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Opened 6 months ago
Last modified 6 months ago
#17753 assigned defect
MemoryError saving session
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
I just saved my current chimerax session
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/backup.cxs
Opened reference as #1, grid size 300,300,300, pixel 2.09, shown at level 2.6,
step 1, values float32
Opened bestrefinedstructure as #3, grid size 300,300,300, pixel 2.08, shown at
level 0.116, step 1, values float32
Log from Thu Apr 17 15:54:33 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\Users\2803976\Downloads\chimeraxsessionmtwithtubulin\session.cxs
> format session
Opened reference as #1, grid size 300,300,300, pixel 2.09, shown at level 2.6,
step 1, values float32
Opened bestrefinedstructure as #3, grid size 300,300,300, pixel 2.08, shown at
level 0.09, step 1, values float32
Log from Wed Apr 16 17:09:40 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\Users\2803976\Downloads\chimeraxsessionmtwithtubulin\session.cxs
> format session
Opened bestrefinedstructure as #7, grid size 300,300,300, pixel 2.08, shown at
level 0.09, step 1, values float32
Opened reference as #3, grid size 300,300,300, pixel 2.09, shown at level 2.6,
step 1, values float32
Log from Wed Apr 16 14:14:18 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\Users\2803976\Downloads\chimeraxsessionmtwithtubulin\session.cxs
> format session
Opened bestrefinedstructure as #7, grid size 300,300,300, pixel 2.08, shown at
level 0.09, step 1, values float32
Opened reference as #3, grid size 300,300,300, pixel 2.09, shown at level 2.6,
step 1, values float32
Log from Tue Apr 8 11:30:02 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\Users\2803976\Downloads\chimeraxsessionmtwithtubulin\session.cxs
> format session
Opened bestrefinedstructure as #7, grid size 300,300,300, pixel 2.08, shown at
level 0.09, step 1, values float32
Opened reference as #3, grid size 300,300,300, pixel 2.09, shown at level 2.6,
step 1, values float32
Log from Fri Apr 4 14:33:48 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\Users\2803976\Downloads\chimeraxsessionmtwithtubulin\session.cxs
> format session
Error opening map
"C:\Users\2803976\Downloads\chimeraxsessionmtwithtubulin\session.cxs": File
session.cxs, format mrc
MRC header value nsymbt (875113504) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "ClipCap" returned None
Opened nonhelical0.mrc as #4, grid size 300,300,300, pixel 2.08, shown at
level 0.139, step 1, values float32
Opened nonhelical14.mrc as #6, grid size 300,300,300, pixel 2.08, shown at
level 0.0867, step 1, values float32
Opened helical0.mrc as #7, grid size 300,300,300, pixel 2.08, shown at level
0.139, step 1, values float32
Opened cryosparc_P45_14pf_3_r1.mrc as #3, grid size 300,300,300, pixel 2.09,
shown at level 2.6, step 1, values float32
Log from Mon Mar 24 11:21:24 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/2803976/Downloads/cryosparc_P45_J170_007_volume_map_sharp.mrc
Opened cryosparc_P45_J170_007_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 2.08, shown at level 0.254, step 2, values float32
> volume #1 step 1
> color #1 #aa00ffff models
> color #1 #0055ffff models
> color #1 blue models
> color #1 #0055ffff models
> set bgColor white
> graphics silhouettes true
> color #1 #aaaaffff models
> color #1 #aa55ffff models
> color #1 #0055ffff models
> color #1 springgreen models
> color #1 #ffaa00ff models
> color #1 #ff5500ff models
> color #1 #aa55ffff models
> color #1 #aaaaffff models
> color #1 #00aaffff models
> color #1 #55aaffff models
> view orient
> ui tool show "Side View"
> volume #1 level 0.1904
> pdb 1TUB
Unknown command: pdb 1TUB
> open pdb 1TUB
'pdb' has no suffix
> open 1TUB
Summary of feedback from opening 1TUB fetched from pdb
---
note | Fetching compressed mmCIF 1tub from http://files.rcsb.org/download/1tub.cif
1tub title:
Tubulin α-β dimer, electron diffraction [more info...]
