #7
2 models selected
> hide #!12 models
> select clear
> color #7.1 #8b8b8b33
> color #7.1 #ffffff33
> transparency #7 0
> transparency #7 80
> hide #!7 models
> show #!12 models
> select add #12
9194 atoms, 8792 bonds, 16 pseudobonds, 1658 residues, 2 models selected
> color #12 #4ce653ff
> show #!7 models
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.49774,-0.863,-0.086504,115.4,0.079212,-0.054088,0.99539,116.43,-0.8637,-0.5023,0.041439,118.45
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.49774,-0.863,-0.086504,121.55,0.079212,-0.054088,0.99539,116.16,-0.8637,-0.5023,0.041439,120.44
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.47996,-0.8441,-0.23903,121.55,0.2081,-0.15514,0.96573,116.16,-0.85225,-0.51325,0.10119,120.44
> view matrix models
> #12,0.39869,-0.86223,0.31243,121.55,-0.29156,0.20383,0.93458,116.16,-0.86951,-0.4637,-0.17013,120.44
> view matrix models
> #12,0.61859,-0.69877,0.35926,121.55,-0.30429,0.2085,0.92948,116.16,-0.7244,-0.68429,-0.083646,120.44
> view matrix models
> #12,0.70905,-0.69075,-0.14186,121.55,0.034559,-0.1669,0.98537,116.16,-0.70432,-0.70357,-0.094467,120.44
> view matrix models
> #12,-0.17806,0.33149,-0.9265,121.55,-0.55862,0.74107,0.3725,116.16,0.81009,0.58389,0.053226,120.44
> view matrix models
> #12,-0.18259,0.3277,-0.92697,121.55,-0.5625,0.73846,0.37186,116.16,0.80638,0.58932,0.049493,120.44
> view matrix models
> #12,-0.20527,0.27832,-0.9383,121.55,-0.51023,0.78769,0.34527,116.16,0.83518,0.54962,-0.019682,120.44
> fitmap #12 inMap #7
Fit molecule hFBP2_tet_5et5.pdb (#12) to map
cryosparc_P25_J145_010_volume_map_sharp.mrc (#7) using 9194 atoms
average map value = 0.05805, steps = 72
shifted from previous position = 2.68
rotated from previous position = 0.308 degrees
atoms outside contour = 5756, contour level = 0.070322
Position of hFBP2_tet_5et5.pdb (#12) relative to
cryosparc_P25_J145_010_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.20163395 0.27558241 -0.93989259 123.13078280
-0.50916966 0.79025709 0.34093986 118.23811674
0.83671381 0.54730984 -0.01902446 119.81114942
Axis 0.10566064 -0.90961563 -0.40179004
Axis point 40.83104314 0.00000000 94.84326700
Rotation angle (degrees) 102.42730003
Shift along axis -142.68008862
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/hFBP2_BC_dimer.pdb
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/hFBP2_AD_dimer.pdb
Chain information for hFBP2_BC_dimer.pdb #13
---
Chain | Description
B C | No description available
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for hFBP2_AD_dimer.pdb #14
---
Chain | Description
A D | No description available
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!12 models
> select subtract #12
Nothing selected
> color #13 #ffaa7fff
> color #14 #aaaaffff
> color #14 #aaffffff
> hide #!14 models
> ui mousemode right select
> ui mousemode right "translate selected models"
> select add #13
4332 atoms, 4396 bonds, 8 pseudobonds, 564 residues, 2 models selected
> view matrix models #13,1,0,0,62.703,0,1,0,114.18,0,0,1,128.16
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.86712,-0.21931,-0.44722,67.923,-0.32569,0.42969,-0.84219,127.46,0.37687,0.87594,0.30117,109.59
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.86712,-0.21931,-0.44722,72.161,-0.32569,0.42969,-0.84219,134.67,0.37687,0.87594,0.30117,122.21
> view matrix models
> #13,0.86712,-0.21931,-0.44722,109.07,-0.32569,0.42969,-0.84219,119.03,0.37687,0.87594,0.30117,119.79
> view matrix models
> #13,0.86712,-0.21931,-0.44722,114.53,-0.32569,0.42969,-0.84219,116.81,0.37687,0.87594,0.30117,120.18
> view matrix models
> #13,0.86712,-0.21931,-0.44722,114.99,-0.32569,0.42969,-0.84219,116.99,0.37687,0.87594,0.30117,123.31
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.69055,0.085692,-0.71819,113.09,-0.667,0.45946,-0.58652,121.61,0.27972,0.88405,0.37444,124.63
> view matrix models
> #13,0.54352,-0.26089,-0.79782,120.4,-0.56495,0.58927,-0.57757,118.17,0.62082,0.76465,0.17289,121.34
> fitmap #14 inMap #7
Fit molecule hFBP2_AD_dimer.pdb (#14) to map
cryosparc_P25_J145_010_volume_map_sharp.mrc (#7) using 4332 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 4332, contour level = 0.070322
Position of hFBP2_AD_dimer.pdb (#14) relative to
cryosparc_P25_J145_010_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> hide #!13 models
> show #!13 models
> fitmap #13 inMap #7
Fit molecule hFBP2_BC_dimer.pdb (#13) to map
cryosparc_P25_J145_010_volume_map_sharp.mrc (#7) using 4332 atoms
average map value = 0.1578, steps = 52
shifted from previous position = 1.69
rotated from previous position = 4.77 degrees
atoms outside contour = 1444, contour level = 0.070322
Position of hFBP2_BC_dimer.pdb (#13) relative to
cryosparc_P25_J145_010_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.50205781 -0.32182458 -0.80272467 121.31747162
-0.53414108 0.61460399 -0.58047846 115.84517910
0.68017002 0.72020197 0.13666700 121.65110006
Axis 0.65562083 -0.74746773 -0.10702023
Axis point 20.66866817 0.00000000 154.70422563
Rotation angle (degrees) 82.72311686
Shift along axis -20.07140003
> select subtract #13
Nothing selected
> show #!14 models
> select add #14
4332 atoms, 4396 bonds, 8 pseudobonds, 564 residues, 2 models selected
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models #14,1,0,0,89.118,0,1,0,154.16,0,0,1,73.276
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.69601,-0.57109,-0.43522,76.149,-0.30626,0.31211,-0.89933,139.43,0.64944,0.75924,0.042328,94.152
> view matrix models
> #14,-0.54821,0.5756,-0.60676,74.704,-0.48169,0.37577,0.79169,137.77,0.6837,0.72628,0.071254,94.172
> view matrix models
> #14,-0.45734,0.6715,-0.58303,77.472,-0.48214,0.36366,0.79705,137.59,0.74725,0.64563,0.15744,93.918
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.45734,0.6715,-0.58303,121.13,-0.48214,0.36366,0.79705,136,0.74725,0.64563,0.15744,116.54
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.53508,0.59518,-0.59954,118.85,-0.47972,0.3701,0.79555,136.14,0.69539,0.71329,0.087489,116.78
> view matrix models
> #14,-0.49892,0.63231,-0.59267,119.94,-0.48079,0.36703,0.79632,136.07,0.72105,0.68225,0.12089,116.7
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> select add #14
4332 atoms, 4396 bonds, 8 pseudobonds, 564 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.49892,0.63231,-0.59267,126.91,-0.48079,0.36703,0.79632,114.67,0.72105,0.68225,0.12089,117.21
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.51336,0.60781,-0.60583,126.33,-0.42353,0.43455,0.79485,116.52,0.74638,0.66463,0.034345,117.33
> select subtract #14
Nothing selected
> hide #!13 models
> ui mousemode right select
> ui mousemode right "translate selected models"
> select add #14
4332 atoms, 4396 bonds, 8 pseudobonds, 564 residues, 2 models selected
> view matrix models
> #14,-0.51336,0.60781,-0.60583,121.5,-0.42353,0.43455,0.79485,115.94,0.74638,0.66463,0.034345,117.77
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.42665,0.52306,-0.73782,121.52,-0.52024,0.52538,0.67329,115.86,0.73981,0.67111,0.047961,117.77
> select subtract #14
Nothing selected
> show #!13 models
> select add #14
4332 atoms, 4396 bonds, 8 pseudobonds, 564 residues, 2 models selected
> select subtract #14
Nothing selected
> fitmap #14 inMap #7
Fit molecule hFBP2_AD_dimer.pdb (#14) to map
cryosparc_P25_J145_010_volume_map_sharp.mrc (#7) using 4332 atoms
average map value = 0.1614, steps = 68
shifted from previous position = 2.71
rotated from previous position = 4.71 degrees
atoms outside contour = 1402, contour level = 0.070322
Position of hFBP2_AD_dimer.pdb (#14) relative to
cryosparc_P25_J145_010_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.35926443 0.54189680 -0.75978743 121.23134418
-0.50728173 0.56996480 0.64637867 115.69528430
0.78332262 0.61764714 0.07012626 119.47665448
Axis -0.01539555 -0.82686246 -0.56219343
Axis point 48.38147272 0.00000000 69.66750031
Rotation angle (degrees) 111.07481506
Shift along axis -164.69950010
> hide #!7 models
> show #!12 models
> save "C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/Chimera
> session_Complex_hFBP2+hALDOA_3 expts.cxs"
Must specify one map, got 0
> help help:user
> hide #!13 models
> show #!13 models
> align #12 toATOMS #14 move chains
Expected a keyword
> align #12 toATOMS #14 move chains each chain
Expected a keyword
> hide #!7 models
> show #!12 models