Chain information for 1tub #2
---
Chain | Description | UniProt
A | TUBULIN | TBA_PIG 1-440
B | TUBULIN | TBB_PIG 1-437
Non-standard residues in 1tub #2
---
GDP — guanosine-5'-diphosphate
GTP — guanosine-5'-triphosphate
TXL — taxotere
> color #2 red
> view orient
> ui mousemode right "translate selected models"
> select add #2
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> view matrix models #2,1,0,0,285.49,0,1,0,165.72,0,0,1,0
> view matrix models #2,1,0,0,335.65,0,1,0,192.7,0,0,1,198.49
> view orient
> view matrix models #2,1,0,0,373.17,0,1,0,174.42,0,0,1,198.49
> view matrix models #2,1,0,0,372.8,0,1,0,239.59,0,0,1,212.86
> view matrix models #2,1,0,0,371.14,0,1,0,246.9,0,0,1,240.9
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.32933,0.85967,-0.39053,283.36,0.16329,0.35551,0.9203,313.05,0.92999,-0.36685,-0.023295,277.7
> hide #!1 models
> view matrix models
> #2,0.46669,0.78286,-0.4115,294.04,0.16439,0.38038,0.9101,311.79,0.86901,-0.49239,0.048825,281.38
> view matrix models
> #2,0.6877,-0.20792,0.69559,383.65,-0.27081,0.81549,0.5115,254.87,-0.6736,-0.54013,0.50451,204.98
> view matrix models
> #2,0.41238,-0.33322,0.84789,377.02,-0.26126,0.84836,0.46047,252.44,-0.87275,-0.41141,0.26279,179.75
> view matrix models
> #2,0.33091,-0.43848,-0.83561,320.12,-0.095622,-0.89651,0.43257,330.77,-0.93881,-0.063239,-0.33859,141.88
> view matrix models
> #2,0.27013,-0.50186,-0.82168,319.42,-0.48215,-0.80921,0.33573,300.66,-0.8334,0.30548,-0.46057,129.57
> view matrix models
> #2,-0.14418,0.94724,-0.28627,254.67,-0.12019,0.27039,0.95522,300.42,0.98222,0.17213,0.074863,262.75
> view matrix models
> #2,0.0039306,-0.15454,-0.98798,283.96,0.12091,0.98081,-0.15294,249.89,0.99266,-0.11886,0.022541,273.18
> show #!1 models
> select subtract #2
Nothing selected
> select add #1
3 models selected
> transparency sel 50
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,0.29959,0,1,0,1.9603,0,0,1,-0.49057
> select subtract #1
Nothing selected
> select add #2
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> view matrix models
> #2,0.0039306,-0.15454,-0.98798,394.86,0.12091,0.98081,-0.15294,247.87,0.99266,-0.11886,0.022541,258.55
> view matrix models
> #2,0.0039306,-0.15454,-0.98798,389.91,0.12091,0.98081,-0.15294,248.65,0.99266,-0.11886,0.022541,375.92
> view matrix models
> #2,0.0039306,-0.15454,-0.98798,389.79,0.12091,0.98081,-0.15294,246.69,0.99266,-0.11886,0.022541,376.61
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.018668,-0.17404,-0.98456,391.57,0.12096,0.97789,-0.17057,246.22,0.99248,-0.1159,0.039307,377.04
> view matrix models
> #2,0.016059,-0.068849,-0.9975,386.8,0.11465,0.99117,-0.066567,248.78,0.99328,-0.11329,0.023811,376.46
> view matrix models
> #2,0.065449,-0.093116,-0.9935,390.89,0.11433,0.98978,-0.085236,248.19,0.99129,-0.108,0.075426,377.86
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 1tub (#2) to map cryosparc_P45_J170_007_volume_map_sharp.mrc (#1)
using 6907 atoms
average map value = 0.2165, steps = 112
shifted from previous position = 9.5
rotated from previous position = 47.2 degrees
atoms outside contour = 2511, contour level = 0.19039
Position of 1tub (#2) relative to cryosparc_P45_J170_007_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
0.01389017 0.66402462 -0.74758167 372.44319503
-0.00213988 0.74767183 0.66406494 274.12853219
0.99990123 -0.00762424 0.01180622 372.15148337
Axis -0.33802179 -0.87940570 -0.33524154
Axis point 28.34962983 0.00000000 238.46714806
Rotation angle (degrees) 96.50649796
Shift along axis -491.72474357
> view matrix models
> #2,0.020161,0.66766,-0.74419,373.09,0.12329,0.737,0.66455,284.13,0.99217,-0.10515,-0.067456,372.42
> fitmap #2 inMap #1
Fit molecule 1tub (#2) to map cryosparc_P45_J170_007_volume_map_sharp.mrc (#1)
using 6907 atoms
average map value = 0.2165, steps = 60
shifted from previous position = 0.197
rotated from previous position = 7.27 degrees
atoms outside contour = 2516, contour level = 0.19039
Position of 1tub (#2) relative to cryosparc_P45_J170_007_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
0.01378486 0.66346803 -0.74807763 372.45601916
-0.00282668 0.74817158 0.66349928 274.08498789
0.99990099 -0.00703167 0.01218885 372.14175374
Axis -0.33742389 -0.87961600 -0.33529214
Axis point 28.44025536 0.00000000 238.67847578
Rotation angle (degrees) 96.48409221
Shift along axis -491.54130326
> ui mousemode right select
> select subtract #2
Nothing selected
> volume #1 level 0.2457
> select clear
> open 1JFF
Summary of feedback from opening 1JFF fetched from pdb
---
notes | Fetching compressed mmCIF 1jff from http://files.rcsb.org/download/1jff.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
1jff title:
Refined structure of alpha-beta tubulin from zinc-induced sheets stabilized
with taxol [more info...]
Chain information for 1jff #3
---
Chain | Description
A | tubulin alpha chain
B | tubulin beta chain
Non-standard residues in 1jff #3
---
GDP — guanosine-5'-diphosphate
GTP — guanosine-5'-triphosphate
MG — magnesium ion
TA1 — TAXOL
ZN — zinc ion
> color #3 springgreen
> color #3 lime
> view orient
> select add #3
6702 atoms, 6858 bonds, 2 pseudobonds, 843 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,356.79,0,1,0,272.44,0,0,1,0
> view matrix models #3,1,0,0,231.95,0,1,0,279.39,0,0,1,213.76
> view matrix models #3,1,0,0,167.41,0,1,0,310.92,0,0,1,201.66
> view matrix models #3,1,0,0,182.41,0,1,0,310.64,0,0,1,201.12
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99038,-0.13642,-0.023291,182.01,0.13632,0.99065,-0.006043,308.04,0.023897,0.00281,0.99971,200.69
> view matrix models
> #3,0.98374,0.1769,0.031134,183.44,-0.17708,0.98419,0.0030129,313.89,-0.030109,-0.0084772,0.99951,201.65
> view matrix models
> #3,0.98437,0.17368,0.029183,183.42,-0.17565,0.95632,0.23365,312.52,0.012672,-0.23513,0.97188,199.84
> view matrix models
> #3,0.99884,-0.0053522,-0.047814,182.64,0.016026,0.97406,0.22574,309.02,0.045365,-0.22625,0.97301,199.26
> view matrix models
> #3,0.96253,-0.23916,-0.12784,182.56,0.26793,0.91145,0.31221,303.49,0.041849,-0.33476,0.94137,198.94
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.96253,-0.23916,-0.12784,209.92,0.26793,0.91145,0.31221,297.65,0.041849,-0.33476,0.94137,210.96
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.91287,0.17384,-0.3694,214.22,0.13105,0.73216,0.6684,297.47,0.38665,-0.65857,0.64559,204.35
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.37435,0.80787,-0.45521,242.23,-0.11874,0.4451,0.88757,299.59,0.91965,0.38632,-0.070696,203.32
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.37435,0.80787,-0.45521,213.23,-0.11874,0.4451,0.88757,292.46,0.91965,0.38632,-0.070696,203.3
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.39549,0.86031,-0.32165,198.24,0.02819,0.33866,0.94048,288.87,0.91804,-0.38102,0.10969,198.48
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.39549,0.86031,-0.32165,256.32,0.02819,0.33866,0.94048,288.53,0.91804,-0.38102,0.10969,239.22
> hide #!1 models
> view orient
> color #3 black
> color #3 #aa55ffff
> color #3 #5555ffff
> color #3 #5500ffff
> color #3 #5555ffff
> hide #2 models
> show #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.26752,0.86291,0.42874,254.83,-0.10556,-0.41603,0.9032,287.42,0.95775,-0.28688,-0.020205,239.62
> view matrix models
> #3,-0.022528,0.37734,0.9258,255.25,-0.12122,-0.92023,0.37212,287.94,0.99237,-0.10385,0.066474,239.45