> align #12 toATOMS #14 move chains each chain matchChainIds true
Expected a keyword
> hide #!14 models
> show #!14 models
> align #12 toATOMS #14 [move chains] [each chain] matchChainIds true
Expected a keyword
> align #12 toATOMS #14 matchChainIds true
Expected a keyword
> show #!14 models
> hide #14.1 models
> show #14.1 models
> hide #!14 models
> show #!14 models
> matchmaker #12 to #14
Parameters
---
Chain pairing | bb
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 hFBP2_AD_dimer.pdb, chain A (#14) with hFBP2_tet_5et5.pdb, chain A
(#12), sequence alignment score = 1416.4
RMSD between 282 pruned atom pairs is 0.000 angstroms; (across all 282 pairs:
0.000)
> hide #!12 models
> show #!12 models
> hide #!14 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> show #!12 models
> show #!14 models
> show #!7 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> hide #!14 models
> hide #!12 models
> show #!14 models
> hide #14.1 models
> show #12.1 models
> hide #12.1 models
> hide #!12 models
> show #!13 models
> hide #!7 models
> ui mousemode right select
> ui tool show "Side View"
[Repeated 1 time(s)]
> set bgColor gray
> set bgColor #80808000
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> select clear
> label #13#!14 text "{0.name} {0.number}{0.insertion_code}"
> select clear
> show #!7 models
Drag select of 7 cryosparc_P25_J145_010_volume_map_sharp.mrc , 1 residues
> select clear
> label #7,13#14.2#!14 text "{0.name} {0.number}{0.insertion_code}"
> close #14.2
> close #13.2
> hide #!7 models
> hide #!13 models
> hide #!14 models
> show #!2 models
> show #!1 models
> show #1.1 models
> show #4 models
> hide #4 models
> show #11 models
> hide #11 models
> help help:user
> fitmap #1 inMap map #2
Invalid "inMap" argument: invalid density map specifier
> ui mousemode right "translate selected models"
> select add #2
12886 atoms, 10880 bonds, 4 pseudobonds, 3611 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #1
3 models selected
> view matrix models #1,1,0,0,164.5,0,1,0,59.721,0,0,1,140.78
> ui mousemode right select
> select add #1.2
3 models selected
> close #1.2
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,154.7,0,1,0,139.13,0,0,1,136.51
> view matrix models #1,1,0,0,135.86,0,1,0,138.25,0,0,1,136.97
> transparency #1.1 70
> view matrix models #1,1,0,0,133.47,0,1,0,136.31,0,0,1,143.65
> ui mousemode right select
> select clear
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,136.37,0,1,0,138.13,0,0,1,137.27
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,136.82,0,1,0,137.03,0,0,1,136.98
> ui mousemode right select
> hide #!1 models
> select subtract #1
Nothing selected
> hide #1.1 models
> molmap #2 2.5
Opened Refined_aldolaseA_noDMSO_cyc_2_real_space_refined.pdb map 2.5 as #15,
grid size 143,104,125, pixel 0.833, shown at level 0.121, step 1, values
float32
> color #15 #aaff00ff models
> color #15 yellow models
> color #15 #ffff7fff models
> color #15 white models
> color #15 #ffff7fff models
> transparency #15.1 50
> show #!1 models
> show #1.1 models
> hide #!2 models
> fitmap #2 inMap map #15
Invalid "inMap" argument: invalid density map specifier
> save "C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/Chimera
> session_Complex_hFBP2+hALDOA_3 expts.cxs"
> fitmap #2 inMap map #15.1
Invalid "inMap" argument: invalid density map specifier
> hide #!15 models
> hide #15.1 models
> hide #!1 models
> hide #1.1 models
> show #15.1 models
> volume #15 level 0.2315
> volume #15 level 0.1814
> volume #15 style image
> volume #15 colorMode opaque8 showOutlineBox true imageMode "box faces"
> volume #15 style mesh
> volume #15 style surface
> volume #15 change image level 0,0 level 1.715,0.8 level 5.577,1
> volume #15 style image
> volume #15 style surface
> close #15.2
> volume #!15 showOutlineBox false
> close #15
> show target m
[Repeated 1 time(s)]
> hide target m
> show #11 models
> hide #11 models
> show #!2 models
> show #!1 models
> show #1.1 models
> hide #!1 models
> hide #1.1 models
> show #!1 models
> show #1.1 models
> fitmap #1 inMap map #2
Invalid "inMap" argument: invalid density map specifier
> open "C:/Users/Jurgen/My Files/CHUM_Inst_du_Cancer/Compounds/Cryo-
> EM/NoDMSO/no_DMSO_P223_J215_sharp-fixed.ccp4"
Opened no_DMSO_P223_J215_sharp-fixed.ccp4 as #15, grid size 256,256,256, pixel
1.07, shown at level 0.6, step 1, values float32
> surface dust #1 size 10.7
> surface dust #15 size 10.7
> hide #!1 models
> hide #1.1 models
> show #!1 models
> hide #!2 models
> show #1.1 models
> hide #!1 models
> show #!2 models
> hide #1.1 models
> transparency #15.1 50
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #!2 models
> fitmap #1 inMap map #15
Invalid "inMap" argument: invalid density map specifier
> select add #1
2 models selected
> fitmap #1 inMap map #15
Invalid "inMap" argument: invalid density map specifier
> ui tool show "Volume Viewer"
> select add #15
4 models selected
> select subtract #1
2 models selected
> hide #!1 models
> ui tool show "Show Volume Menu"
> hide #1.1 models
No map chosen to save
> hide #15.1 models
> select subtract #15.1
1 model selected
> select add #15
2 models selected
> show #15.1 models
> ui tool show "Volume Viewer"
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/cryosparc_P25_J143_009_volume_map_sharp.mrc
Opened cryosparc_P25_J143_009_volume_map_sharp.mrc as #16, grid size
176,176,176, pixel 1.36, shown at level 0.0494, step 1, values float32
> close #16
> ui autostart true "Volume Viewer"
> ui favorite true "Volume Viewer"
> ui tool show "Volume Viewer"
> ui tool show "Model Panel"
> ui tool show "Show Volume Menu"
> select add #1
4 models selected
> show target m
> hide target m
> show #!15 models
> show #15.1 models
> view clip false
> log metadata #2
No models had metadata
> log chains #2
Chain information for Refined_aldolaseA_noDMSO_cyc_2_real_space_refined.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> log metadata #4
The model has no metadata
> log chains #4
Chain information for 4_ALDOA_real_space_refined_051.pdb #4
---
Chain | Description
A B C D | No description available
> log metadata #8
The model has no metadata
> log chains #8
Chain information for RMATet_dim_AB.pdb #8
---
Chain | Description
A B | No description available
> log metadata #9
The model has no metadata
> log chains #9
Chain information for RMATet_dim_AC.pdb #9
---
Chain | Description
A C | No description available
> log metadata #10
The model has no metadata
> log chains #10
Chain information for RMATet_dim_AD.pdb #10
---
Chain | Description
A D | No description available
> log metadata #11
The model has no metadata
> log chains #11
Chain information for RMATet.pdb #11
---
Chain | Description
A B C D | No description available
> log metadata #12
No models had metadata
> log chains #12
Chain information for hFBP2_tet_5et5.pdb #12
---
Chain | Description
A B C D | No description available
> log metadata #13
No models had metadata
> log chains #13
Chain information for hFBP2_BC_dimer.pdb #13
---
Chain | Description
B C | No description available
> log metadata #14
No models had metadata
> log chains #14
Chain information for hFBP2_AD_dimer.pdb #14
---
Chain | Description
A D | No description available
> close #15
> show target m
[Repeated 2 time(s)]
> view clip false
> show target m
> ui tool show "Map Statistics"
> measure mapstats sel
Map no_DMSO_P223_J215_sharp.mrc #1, minimum -6.286, maximum 7.943, mean
-1.155e-05, SD 0.2543, RMS 0.2543
> ui tool show "Volume Viewer"
> show target m
> hide target m
> show #15
> log metadata #2
No models had metadata
> log chains #2
Chain information for Refined_aldolaseA_noDMSO_cyc_2_real_space_refined.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> log metadata #4
The model has no metadata
> log chains #4
Chain information for 4_ALDOA_real_space_refined_051.pdb #4
---
Chain | Description
A B C D | No description available
> log metadata #8
The model has no metadata
> log chains #8
Chain information for RMATet_dim_AB.pdb #8
---
Chain | Description
A B | No description available
> log metadata #9
The model has no metadata
> log chains #9
Chain information for RMATet_dim_AC.pdb #9
---
Chain | Description
A C | No description available
> log metadata #10
The model has no metadata
> log chains #10
Chain information for RMATet_dim_AD.pdb #10
---
Chain | Description