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.022528,0.37734,0.9258,254.87,-0.12122,-0.92023,0.37212,286.25,0.99237,-0.10385,0.066474,233.36
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.022528,0.37734,0.9258,241.99,-0.12122,-0.92023,0.37212,313.99,0.99237,-0.10385,0.066474,230.4
> view matrix models
> #3,-0.022528,0.37734,0.9258,199.74,-0.12122,-0.92023,0.37212,287.55,0.99237,-0.10385,0.066474,228.29
> view matrix models
> #3,-0.022528,0.37734,0.9258,202.9,-0.12122,-0.92023,0.37212,291.2,0.99237,-0.10385,0.066474,266.35
> fitmap #3 inMap #1
Fit molecule 1jff (#3) to map cryosparc_P45_J170_007_volume_map_sharp.mrc (#1)
using 6702 atoms
average map value = 0.2151, steps = 108
shifted from previous position = 10.1
rotated from previous position = 39.3 degrees
atoms outside contour = 4040, contour level = 0.24566
Position of 1jff (#3) relative to cryosparc_P45_J170_007_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.00829459 -0.28658754 0.95801815 192.04897540
-0.00184304 -0.95804510 -0.28661156 288.36595107
0.99996390 -0.00414299 0.00741840 262.53458423
Axis 0.70044382 -0.10401384 0.70608752
Axis point -57.16921537 162.72592835 0.00000000
Rotation angle (degrees) 168.36738989
Shift along axis 289.89785900
> view orient
> show #2 models
> select subtract #3
Nothing selected
> lighting flat
> undo
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> hide sel atoms
> view matrix models
> #3,-0.0082946,-0.28659,0.95802,192.23,-0.001843,-0.95805,-0.28661,290.67,0.99996,-0.004143,0.0074184,262.01
> fitmap #3 inMap #1
Fit molecule 1jff (#3) to map cryosparc_P45_J170_007_volume_map_sharp.mrc (#1)
using 6702 atoms
average map value = 0.2151, steps = 44
shifted from previous position = 0.396
rotated from previous position = 0.0229 degrees
atoms outside contour = 4051, contour level = 0.24566
Position of 1jff (#3) relative to cryosparc_P45_J170_007_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.00839050 -0.28675685 0.95796666 192.05169911
-0.00149591 -0.95799571 -0.28677864 288.33240042
0.99996368 -0.00383925 0.00760910 262.52731383
Axis 0.70039598 -0.10396060 0.70614280
Axis point -57.18068224 162.69600091 0.00000000
Rotation angle (degrees) 168.34692196
Shift along axis 289.91880244
> select subtract #3
Nothing selected
> mmaker #3 to #2
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 1tub, chain A (#2) with 1jff, chain A (#3), sequence alignment
score = 1992.8
RMSD between 349 pruned atom pairs is 0.996 angstroms; (across all 412 pairs:
2.459)
> view orient
> select add #3
6702 atoms, 6858 bonds, 2 pseudobonds, 843 residues, 3 models selected
> select add #2
13609 atoms, 13927 bonds, 2 pseudobonds, 1713 residues, 4 models selected
> hide sel atoms
> select subtract #3
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> select subtract #2
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:84-121
290 atoms, 297 bonds, 38 residues, 1 model selected
> select #2/B:84-278
1505 atoms, 1539 bonds, 195 residues, 1 model selected
> select add #2
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> select subtract #2
Nothing selected
> open 8c5c
Summary of feedback from opening 8c5c fetched from pdb
---
notes | Fetching compressed mmCIF 8c5c from http://files.rcsb.org/download/8c5c.cif
Fetching CCD TA1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/TA1/TA1.cif
Fetching CCD GDP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GDP/GDP.cif
Fetching CCD GTP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GTP/GTP.cif
8c5c title:
microtubule decorated with tubulin oligomers in presence of APC C-terminal
domain. (here only map corresponding to the 13-pf microtubule is represented)
[more info...]