A D | No description available
> log metadata #11
The model has no metadata
> log chains #11
Chain information for RMATet.pdb #11
---
Chain | Description
A B C D | No description available
> log metadata #12
No models had metadata
> log chains #12
Chain information for hFBP2_tet_5et5.pdb #12
---
Chain | Description
A B C D | No description available
> log metadata #13
No models had metadata
> log chains #13
Chain information for hFBP2_BC_dimer.pdb #13
---
Chain | Description
B C | No description available
> log metadata #14
No models had metadata
> log chains #14
Chain information for hFBP2_AD_dimer.pdb #14
---
Chain | Description
A D | No description available
> volume sel show
> volume sel style surface
[Repeated 1 time(s)]
> hide #!1 models
> hide #1.1 models
> ui tool show "Map Statistics"
> hide #!3 models
> save "C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/Chimera
> session_Complex_hFBP2+hALDOA_3 expts.cxs"
——— End of log from Mon Aug 26 22:00:46 2024 ———
opened ChimeraX session
> ui windowfill toggle
[Repeated 1 time(s)]
> open "C:/Users/Jurgen/My Files/CHUM_Inst_du_Cancer/Compounds/Cryo-
> EM/NoDMSO/no_DMSO_P223_J215_sharp-fixed.ccp4"
Opened no_DMSO_P223_J215_sharp-fixed.ccp4 as #15, grid size 256,256,256, pixel
1.07, shown at level 0.6, step 1, values float32
> surface dust #1 size 10.7
> surface dust #7 size 13.6
> surface dust #15 size 10.7
> hide #!1 models
> hide #!7 models
> show #!2 models
> select add #15
2 models selected
> transparency #15.1 70
> hide #!2 models
> volume #15 save recentered-noDMSO_P223_J215_sharp.mrc
Expected a keyword
> volume #15 save recentered_noDMSO_P223_J215_sharp.mrc
Expected a keyword
> volume #15 save mymap.mrc
Expected a keyword
> volume #16 save mymap.mrc
Expected a keyword
> save "C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/Chimera
> session_Complex_hFBP2+hALDOA_3 expts.cxs"
> save recentered_no_DMSO_P223_J215_sharp.mrc #15
> save as recentered_no_DMSO_P223_J215_sharp.mrc #15
Cannot determine format for 'as'
> save
> C:\Users\Jurgen\Desktop\cryoEM_ALDOA_hFBP2_Transfer\Transfer\recentered_no_DMSO_P223_J215_sharp.mrc
> #15
> open
> C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/recentered_no_DMSO_P223_J215_sharp.mrc
Opened recentered_no_DMSO_P223_J215_sharp.mrc as #16, grid size 256,256,256,
pixel 1.07, shown at level 0.6, step 1, values float32
> hide #!15 models
> surface dust #16 size 10.7
> transparency #16 80
> show #!2 models
> hide #!2 models
> show #!1 models
> select subtract #15
Nothing selected
> fitmap #1 inMap map #16
Invalid "inMap" argument: invalid density map specifier
> help help:user
> fitmap #1 inMap #16
Fit map no_DMSO_P223_J215_sharp.mrc in map
recentered_no_DMSO_P223_J215_sharp.mrc using 297671 points
correlation = 1, correlation about mean = 0.9999, overlap = 4.78e+05
steps = 44, shift = 0.223, angle = 0.00624 degrees
Position of no_DMSO_P223_J215_sharp.mrc (#1) relative to
recentered_no_DMSO_P223_J215_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.99999999 -0.00002638 0.00010406 136.83859299
0.00002637 1.00000000 0.00001820 136.85090168
-0.00010406 -0.00001819 0.99999999 136.83979353
Axis -0.16712202 0.95571480 0.24223840
Axis point 986740.79896265 0.00000000 -1541574.22521994
Rotation angle (degrees) 0.00623819
Shift along axis 141.06954301
> save "C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/Chimera
> session_Complex_hFBP2+hALDOA_3 expts.cxs"
> hide #!1 models
> cd C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer
Current working directory is:
C:\Users\Jurgen\Desktop\cryoEM_ALDOA_hFBP2_Transfer\Transfer
> show #!6 models
> show #!5 models
> hide #!16 models
> show #!16 target m
> hide #!16 models
> hide #!5 models
> show #!5 models
> volume #6 level 0.07026
> volume #5 level 0.04944
> show #!16 models
> select add #6
2 models selected
> transparency #6.1 80
> transparency #6.1 50
> fitmap #6 inMap #16
Fit map cryosparc_P25_J144_009_volume_map_sharp.mrc in map
recentered_no_DMSO_P223_J215_sharp.mrc using 68903 points
correlation = 0.08464, correlation about mean = 0.03974, overlap = 2671
steps = 120, shift = 3.19, angle = 5.78 degrees
Position of cryosparc_P25_J144_009_volume_map_sharp.mrc (#6) relative to
recentered_no_DMSO_P223_J215_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.99521122 -0.09525888 0.02191755 12.21268928
0.09576541 0.99512995 -0.02335315 -6.90818321
-0.01958622 0.02534026 0.99948699 0.16517651
Axis 0.24170931 0.20602061 0.94822577
Axis point 81.85516676 119.81398359 0.00000000
Rotation angle (degrees) 5.78104840
Shift along axis 1.68531720
> set bgColor gray
> set bgColor #80808000
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> show #!6 models
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.99521,-0.095259,0.021918,22.918,0.095765,0.99513,-0.023353,-6.1021,-0.019586,0.02534,0.99949,15.972
> ui mousemode right "rotate selected models"
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.9804,-0.053401,0.18963,-0.92717,0.066441,0.99579,-0.063082,2.296,-0.18547,0.074445,0.97983,32.805
> view matrix models
> #6,0.99198,-0.11201,-0.058569,35.227,0.11183,0.99371,-0.0063751,-9.9872,0.058914,-0.00022595,0.99826,9.5804
> view matrix models
> #6,0.98263,-0.057003,0.17659,0.83642,0.068513,0.99586,-0.059775,1.6279,-0.17245,0.070836,0.98247,31.32
> view matrix models
> #6,0.012041,-0.3137,0.94945,57.485,-0.83482,0.51949,0.18222,141.95,-0.55039,-0.79481,-0.25562,335.83
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right select
> ui mousemode right "translate selected models"
> select add #6
2 models selected
> view matrix models
> #6,0.012041,-0.3137,0.94945,50.643,-0.83482,0.51949,0.18222,82.092,-0.55039,-0.79481,-0.25562,345.3
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.012041,-0.3137,0.94945,55.053,-0.83482,0.51949,0.18222,69.379,-0.55039,-0.79481,-0.25562,352.28
> ui mousemode right "rotate selected models"
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.27666,-0.4738,0.83604,55.967,-0.94658,-0.28433,0.15211,185.61,0.16565,-0.83347,-0.52716,301.95
> view matrix models
> #6,0.24824,-0.51009,0.82352,65.463,-0.96848,-0.11249,0.22226,158.61,-0.02074,-0.85274,-0.52193,326.67
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> select add #16
2 models selected
> transparency #16.1 50
> select add #6
4 models selected
> select subtract #16
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.33937,-0.35291,0.87194,28.986,-0.83994,0.30363,0.4498,63.778,-0.42348,-0.88502,-0.19338,340.09
> ui mousemode right select
> select clear
> volume #6 level 0.1237
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.33937,-0.35291,0.87194,35.389,-0.83994,0.30363,0.4498,62.155,-0.42348,-0.88502,-0.19338,316.58
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.80309,-0.44286,-0.39866,145.43,-0.54654,-0.814,-0.19674,244.79,-0.23738,0.37588,-0.89575,222.54
> view matrix models
> #6,0.98146,0.079523,-0.17436,30.925,-0.017171,-0.86969,-0.4933,223.18,-0.19087,0.48715,-0.85221,197.63
> view matrix models
> #6,0.94972,0.31191,-0.027321,-12.183,0.23781,-0.77534,-0.58506,191.4,-0.20367,0.54915,-0.81053,186.36
> view matrix models
> #6,0.92908,0.16113,0.33294,-34.981,0.33262,-0.75767,-0.56151,174.69,0.16178,0.63243,-0.75753,124.68
> view matrix models
> #6,0.91499,0.21421,0.34191,-40.975,0.34419,-0.85659,-0.38443,163.91,0.21053,0.46943,-0.8575,151.28
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> select add #6
2 models selected
> select subtract #6
Nothing selected
> select add #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.9705,-0.12232,-0.20775,61.535,-0.18412,-0.93235,-0.31117,229.15,-0.15564,0.34024,-0.92737,220.84
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> select add #6
2 models selected
> view matrix models
> #6,0.9705,-0.12232,-0.20775,69.003,-0.18412,-0.93235,-0.31117,219.71,-0.15564,0.34024,-0.92737,223.93
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.82095,0.56394,0.089489,166.6,-0.52236,-0.67845,-0.51657,254.67,-0.2306,-0.47083,0.85155,116.34
> view matrix models
> #6,-0.44137,0.83184,0.3365,56.391,-0.89715,-0.40162,-0.1839,225.33,-0.017831,-0.38306,0.92355,70.492
> view matrix models
> #6,-0.30169,0.90883,0.28812,35.594,-0.95054,-0.26332,-0.16472,212.28,-0.073835,-0.32356,0.94332,67.514
> view matrix models
> #6,-0.4379,0.89171,0.11443,75.705,-0.85004,-0.36923,-0.37564,239.01,-0.29271,-0.26176,0.91967,89.534
> view matrix models
> #6,-0.63912,0.61528,0.46147,92.335,-0.74864,-0.63517,-0.18998,237,0.17622,-0.4669,0.86657,64.142
> view matrix models
> #6,-0.39558,0.75203,0.52722,37.368,-0.85933,-0.50567,0.076519,201.77,0.32414,-0.42279,0.84627,42.993
> view matrix models
> #6,-0.53877,0.77342,0.33399,75.925,-0.84218,-0.50465,-0.1899,232.18,0.021676,-0.3836,0.92325,65.753
> view matrix models
> #6,-0.46287,0.80375,0.37383,57.959,-0.88528,-0.39774,-0.241,230.39,-0.045018,-0.44249,0.89564,84.657
> view matrix models
> #6,-0.46883,0.80826,0.35625,60.279,-0.88254,-0.41204,-0.22659,230.07,-0.036358,-0.42063,0.9065,79.539
> ui mousemode right select
> select clear
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.46883,0.80826,0.35625,63.646,-0.88254,-0.41204,-0.22659,231.54,-0.036358,-0.42063,0.9065,97.666
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.40648,0.81512,0.41274,48.227,-0.86127,-0.49263,0.12467,195.95,0.30495,-0.30481,0.90228,41.898
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> select add #6
2 models selected
> view matrix models
> #6,-0.40648,0.81512,0.41274,42.855,-0.86127,-0.49263,0.12467,286.09,0.30495,-0.30481,0.90228,34.165
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.12675,0.91101,0.39243,-0.90831,-0.95834,-0.21456,0.18855,255.48,0.25597,-0.35218,0.90025,46.326
> ui mousemode right select
> select clear
> fitmap #6 inMap #16
Fit map cryosparc_P25_J144_009_volume_map_sharp.mrc in map
recentered_no_DMSO_P223_J215_sharp.mrc using 45805 points
correlation = 0.1739, correlation about mean = 0.07115, overlap = 6589
steps = 128, shift = 2.89, angle = 5.15 degrees
Position of cryosparc_P25_J144_009_volume_map_sharp.mrc (#6) relative to
recentered_no_DMSO_P223_J215_sharp.mrc (#16) coordinates:
Matrix rotation and translation
-0.04753249 0.92534041 0.37614596 -9.57265106
-0.95547835 -0.15190522 0.25295437 240.75923119
0.29120744 -0.34737578 0.89136317 39.88058249
Axis -0.30379081 0.04298226 -0.95176871
Axis point 97.61627192 128.96085771 0.00000000
Rotation angle (degrees) 98.86096551
Shift along axis -24.70063217
> fitmap #6 inMap #16
Fit map cryosparc_P25_J144_009_volume_map_sharp.mrc in map
recentered_no_DMSO_P223_J215_sharp.mrc using 45805 points
correlation = 0.1739, correlation about mean = 0.07119, overlap = 6588
steps = 44, shift = 0.0113, angle = 0.0122 degrees
Position of cryosparc_P25_J144_009_volume_map_sharp.mrc (#6) relative to
recentered_no_DMSO_P223_J215_sharp.mrc (#16) coordinates:
Matrix rotation and translation
-0.04752613 0.92537299 0.37606660 -9.57366799
-0.95553647 -0.15180887 0.25279265 240.76680423
0.29101774 -0.34733110 0.89144253 39.89505887
Axis -0.30368200 0.04303747 -0.95180093
Axis point 97.62647092 128.96609990 0.00000000
Rotation angle (degrees) 98.85568644
Shift along axis -24.70280920
> show #!2 models
> hide #!16 models
> hide #!6 models
> show #!16 models
> select clear
> show #!6 models
> hide #!6 models
> hide #!2 models
> show #!3 models
> select add #3
2 models selected
> volume #3 level 0.1947
> hide #!16 models
> volume #6 level 0.1344
> volume #3 level 0.1022
> show #4 models
> show #!16 models
> hide #4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
Drag select of 16 recentered_no_DMSO_P223_J215_sharp.mrc
> select clear
> show #!3 models
> ui mousemode right "rotate selected models"
> select add #3
2 models selected
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.2352,0.9673,0.094938,-45.02,-0.94537,0.25036,-0.20878,249.87,-0.22572,-0.040646,0.97334,37.934
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.2352,0.9673,0.094938,-34.161,-0.94537,0.25036,-0.20878,254.09,-0.22572,-0.040646,0.97334,41.931
> view matrix models
> #3,0.2352,0.9673,0.094938,-34.337,-0.94537,0.25036,-0.20878,254.39,-0.22572,-0.040646,0.97334,42.184
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.65539,0.74651,0.11482,107.76,-0.74089,-0.60589,-0.28978,354.66,-0.14675,-0.27499,0.95018,66.791
> ui mousemode right "translate selected models"
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.65539,0.74651,0.11482,148.82,-0.74089,-0.60589,-0.28978,275.6,-0.14675,-0.27499,0.95018,56.39
> ui mousemode right select
> select clear
> ui mousemode right "rotate selected models"
> select add #3
2 models selected
> view matrix models
> #3,-0.61861,0.78096,0.086121,143.03,-0.78396,-0.62082,-0.0014993,246.79,0.052294,-0.068442,0.99628,-3.1108
> volume #3 level 0.1211
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.61861,0.78096,0.086121,144.96,-0.78396,-0.62082,-0.0014993,244.98,0.052294,-0.068442,0.99628,7.7005
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.47593,0.86235,0.17273,-18.75,-0.87462,0.44346,0.1959,87.191,0.092333,-0.24431,0.96529,30.325
> view matrix models
> #3,0.63155,0.7735,-0.053229,1.6829,-0.65341,0.56795,0.50049,3.2044,0.41736,-0.28131,0.86411,6.034
> view matrix models
> #3,0.35342,0.91769,-0.18151,34.287,-0.74367,0.39333,0.5406,33.559,0.56749,-0.056073,0.82147,-38.632
> view matrix models
> #3,0.14351,0.98334,0.11159,15.565,-0.97516,0.12129,0.18534,145.32,0.16871,-0.13542,0.97632,4.2468
> view matrix models
> #3,0.67106,-0.69845,0.24868,158.5,-0.73324,-0.57563,0.36195,186.42,-0.10966,-0.42524,-0.89842,316.2
> view matrix models
> #3,-0.14838,-0.98506,-0.087361,345.94,-0.84125,0.17217,-0.51249,209.11,0.51988,-0.002552,-0.85423,171.68
> view matrix models
> #3,0.11728,-0.97293,0.19915,273.75,-0.96995,-0.15526,-0.18734,229.25,0.21319,-0.17119,-0.9619,247.89
> view matrix models
> #3,-0.11546,-0.99237,0.043221,326.2,-0.98937,0.11877,0.083908,160.3,-0.088401,-0.033074,-0.99554,272.41
> view matrix models
> #3,-0.038798,-0.99566,0.084586,311.5,-0.99925,0.038548,-0.0045824,183.64,0.0013019,-0.0847,-0.99641,267.92
> view matrix models
> #3,-0.031766,-0.99615,0.08172,311.02,-0.99949,0.031894,0.00026091,183.97,-0.0028663,-0.08167,-0.99666,268.08
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.031766,-0.99615,0.08172,265.31,-0.99949,0.031894,0.00026091,264.2,-0.0028663,-0.08167,-0.99666,278.89
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.3005,-0.14686,0.94241,-1.7108,-0.95313,-0.0097338,0.30241,225.73,-0.035238,-0.98911,-0.1429,298.68
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.29959,-0.10803,0.94793,-7.5664,-0.95352,-0.06743,0.29368,234.72,0.032193,-0.99186,-0.12321,287.84
> view matrix models
> #3,0.27596,-0.35962,0.89136,36.819,-0.92911,-0.33732,0.15156,286.17,0.24617,-0.86999,-0.42721,281.93
> view matrix models
> #3,0.25991,0.025723,0.96529,-22.794,-0.94131,-0.21619,0.25922,257.7,0.21536,-0.97601,-0.031979,250.46
> view matrix models
> #3,0.26769,-0.090181,0.95927,-7.2924,-0.96267,0.016412,0.27018,227.48,-0.040109,-0.99579,-0.082421,292.59
> ui mousemode right select
> fitmap #3 inMap #16
Fit map cryosparc_P352_J79_007_WT_volume_map.mrc in map
recentered_no_DMSO_P223_J215_sharp.mrc using 287754 points
correlation = 0.2735, correlation about mean = 0.1183, overlap = 2.637e+04
steps = 112, shift = 5.05, angle = 18.7 degrees
Position of cryosparc_P352_J79_007_WT_volume_map.mrc (#3) relative to
recentered_no_DMSO_P223_J215_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.27244541 -0.05255255 0.96073499 -15.91067080
-0.92129433 -0.30219820 0.24473047 264.37987657
0.27747117 -0.95179540 -0.13074887 248.61376855
Axis -0.73457164 0.41946960 -0.53333831
Axis point 0.00000000 212.98991856 35.86391570
Rotation angle (degrees) 125.46818680
Shift along axis -10.00839786
> fitmap #3 inMap #16
Fit map cryosparc_P352_J79_007_WT_volume_map.mrc in map
recentered_no_DMSO_P223_J215_sharp.mrc using 287754 points
correlation = 0.2735, correlation about mean = 0.1183, overlap = 2.637e+04
steps = 36, shift = 0.0138, angle = 0.00556 degrees
Position of cryosparc_P352_J79_007_WT_volume_map.mrc (#3) relative to
recentered_no_DMSO_P223_J215_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.27240914 -0.05264181 0.96074039 -15.89369951
-0.92131414 -0.30218466 0.24467260 264.40119382
0.27744100 -0.95179476 -0.13081751 248.63153165
Axis -0.73456508 0.41950820 -0.53331698
Axis point 0.00000000 213.00660510 35.86484538
Rotation angle (degrees) 125.47140066
Shift along axis -10.00599207
> show #!6 models
> hide #!3 models
> fitmap #6 inMap #16
Fit map cryosparc_P25_J144_009_volume_map_sharp.mrc in map
recentered_no_DMSO_P223_J215_sharp.mrc using 43744 points
correlation = 0.1756, correlation about mean = 0.06744, overlap = 6580