Chain information for 8c5c #4
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z | Tubulin alpha-1B chain | TBA1B_BOVIN 1-451
a b c d e f g h i j k l m n o p q r s t u v w x y z | Tubulin beta chain | A0A452DIL8_BOVIN 1-446
Non-standard residues in 8c5c #4
---
GDP — guanosine-5'-diphosphate
GTP — guanosine-5'-triphosphate
MG — magnesium ion
TA1 — TAXOL
> select add #4
178971 atoms, 183067 bonds, 30 pseudobonds, 22672 residues, 2 models selected
> close #4
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select
> #2/A:12-23,74-79,111-127,146-161,182-193,206-215,225-239,252-259,288-295,325-337,385-397,418-433
1150 atoms, 1154 bonds, 146 residues, 1 model selected
> select #2/A:27-53
203 atoms, 208 bonds, 27 residues, 1 model selected
> view matrix models
> #2,0.013785,0.66347,-0.74808,371.44,-0.0028267,0.74817,0.6635,275.68,0.9999,-0.0070317,0.012189,382.99
> fitmap #2 inMap #1
Fit molecule 1tub (#2) to map cryosparc_P45_J170_007_volume_map_sharp.mrc (#1)
using 6907 atoms
average map value = 0.2165, steps = 88
shifted from previous position = 11.4
rotated from previous position = 0.0409 degrees
atoms outside contour = 4217, contour level = 0.24566
Position of 1tub (#2) relative to cryosparc_P45_J170_007_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
0.01371964 0.66398929 -0.74761620 372.44140161
-0.00269008 0.74770838 0.66402180 274.11789350
0.99990226 -0.00709900 0.01204448 372.13982603
Axis -0.33773373 -0.87941833 -0.33549863
Axis point 28.45869855 0.00000000 238.50279080
Rotation angle (degrees) 96.50349099
Shift along axis -491.70272647
> ui mousemode right select
Drag select of 1 cryosparc_P45_J170_007_volume_map_sharp.mrc , 13 residues
Drag select of 1 cryosparc_P45_J170_007_volume_map_sharp.mrc
> select add #1
3 models selected
Drag select of 1 cryosparc_P45_J170_007_volume_map_sharp.mrc
> view orient
> select subtract #1
Nothing selected
> select #2/A:27-53
203 atoms, 208 bonds, 27 residues, 1 model selected
> hide #2 models
> hide #!3 models
> open C:/Users/2803976/Downloads/cryosparc_P45_J170_007_volume_map_sharp.mrc
Opened cryosparc_P45_J170_007_volume_map_sharp.mrc as #4, grid size
300,300,300, pixel 2.08, shown at level 0.254, step 2, values float32
> volume #4 level 0.1902
> hide #!4 models
> show #!4 models
> hide #!1 models
> color #4 lime models
> color #4 springgreen models
> color #4 #aaff00ff models
> color #4 #aaff7fff models
> volume #4 level 0.14
> transparency #4.1 50
> volume #4 step 1
> color #4 lime models
> color #4 springgreen models
> color #4 #5555ffff models
> color #4 magenta models
> color #4 #5555ffff models
> show #!1 models
> show #2 models
> select add #4
203 atoms, 208 bonds, 27 residues, 4 models selected
> select add #2
6907 atoms, 7069 bonds, 870 residues, 4 models selected
> select subtract #2
3 models selected
> transparency sel 50
> select subtract #4
Nothing selected
Drag select of 5 cryosparc_P45_J170_007_volume_map_sharp.mrc
> fitmap #2 inMap #4
Fit molecule 1tub (#2) to map cryosparc_P45_J170_007_volume_map_sharp.mrc (#4)
using 6907 atoms
average map value = 0.2165, steps = 48
shifted from previous position = 2.07
rotated from previous position = 0.0395 degrees
atoms outside contour = 1313, contour level = 0.14005
Position of 1tub (#2) relative to cryosparc_P45_J170_007_volume_map_sharp.mrc
(#4) coordinates:
Matrix rotation and translation
0.01389713 0.66412702 -0.74749057 372.44253758
-0.00205346 0.74758015 0.66416843 274.14215889
0.99990132 -0.00769509 0.01175298 372.15316740