steps = 44, shift = 0.0294, angle = 0.0609 degrees
Position of cryosparc_P25_J144_009_volume_map_sharp.mrc (#6) relative to
recentered_no_DMSO_P223_J215_sharp.mrc (#16) coordinates:
Matrix rotation and translation
-0.04659418 0.92528623 0.37639656 -9.72222012
-0.95568396 -0.15094249 0.25275389 240.70314586
0.29068393 -0.34793929 0.89131425 40.00153479
Axis -0.30393024 0.04336767 -0.95170671
Axis point 97.60769370 129.01703189 0.00000000
Rotation angle (degrees) 98.80726900
Shift along axis -24.67611827
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> ui mousemode right "rotate selected models"
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.43655,0.039549,0.89881,-41.861,0.84597,0.32198,-0.42506,35.256,-0.30621,0.94592,0.1071,36.307
> view matrix models
> #3,0.40778,0.10248,0.90731,-47.759,0.85233,0.31369,-0.4185,34.731,-0.3275,0.94398,0.040573,47.722
> view matrix models
> #3,0.38185,0.15562,0.91103,-52.092,0.84273,0.3461,-0.41234,30.792,-0.37948,0.9252,0.0010146,61.994
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.38185,0.15562,0.91103,-51.841,0.84273,0.3461,-0.41234,33.313,-0.37948,0.9252,0.0010146,62.315
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.23139,0.068989,0.97041,-28.08,0.89679,0.37154,-0.24025,1.1437,-0.37712,0.92585,0.024102,59.009
> view matrix models
> #3,0.27697,0.10727,0.95487,-37.223,0.88337,0.36259,-0.29697,11.254,-0.37808,0.92575,0.005673,61.472
> ui mousemode right select
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!2 models
> show #!3 models
> hide #!2 models
> fitmap #3 inMap #16
Fit map cryosparc_P352_J79_007_WT_volume_map.mrc in map
recentered_no_DMSO_P223_J215_sharp.mrc using 287754 points
correlation = 0.2735, correlation about mean = 0.1183, overlap = 2.637e+04
steps = 100, shift = 3.81, angle = 9.92 degrees
Position of cryosparc_P352_J79_007_WT_volume_map.mrc (#3) relative to
recentered_no_DMSO_P223_J215_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.27246683 -0.05243446 0.96073537 -15.92916449
0.92128661 0.30217587 -0.24478709 10.38647739
-0.27747577 0.95180900 0.13064007 26.15335219
Axis 0.60490168 0.62593886 0.49223419
Axis point 1.72491733 0.00000000 24.01849258
Rotation angle (degrees) 98.47388519
Shift along axis 9.73929568
> fitmap #3 inMap #16
Fit map cryosparc_P352_J79_007_WT_volume_map.mrc in map
recentered_no_DMSO_P223_J215_sharp.mrc using 287754 points
correlation = 0.2735, correlation about mean = 0.1183, overlap = 2.637e+04
steps = 44, shift = 0.0161, angle = 0.0118 degrees
Position of cryosparc_P352_J79_007_WT_volume_map.mrc (#3) relative to
recentered_no_DMSO_P223_J215_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.27238137 -0.05262123 0.96074939 -15.89400644
0.92131968 0.30218468 -0.24465171 10.34843972
-0.27744987 0.95179589 0.13079045 26.12546942
Axis 0.60482326 0.62592939 0.49234259
Axis point 1.74646289 0.00000000 23.98948871
Rotation angle (degrees) 98.47174972
Shift along axis 9.72700912
> ui mousemode right select
> select subtract #3
Nothing selected
> show #4 models
> hide #!3 models
> show #!3 models
> hide #!16 models
> hide #!3 models
> select add #4
10472 atoms, 10672 bonds, 1372 residues, 1 model selected
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> select clear
> label height 2
> label height 1
> label height 0.9
[Repeated 1 time(s)]Drag select of 22 residues
Drag select of 5 residues
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide labels
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select add #4
10472 atoms, 10672 bonds, 1372 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #4
10472 atoms, 10672 bonds, 1372 residues, 2 models selected
> hide labels
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> label hide
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label #4
> label hide #4
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label hide chains
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label hide residues
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label hide model #4
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label hide models #4
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> ui mousemode right label
[Repeated 1 time(s)]
> label hide #4
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label hide
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label delete models #4
Expected a keyword
> label delete models #4
Expected a keyword
> label delete #4
> show #!3 models
> color red chain A
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /A red target c
> color /B cyan target c
> color /C orange target c
> select add #3
10472 atoms, 10672 bonds, 1372 residues, 3 models selected
> select subtract #4
2 models selected
> transparency #3.1 70
> transparency #3.1 60
> ui mousemode right select
> select subtract #3
Nothing selected
> select add #4
10472 atoms, 10672 bonds, 1372 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.42686,-0.41482,-0.80356,229.55,0.24196,0.90858,-0.3405,26.091,0.87135,-0.049079,0.48821,-35.318
> view matrix models
> #4,0.048278,0.21674,0.97503,-36.706,-0.50379,0.84819,-0.1636,103.57,-0.86248,-0.48332,0.15014,280.41
> view matrix models
> #4,-0.12128,0.18715,0.97482,-11.772,-0.52534,0.82115,-0.22301,117.48,-0.8422,-0.53916,-0.0012671,304.83
> view matrix models
> #4,0.068586,0.21955,0.97319,-39.353,-0.50048,0.85143,-0.15681,101.85,-0.86303,-0.4763,0.16828,277.21
> view matrix models
> #4,0.043896,-0.50449,-0.8623,296.41,0.21612,0.84749,-0.48482,56,0.97538,-0.16508,0.14623,11.29
> view matrix models
> #4,0.10862,0.22463,0.96837,-44.36,-0.49348,0.85782,-0.14363,98.441,-0.86295,-0.46227,0.20403,270.73
> view matrix models
> #4,-0.078158,0.19573,0.97754,-18.596,-0.52091,0.82802,-0.20744,114.01,-0.85003,-0.52542,0.037238,299.01
> view matrix models
> #4,0.15616,0.22986,0.96061,-49.936,-0.48437,0.8654,-0.12833,94.335,-0.86081,-0.44525,0.24648,262.73
> ui mousemode right select
> hide #4 models
> show #4 models
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.15616,0.22986,0.96061,-45.819,-0.48437,0.8654,-0.12833,93.362,-0.86081,-0.44525,0.24648,271.94
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.064257,0.13,-0.98943,244.36,0.93121,0.36426,-0.012616,-28.245,0.35877,-0.92218,-0.14447,236.05
> view matrix models
> #4,-0.1379,0.28302,-0.94915,227.61,-0.9893,-0.085525,0.11823,252.6,-0.047715,0.95529,0.29179,-23.417
> view matrix models
> #4,-0.24411,0.2244,-0.94343,247.89,-0.8998,-0.41519,0.13407,284.1,-0.36162,0.88162,0.30327,23.775
> view matrix models
> #4,-0.40865,0.15889,-0.89875,271.32,-0.83259,-0.46831,0.29578,262.3,-0.3739,0.86916,0.32366,24.364
> ui mousemode right "translate selected models"
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.40865,0.15889,-0.89875,281.26,-0.83259,-0.46831,0.29578,261.2,-0.3739,0.86916,0.32366,25.751
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.35808,0.026322,-0.93332,297.36,-0.83522,-0.45585,0.30759,258.33,-0.41735,0.88967,0.18521,46.052
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.35808,0.026322,-0.93332,303.95,-0.83522,-0.45585,0.30759,267.11,-0.41735,0.88967,0.18521,47.876
> view matrix models
> #4,-0.35808,0.026322,-0.93332,301.04,-0.83522,-0.45585,0.30759,267.56,-0.41735,0.88967,0.18521,46.404
> view matrix models
> #4,-0.35808,0.026322,-0.93332,301.07,-0.83522,-0.45585,0.30759,267.52,-0.41735,0.88967,0.18521,46.903
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.35524,0.018984,-0.93458,301.87,-0.83541,-0.45502,0.3083,267.34,-0.4194,0.89028,0.1775,48.059
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.35524,0.018984,-0.93458,299.34,-0.83541,-0.45502,0.3083,267.69,-0.4194,0.89028,0.1775,47.396
> view matrix models
> #4,-0.35524,0.018984,-0.93458,299.25,-0.83541,-0.45502,0.3083,267.81,-0.4194,0.89028,0.1775,45.9
> view matrix models
> #4,-0.35524,0.018984,-0.93458,299.78,-0.83541,-0.45502,0.3083,267.72,-0.4194,0.89028,0.1775,46.365
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.3523,0.011411,-0.93582,300.6,-0.83561,-0.45415,0.30903,267.53,-0.42148,0.89085,0.16953,47.565
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> fitmap #4 inMap #3
Fit molecule 4_ALDOA_real_space_refined_051.pdb (#4) to map
cryosparc_P352_J79_007_WT_volume_map.mrc (#3) using 10472 atoms
average map value = 0.1427, steps = 224
shifted from previous position = 2.98
rotated from previous position = 13.5 degrees
atoms outside contour = 5063, contour level = 0.12115
Position of 4_ALDOA_real_space_refined_051.pdb (#4) relative to
cryosparc_P352_J79_007_WT_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.87580645 -0.47532166 -0.08385947 316.13785845
-0.47612004 0.82228539 0.31169931 44.87804858
-0.07920101 0.31291543 -0.94647300 221.85194471
Axis 0.24918822 -0.95453820 -0.16359115
Axis point 163.78503018 0.00000000 107.28241483
Rotation angle (degrees) 179.86018875
Shift along axis -0.35299743
> fitmap #4 inMap #3
Fit molecule 4_ALDOA_real_space_refined_051.pdb (#4) to map
cryosparc_P352_J79_007_WT_volume_map.mrc (#3) using 10472 atoms
average map value = 0.1427, steps = 44
shifted from previous position = 0.0384
rotated from previous position = 0.119 degrees
atoms outside contour = 5081, contour level = 0.12115
Position of 4_ALDOA_real_space_refined_051.pdb (#4) relative to
cryosparc_P352_J79_007_WT_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.87665783 -0.47375147 -0.08384882 316.05749381
-0.47454805 0.82276422 0.31283095 44.47208663
-0.07921631 0.31403599 -0.94610052 221.67873167
Axis 0.24833262 -0.95466360 -0.16415945
Axis point 163.67210464 0.00000000 107.21663087
Rotation angle (degrees) 179.86098569
Shift along axis -0.35915469
> hide #!3 models
> hide #4 models
> show #4 models
> hide #4 models
> show #!6 models
> show #!5 models
> volume #5 level 0.195
> select clear
> select add #5
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.1011,-0.15997,0.98193,36.09,0.99449,0.011165,0.10421,-14.264,-0.027634,0.98706,0.15796,-15.125
> view matrix models
> #5,-0.092112,-0.10223,0.99049,27.053,0.99029,-0.11338,0.080392,4.0242,0.10409,0.98828,0.11168,-25.746
> view matrix models
> #5,0.21294,0.22139,-0.95165,181.88,-0.89488,0.43519,-0.099,188.06,0.39223,0.8727,0.29079,-68.081
> view matrix models
> #5,0.21927,0.24323,-0.94486,177.68,-0.89123,0.44401,-0.092521,185.78,0.39703,0.86238,0.31413,-70.196
> view matrix models
> #5,-0.41626,-0.10218,0.90349,76.682,0.90837,-0.0030491,0.41816,-39.401,-0.039973,0.99476,0.094085,-6.9676
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.41626,-0.10218,0.90349,90.173,0.90837,-0.0030491,0.41816,-32.852,-0.039973,0.99476,0.094085,-5.5409
> ui mousemode right "rotate selected models"
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.40273,-0.14851,0.90319,94.129,0.89191,0.15805,0.42369,-50.85,-0.20567,0.9762,0.068807,19.78
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.40273,-0.14851,0.90319,99.393,0.89191,0.15805,0.42369,-48.065,-0.20567,0.9762,0.068807,21.972
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.40315,-0.23045,0.88564,111.36,0.89147,0.11976,0.43697,-44.992,-0.20676,0.96569,0.15715,12.873
> view matrix models
> #5,-0.38032,-0.25732,0.88834,111.5,0.85155,0.27733,0.44491,-60.01,-0.36085,0.92567,0.11364,41.526
> view matrix models
> #5,-0.33365,-0.65342,0.6795,178.19,0.87464,0.054342,0.48172,-40.414,-0.35169,0.75504,0.55338,8.6732
> view matrix models
> #5,-0.41274,0.03287,0.91025,77.996,0.90986,-0.03166,0.41371,-26.284,0.042418,0.99896,-0.01684,-0.66896
> view matrix models
> #5,-0.24577,-0.19143,0.95024,79.926,0.77255,0.5534,0.3113,-67.701,-0.58545,0.81062,0.011876,94.656
> view matrix models
> #5,0.067928,-0.025011,0.99738,16.316,0.84069,0.53975,-0.043721,-32.159,-0.53724,0.84145,0.05769,79.668
> view matrix models
> #5,-0.051024,-0.086003,0.99499,38.344,0.82894,0.55202,0.090223,-48.115,-0.55701,0.82939,0.043125,85.243
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.051024,-0.086003,0.99499,38.823,0.82894,0.55202,0.090223,-38.944,-0.55701,0.82939,0.043125,84.359
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.017661,-0.16303,0.98646,40.752,0.76367,0.63903,0.091936,-41.678,-0.64537,0.75171,0.13578,93.391
> view matrix models
> #5,0.093031,-0.23686,0.96708,42.779,0.79129,0.60712,0.072579,-38.898,-0.60433,0.75848,0.24391,74.761
> view matrix models
> #5,0.25944,-0.13247,0.95663,11.313,0.77709,0.61679,-0.12533,-14.832,-0.57344,0.7759,0.26296,66.662
> ui mousemode right select
> fitmap #5 inMap #6
Fit map cryosparc_P25_J143_009_volume_map_sharp.mrc in map
cryosparc_P25_J144_009_volume_map_sharp.mrc using 23679 points
correlation = 0.169, correlation about mean = 0.04145, overlap = 913
steps = 60, shift = 2.55, angle = 3.73 degrees
Position of cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) relative to
cryosparc_P25_J144_009_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.91767456 -0.33958072 0.20629674 241.24172276
0.35067403 -0.44807177 0.82234994 39.02753646
-0.18681844 0.82699253 0.53026620 -33.73978162
Axis 0.00584441 0.49488097 0.86894112
Axis point 115.57644240 57.87709828 0.00000000
Rotation angle (degrees) 156.59789904
Shift along axis -8.59398221
> volume #5 level 0.2262
> fitmap #5 inMap #6
Fit map cryosparc_P25_J143_009_volume_map_sharp.mrc in map
cryosparc_P25_J144_009_volume_map_sharp.mrc using 20831 points
correlation = 0.1735, correlation about mean = 0.04151, overlap = 882
steps = 36, shift = 0.0368, angle = 0.141 degrees
Position of cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) relative to
cryosparc_P25_J144_009_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.91784675 -0.33844496 0.20739420 241.01542886
0.35132617 -0.44950661 0.82128785 39.25061903
-0.18473567 0.82667940 0.53148275 -34.12944671
Axis 0.00679498 0.49420231 0.86932037
Axis point 115.46365061 58.00798356 0.00000000
Rotation angle (degrees) 156.62607965
Shift along axis -8.63398246
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.29093,-0.070027,0.95418,0.67709,0.70866,0.6858,-0.16574,-8.7423,-0.64277,0.72441,0.24915,85.133
> view matrix models
> #5,0.45517,0.028168,0.88996,-23.389,0.62947,0.69673,-0.344,20.746,-0.62975,0.71678,0.2994,78.495
> view matrix models
> #5,0.37181,0.18722,0.90923,-34.67,0.6307,0.66774,-0.3954,30.192,-0.68116,0.72047,0.13019,104.41
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.37181,0.18722,0.90923,-36.519,0.6307,0.66774,-0.3954,30.813,-0.68116,0.72047,0.13019,103.38
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.37607,0.21135,0.90216,-39.092,0.59506,0.69124,-0.40999,34.047,-0.71026,0.69103,0.13419,109.97
> view matrix models
> #5,0.28734,0.34145,0.8949,-43.09,0.63434,0.63221,-0.44489,40.523,-0.71767,0.6955,-0.034933,130.44
> ui mousemode right select
> fitmap #5 inMap #6
Fit map cryosparc_P25_J143_009_volume_map_sharp.mrc in map
cryosparc_P25_J144_009_volume_map_sharp.mrc using 20831 points
correlation = 0.1895, correlation about mean = 0.05367, overlap = 970.8
steps = 60, shift = 2.19, angle = 5.45 degrees
Position of cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) relative to
cryosparc_P25_J144_009_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.86216854 -0.33227478 0.38243808 213.11889451
0.41943184 -0.04475468 0.90668295 -30.80111711
-0.28415198 0.94212022 0.17795269 3.84865105
Axis 0.03524987 0.66306498 0.74773142
Axis point 110.82214635 21.37701014 0.00000000
Rotation angle (degrees) 149.82398050
Shift along axis -10.03297144
> hide #!5 models
> show #!5 models
> hide #!6 models
> select clear
> volume #5 level 0.2677
> show #4 models
> show #!16 models
> hide #!5 models
> show #!5 models
> hide #4 models
> fitmap #5 inMap #16
Fit map cryosparc_P25_J143_009_volume_map_sharp.mrc in map
recentered_no_DMSO_P223_J215_sharp.mrc using 17698 points
correlation = 0.189, correlation about mean = 0.05397, overlap = 2823
steps = 72, shift = 1.53, angle = 7.07 degrees
Position of cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) relative to
recentered_no_DMSO_P223_J215_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.25278723 0.23923791 0.93747738 -34.73626035
0.72835578 0.59074746 -0.34715315 20.15627515
-0.63686457 0.77057295 -0.02491690 110.77164212
Axis 0.56117561 0.79042827 0.24557091
Axis point 36.10307237 0.00000000 79.98040959
Rotation angle (degrees) 95.20336711
Shift along axis 23.64124087
> show #4 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!6 models
> select add #5
2 models selected
> hide #!16 models
> hide #!6 models
> select clear
> save "C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/Chimera
> session_Complex_hFBP2+hALDOA_3 expts.cxs"
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 2 time(s)]
"Unable to get device information for 4352:" "The operation completed
successfully."