Axis -0.33811220 -0.87936686 -0.33525224
Axis point 28.34147208 0.00000000 238.42908724
Rotation angle (degrees) 96.51047571
Shift along axis -491.76407779
Drag select of 1 cryosparc_P45_J170_007_volume_map_sharp.mrc
[Repeated 2 time(s)]
> ui mousemode right "translate selected atoms"
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-3.4556,0,1,0,6.7742,0,0,1,-9.5239
> undo
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right rotate
[Repeated 1 time(s)]
> volume #1 level 0.1423
> open C:/Users/2803976/Downloads/cryosparc_P45_J170_007_volume_map_sharp.mrc
Opened cryosparc_P45_J170_007_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 2.08, shown at level 0.254, step 2, values float32
> color #5 magenta models
> select add #5
5 models selected
> select add #1
6 models selected
> select subtract #1
3 models selected
> transparency sel 50
> hide #!1 models
> volume #5 step 1
> volume #5 level 0.1457
> graphics silhouettes false
> graphics silhouettes true
> transparency sel 0
> transparency sel 50
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.1555
> volume #1 level 0.1397
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #2 models
> fitmap #1 inMap #4
Fit map cryosparc_P45_J170_007_volume_map_sharp.mrc in map
cryosparc_P45_J170_007_volume_map_sharp.mrc using 905685 points
correlation = 1, correlation about mean = 1, overlap = 4.979e+04
steps = 44, shift = 2.03, angle = 0.00475 degrees
Position of cryosparc_P45_J170_007_volume_map_sharp.mrc (#1) relative to
cryosparc_P45_J170_007_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
1.00000000 0.00000907 -0.00007571 0.01912872
-0.00000907 1.00000000 0.00003256 0.00873611
0.00007571 -0.00003256 1.00000000 -0.01402737
Axis -0.39266034 -0.91315025 -0.10942801
Axis point 205.44594145 0.00000000 180.27599159
Rotation angle (degrees) 0.00475060
Shift along axis -0.01395348
> fitmap #2 inMap #4
Fit molecule 1tub (#2) to map cryosparc_P45_J170_007_volume_map_sharp.mrc (#4)
using 6907 atoms
average map value = 0.2165, steps = 44
shifted from previous position = 0.0245
rotated from previous position = 0.0399 degrees
atoms outside contour = 1310, contour level = 0.14005
Position of 1tub (#2) relative to cryosparc_P45_J170_007_volume_map_sharp.mrc
(#4) coordinates:
Matrix rotation and translation
0.01370715 0.66402800 -0.74758205 372.43965742
-0.00270777 0.74767420 0.66406021 274.11780425
0.99990239 -0.00707809 0.01204651 372.13864428
Axis -0.33774340 -0.87940346 -0.33552788
Axis point 28.46553147 0.00000000 238.49127826
Rotation angle (degrees) 96.50477810
Shift along axis -491.71207093
> show #2 models
> hide #!1 models
> hide #2 models
> show #!4 models
> hide #!4 models
> close #4
> close #5
> open C:/Users/2803976/Downloads/cryosparc_P45_14pf_3_r1.mrc
Opened cryosparc_P45_14pf_3_r1.mrc as #4, grid size 300,300,300, pixel 2.09,
shown at level 3.4, step 2, values float32
> color #4 #5500ffff models
> color #4 blue models
> color #4 #aa00ffff models
> transparency #4.1 50
> volume #4 level 2.357
> show #!1 models
> fitmap #4 inMap #1
Fit map cryosparc_P45_14pf_3_r1.mrc in map
cryosparc_P45_J170_007_volume_map_sharp.mrc using 53459 points
correlation = 0.9194, correlation about mean = 0.3519, overlap = 5.062e+04
steps = 64, shift = 2.67, angle = 0.122 degrees
Position of cryosparc_P45_14pf_3_r1.mrc (#4) relative to
cryosparc_P45_J170_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999776 -0.00047623 0.00206150 -1.98631589
0.00047507 0.99999973 0.00056181 -1.92060634