> show #8 models
> select add #8
5400 atoms, 5336 bonds, 850 residues, 1 model selected
> ui mousemode right "translate selected models"
> show #4 models
> help help:user
> ui tool show Matchmaker
> matchmaker #8 to #4
Parameters
---
Chain pairing | bb
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 4_ALDOA_real_space_refined_051.pdb, chain B (#4) with
RMATet_dim_AB.pdb, chain A (#8), sequence alignment score = 1723.6
RMSD between 275 pruned atom pairs is 1.272 angstroms; (across all 343 pairs:
1.624)
> hide #8 models
> show #8 models
> hide #8 models
> hide #!5 models
> hide #4 models
> show #4 models
> hide #4 models
> show #8 models
> show #4 models
> hide #4 models
> show #4 models
> matchmaker #8/A to #4/A pairing ss
Parameters
---
Chain pairing | ss
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 4_ALDOA_real_space_refined_051.pdb, chain A (#4) with
RMATet_dim_AB.pdb, chain A (#8), sequence alignment score = 1699
RMSD between 275 pruned atom pairs is 1.290 angstroms; (across all 343 pairs:
1.810)
> matchmaker #8/A to #4/A pairing ss cutoffDistance 1.8
Parameters
---
Chain pairing | ss
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 | 1.8
Matchmaker 4_ALDOA_real_space_refined_051.pdb, chain A (#4) with
RMATet_dim_AB.pdb, chain A (#8), sequence alignment score = 1699
RMSD between 248 pruned atom pairs is 1.206 angstroms; (across all 343 pairs:
1.818)
> matchmaker #8 to #2/A pairing bs cutoffDistance 1.8
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 | 1.8
Matchmaker Refined_aldolaseA_noDMSO_cyc_2_real_space_refined.pdb, chain A (#2)
with RMATet_dim_AB.pdb, chain A (#8), sequence alignment score = 1741
RMSD between 343 pruned atom pairs is 0.250 angstroms; (across all 343 pairs:
0.250)
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #4 models
> show #4 models
> matchmaker #8/A to #4/A pairing ss cutoffDistance 1.8
Parameters
---
Chain pairing | ss
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 | 1.8
Matchmaker 4_ALDOA_real_space_refined_051.pdb, chain A (#4) with
RMATet_dim_AB.pdb, chain A (#8), sequence alignment score = 1699
RMSD between 248 pruned atom pairs is 1.206 angstroms; (across all 343 pairs:
1.818)
> show #!2 models
> hide #4 models
> show #!6 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #8 models
> show #11 models
> hide #11 models
> show #11 models
> show #!16 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #4 models
> hide #!16 models
> hide #!6 models
> show #!16 models
> show #8 models
> select subtract #8
Nothing selected
> hide #4 models
> show #4 models
> hide #8 models
> hide #4 models
> show #4 models
> show #!3 models
> hide #4 models
> show #4 models
> hide #!16 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!3 models
> volume #3 level 0.05182
> hide #!3 models
> show #!6 models
> hide #4 models
> show #11 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #4 models
No reference and/or match structure/chain chosen
> select add #11
10800 atoms, 10672 bonds, 1700 residues, 1 model selected
> show #!6 models
> hide #!6 models
> hide #4 models
> show #4 models
> hide #11 models
> show #11 models
> matchmaker #11/A to #4/D pairing ss
Parameters
---
Chain pairing | ss
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 4_ALDOA_real_space_refined_051.pdb, chain D (#4) with RMATet.pdb,
chain A (#11), sequence alignment score = 1535.8
RMSD between 146 pruned atom pairs is 1.243 angstroms; (across all 343 pairs:
5.827)
> hide #11 models
> hide #4 models
> show #4 models
> show #11 models
> hide #4 models
> ui mousemode right select
> select clear
> show #4 models
> hide #4 models
> show #4 models
> matchmaker #11/A to #4/A pairing ss
Parameters
---
Chain pairing | ss
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 4_ALDOA_real_space_refined_051.pdb, chain A (#4) with RMATet.pdb,
chain A (#11), sequence alignment score = 1699
RMSD between 275 pruned atom pairs is 1.290 angstroms; (across all 343 pairs:
1.810)
> matchmaker #11/B#11/C#11/D to #4/C#4/D#4/B pairing ss
Parameters
---
Chain pairing | ss
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 4_ALDOA_real_space_refined_051.pdb, chain C (#4) with RMATet.pdb,
chain B (#11), sequence alignment score = 1651
Matchmaker 4_ALDOA_real_space_refined_051.pdb, chain D (#4) with RMATet.pdb,
chain C (#11), sequence alignment score = 1535.8
Matchmaker 4_ALDOA_real_space_refined_051.pdb, chain B (#4) with RMATet.pdb,
chain D (#11), sequence alignment score = 1723.6
RMSD between 285 pruned atom pairs is 1.409 angstroms; (across all 1029 pairs:
44.337)
> hide #4 models
> show #4 models
> hide #11 models
> show #11 models
> hide #11 models
> matchmaker #11/B to #4/B pairing ss
Parameters
---
Chain pairing | ss
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 4_ALDOA_real_space_refined_051.pdb, chain B (#4) with RMATet.pdb,
chain B (#11), sequence alignment score = 1723.6
RMSD between 275 pruned atom pairs is 1.272 angstroms; (across all 343 pairs:
1.624)
> show #11 models
> show #!16 models
> hide #4 models
> hide #!16 models
> show #!16 models
> hide #11 models
> show #11 models
> show #!5 models
> hide #11 models
> hide #!16 models
> show #8 models
> select add #8
5400 atoms, 5336 bonds, 850 residues, 1 model selected
> fitmap #8 inMap #5
Fit molecule RMATet_dim_AB.pdb (#8) to map
cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) using 5400 atoms
average map value = 0.09979, steps = 84
shifted from previous position = 2.62
rotated from previous position = 5.26 degrees
atoms outside contour = 4093, contour level = 0.26775
Position of RMATet_dim_AB.pdb (#8) relative to
cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.68647086 0.01478304 0.72700703 -12.60252995
0.70789128 -0.24220459 -0.66349595 142.22690288
0.16627595 0.97011257 -0.17673117 32.67876612
Axis 0.87779014 0.30129875 0.37242924
Axis point 0.00000000 66.95017181 69.05199060
Rotation angle (degrees) 111.48344947
Shift along axis 43.96093978
> fitmap #8 inMap #5
Fit molecule RMATet_dim_AB.pdb (#8) to map
cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) using 5400 atoms
average map value = 0.09971, steps = 60
shifted from previous position = 0.0243
rotated from previous position = 0.0313 degrees
atoms outside contour = 4092, contour level = 0.26775
Position of RMATet_dim_AB.pdb (#8) relative to
cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.68677238 0.01478032 0.72672225 -12.62046816
0.70767342 -0.24186658 -0.66385156 142.24066589
0.16595789 0.97019694 -0.17656692 32.67543949
Axis 0.87787742 0.30126546 0.37225040
Axis point 0.00000000 66.95206783 69.07960662
Rotation angle (degrees) 111.45870564
Shift along axis 43.93642126
> transparency sel 60
> select add #5
5400 atoms, 5336 bonds, 850 residues, 3 models selected
> select subtract #8
2 models selected
> select add #8
5400 atoms, 5336 bonds, 850 residues, 3 models selected
> transparency (#8 & sel) 70
> select subtract #8
2 models selected
> hide #8 models
> transparency #5.1 100
> transparency #5.1 70
> show #8 models
> select add #8
5400 atoms, 5336 bonds, 850 residues, 3 models selected
> select subtract #5
5400 atoms, 5336 bonds, 850 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.511,0.85935,0.019959,9.1815,0.81966,-0.49414,0.28981,80.586,0.25891,-0.13173,-0.95688,204
> view matrix models
> #8,0.52446,0.84379,0.11387,0.060581,0.79076,-0.53229,0.30227,85.554,0.31566,-0.068484,-0.9464,191.85
> view matrix models
> #8,0.44795,0.88399,0.13381,1.1211,0.8384,-0.46731,0.28056,77.285,0.31054,-0.013485,-0.95046,187.5
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.44795,0.88399,0.13381,1.583,0.8384,-0.46731,0.28056,78.606,0.31054,-0.013485,-0.95046,188.47
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.42592,0.8959,0.12634,3.1787,0.85028,-0.44407,0.28253,75.136,0.30922,-0.012914,-0.9509,188.58
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.42592,0.8959,0.12634,-0.66756,0.85028,-0.44407,0.28253,75.042,0.30922,-0.012914,-0.9509,188.36
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.41182,0.91053,-0.036491,15.489,0.8706,-0.3813,0.31092,64.425,0.26919,-0.15981,-0.94974,205.77
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.41182,0.91053,-0.036491,15.795,0.8706,-0.3813,0.31092,65.731,0.26919,-0.15981,-0.94974,207.84
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.34852,0.93346,-0.084799,24.133,0.89469,-0.30434,0.32698,54.663,0.27941,-0.18983,-0.94122,208.91
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.34852,0.93346,-0.084799,24.212,0.89469,-0.30434,0.32698,51.151,0.27941,-0.18983,-0.94122,209.97
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.32726,0.94114,-0.084581,25.369,0.91962,-0.29664,0.25748,55.129,0.21724,-0.16205,-0.96257,215.05
> view matrix models
> #8,0.34935,0.92508,-0.14896,31.347,0.92191,-0.31094,0.23109,58.92,0.16746,-0.21805,-0.96146,224.72
> view matrix models
> #8,0.3999,0.9089,-0.11827,25.275,0.90261,-0.36809,0.22318,66.865,0.15931,-0.196,-0.96758,223.97
> fitmap #8 inMap #5
Fit molecule RMATet_dim_AB.pdb (#8) to map
cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) using 5400 atoms
average map value = 0.09696, steps = 112
shifted from previous position = 1.79
rotated from previous position = 9.62 degrees
atoms outside contour = 4083, contour level = 0.26775
Position of RMATet_dim_AB.pdb (#8) relative to
cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.77168574 0.07834211 0.63116054 -19.70527528
0.63555724 -0.13217938 -0.76065472 151.67980827
0.02383511 0.98812505 -0.15179184 38.17602052
Axis 0.90456718 0.31414284 0.28822298
Axis point 0.00000000 68.02848582 81.29005606
Rotation angle (degrees) 104.84130822
Shift along axis 40.82758741
> ui mousemode right select
> show #9 models
> hide #8 models
> select subtract #8
Nothing selected
> show #8 models
> hide #!5 models
> matchmaker #9/A to #8/A pairing ss
Parameters
---
Chain pairing | ss
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 RMATet_dim_AB.pdb, chain A (#8) with RMATet_dim_AC.pdb, chain A
(#9), sequence alignment score = 1788.4
RMSD between 343 pruned atom pairs is 0.001 angstroms; (across all 343 pairs:
0.001)
> select add #9
5401 atoms, 5336 bonds, 851 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.51962,0.8047,-0.28714,38.212,0.85067,-0.5186,0.086061,98.111,-0.079656,-0.28898,-0.95402,251.41
> view matrix models
> #9,-0.15891,0.014764,-0.98718,212.36,0.9872,-0.011524,-0.15908,70.316,-0.013725,-0.99982,-0.012744,218.1
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.15891,0.014764,-0.98718,230.5,0.9872,-0.011524,-0.15908,73.962,-0.013725,-0.99982,-0.012744,199.83
> view matrix models
> #9,-0.15891,0.014764,-0.98718,232.6,0.9872,-0.011524,-0.15908,73.732,-0.013725,-0.99982,-0.012744,199.67
> view matrix models
> #9,-0.15891,0.014764,-0.98718,229.81,0.9872,-0.011524,-0.15908,74.08,-0.013725,-0.99982,-0.012744,199.66
> show #!5 models
> hide #8 models
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.15891,0.014764,-0.98718,229.8,0.9872,-0.011524,-0.15908,67.76,-0.013725,-0.99982,-0.012744,201.38
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.27678,-0.16982,-0.94581,249.69,0.74729,-0.65681,-0.10076,130.2,-0.6041,-0.73469,0.3087,204.15
> view matrix models
> #9,-0.27023,-0.27509,-0.92266,254.89,0.90067,-0.41089,-0.14129,102.77,-0.34024,-0.86919,0.3588,187.64
> view matrix models
> #9,-0.27222,-0.2508,-0.92898,253.81,0.88221,-0.45053,-0.13689,106.84,-0.3842,-0.85681,0.3439,191.68
> view matrix models
> #9,-0.27007,-0.32159,-0.90755,257,0.87319,-0.47897,-0.090122,105.71,-0.40571,-0.8168,0.41016,184.93
> view matrix models
> #9,-0.24064,-0.18737,-0.95236,248.5,0.9151,-0.37086,-0.15826,100.06,-0.32354,-0.90959,0.26071,197.53
> view matrix models
> #9,-0.10121,-0.20344,-0.97384,239.82,0.93279,-0.35977,-0.021783,86.187,-0.34593,-0.91059,0.22618,202.41
> show #8 models
> hide #9 models
> show #9 models
> fitmap #9 inMap #5
Fit molecule RMATet_dim_AC.pdb (#9) to map
cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) using 5401 atoms
average map value = 0.08885, steps = 72
shifted from previous position = 2.13
rotated from previous position = 4.63 degrees
atoms outside contour = 4191, contour level = 0.26775
Position of RMATet_dim_AC.pdb (#9) relative to
cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.90690135 0.21020905 -0.36516036 58.22542004
0.21599052 -0.97606358 -0.02545540 175.78411968
-0.36177069 -0.05578564 -0.93059655 228.99975444
Axis -0.97644656 -0.10912662 0.18612765
Axis point 0.00000000 85.57383288 119.36473648
Rotation angle (degrees) 179.11010783
Shift along axis -33.41355265
> hide #8 models
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.058226,-0.23267,-0.97081,239.55,0.91373,-0.40413,0.042055,85.433,-0.40212,-0.88461,0.23613,202.67
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.055453,-0.24115,-0.9689,239.78,0.90701,-0.41787,0.052094,86.151,-0.41744,-0.87592,0.2419,202.83
> view matrix models
> #9,-0.02588,-0.283,-0.95877,239.51,0.9014,-0.42127,0.10002,82.804,-0.43221,-0.86165,0.266,200.97
> view matrix models
> #9,0.099319,-0.16074,-0.98199,222.03,0.87803,-0.45018,0.16249,81.579,-0.46819,-0.87835,0.096422,219.6
> hide #!5 models
> show #8 models
> hide #9 models
> select subtract #9
Nothing selected
> show #10 models
> select add #10
5403 atoms, 5336 bonds, 853 residues, 1 model selected
> matchmaker #10/A to #8/A pairing ss
Parameters
---
Chain pairing | ss
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 RMATet_dim_AB.pdb, chain A (#8) with RMATet_dim_AD.pdb, chain A
(#10), sequence alignment score = 1788.4
RMSD between 343 pruned atom pairs is 0.001 angstroms; (across all 343 pairs:
0.001)
> view matrix models
> #10,-0.27458,-0.63045,-0.72604,275.48,-0.825,0.54232,-0.15892,179.32,0.49394,0.55535,-0.66903,101.24
> ui mousemode right "translate selected models"
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.27458,-0.63045,-0.72604,275.33,-0.825,0.54232,-0.15892,174.21,0.49394,0.55535,-0.66903,83.844
> show #!5 models
> hide #8 models
> view matrix models
> #10,-0.27458,-0.63045,-0.72604,274.45,-0.825,0.54232,-0.15892,164.6,0.49394,0.55535,-0.66903,82.865
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.399,-0.51633,-0.75776,276.43,-0.75042,0.65877,-0.053744,138.77,0.52694,0.5472,-0.65032,79.393
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.399,-0.51633,-0.75776,277.19,-0.75042,0.65877,-0.053744,141.11,0.52694,0.5472,-0.65032,79.527
> fitmap #10 inMap #5
Fit molecule RMATet_dim_AD.pdb (#10) to map
cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) using 5403 atoms
average map value = 0.08309, steps = 76
shifted from previous position = 2.45
rotated from previous position = 3.45 degrees
atoms outside contour = 4295, contour level = 0.26775
Position of RMATet_dim_AD.pdb (#10) relative to
cryosparc_P25_J143_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.98065771 0.03646204 0.19230439 182.90213119
-0.10749039 0.72075312 -0.68480709 116.58625950
-0.16357346 -0.69223222 -0.70289279 254.15037978
Axis -0.01933823 0.92685802 -0.37491366
Axis point 106.13246955 0.00000000 141.08531981
Rotation angle (degrees) 168.93159716
Shift along axis 9.23745839
> hide #10 models
> select subtract #10
Nothing selected
> show #8 models
> hide #!5 models
> select add #8
5400 atoms, 5336 bonds, 850 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
5400 atoms, 5336 bonds, 850 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
5400 atoms, 5336 bonds, 850 residues, 1 model selected
> show #!5 models
> show #!6 models
> select subtract #8
Nothing selected
> show #4 models
> show #!16 models
> hide #4 models
> hide #!5 models
> hide #8 models
> hide #!16 models
> volume #6 step 8
> volume #6 step 2
> volume #6 step 1
> show #!2 models
> hide #!5 target m
> show #!5 target m
> view #5 clip false
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!16 models
> hide #!16 models
> show #!3 models
> save "C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/Chimera
> session_Complex_hFBP2+hALDOA_3 expts.cxs"
> hide #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #4 models
> hide #4 models
> show #!6 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #4 models
> hide #!1 models
> show #8 models
> hide #8 models
> show #8 models
> save "C:/Users/Jurgen/Desktop/cryoEM_ALDOA_hFBP2_Transfer/Transfer/Chimera
> session_Complex_hFBP2+hALDOA_3 expts.cxs"
OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce RTX 4080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_CA.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 137,167,732,736
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700K
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
File attachment: Volume Viewer_Screenshot 2024-08-27 025252.png
Attachments (1)
Change History (3)
by , 14 months ago
| Attachment: | Volume Viewer_Screenshot 2024-08-27 025252.png added |
|---|
comment:1 by , 14 months ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Volume Viewer menu |
comment:2 by , 14 months ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
The Volume Viewer panel does not have menus except for the context menu on the histogram that has a few entries like showing the volume outline box. So I'm not sure what you are asking about. Our old Chimera program had a Volume Viewer panel that had menus but that is a different (and much less capable) program.
If you want to save a map use the ChimeraX menu entry File / Save... or the equivalent toolbar button Save and choose a map file format like MRC in the Save panel that appears.
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