-0.00206176 -0.00056083 0.99999772 -0.71948505
Axis -0.25642948 0.94182170 0.21729199
Axis point -196.79828842 0.00000000 1144.41200581
Rotation angle (degrees) 0.12541942
Shift along axis -1.45585712
> show #2 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> volume #4 level 2.617
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!4 models
> volume #4 level 2.435
> volume #4 step 1
> volume #4 level 2.168
> ui mousemode right "translate selected models"
> select add #2
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> view matrix models
> #2,0.013707,0.66403,-0.74758,366.5,-0.0027078,0.74767,0.66406,274.62,0.9999,-0.0070781,0.012047,335.15
> fitmap #2 inMap #4
Fit molecule 1tub (#2) to map cryosparc_P45_14pf_3_r1.mrc (#4) using 6907
atoms
average map value = 3.375, steps = 72
shifted from previous position = 5.7
rotated from previous position = 0.827 degrees
atoms outside contour = 1953, contour level = 2.1678
Position of 1tub (#2) relative to cryosparc_P45_14pf_3_r1.mrc (#4)
coordinates:
Matrix rotation and translation
-0.00082299 0.66934696 -0.74294950 371.61454644
-0.00609582 0.74293259 0.66933849 276.70225668
0.99998108 0.00507974 0.00346879 332.56914024
Axis -0.33484979 -0.87860332 -0.34048761
Axis point 48.51680354 0.00000000 218.14131156
Rotation angle (degrees) 97.30844487
Shift along axis -480.78224921
> select subtract #2
Nothing selected
> show #!1 models
> select add #1
3 models selected
> select add #4
6 models selected
> hide #!4 models
> view matrix models
> #1,1,9.0743e-06,-7.5712e-05,1.3859,-9.0718e-06,1,3.2557e-05,0.90474,7.5713e-05,-3.2557e-05,1,-41.356,#4,1,-0.00046711,0.0019858,-0.6004,0.00046593,1,0.00059435,-1.0159,-0.0019861,-0.00059342,1,-42.075
> show #!4 models
> undo
[Repeated 2 time(s)]
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> select subtract #1
2 models selected
> select add #2
6907 atoms, 7069 bonds, 870 residues, 3 models selected
> select add #4
6907 atoms, 7069 bonds, 870 residues, 4 models selected
> hide #!1 models
> show #!1 models
> hide #!4 models
> view matrix models
> #2,0.0011656,0.66901,-0.74325,368.88,-0.0055019,0.74325,0.66899,274.81,0.99998,0.0033095,0.0045471,372.33,#4,1,-0.00046711,0.0019858,-3.2615,0.00046593,1,0.00059435,-2.2622,-0.0019861,-0.00059342,1,40.667
> show #!4 models
> fitmap #2 inMap #1
Fit molecule 1tub (#2) to map cryosparc_P45_J170_007_volume_map_sharp.mrc (#1)
using 6907 atoms
average map value = 0.2165, steps = 48
shifted from previous position = 2.92
rotated from previous position = 0.847 degrees
atoms outside contour = 1304, contour level = 0.13968
Position of 1tub (#2) relative to cryosparc_P45_J170_007_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
0.01393806 0.66386910 -0.74771889 372.45615487
-0.00218597 0.74780998 0.66390923 274.13892754
0.99990047 -0.00761911 0.01187422 372.15478200
Axis -0.33793592 -0.87946155 -0.33518158
Axis point 28.34320998 0.00000000 238.51847596
Rotation angle (degrees) 96.49917291
Shift along axis -491.70038932
> fitmap #4 inMap #1
Fit map cryosparc_P45_14pf_3_r1.mrc in map
cryosparc_P45_J170_007_volume_map_sharp.mrc using 461443 points
correlation = 0.9235, correlation about mean = 0.3864, overlap = 4.236e+05
steps = 44, shift = 1.62, angle = 0.195 degrees
Position of cryosparc_P45_14pf_3_r1.mrc (#4) relative to
cryosparc_P45_J170_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999438 0.00291099 0.00166466 -2.79825979
-0.00291191 0.99999561 0.00055267 -0.81953706
-0.00166304 -0.00055751 0.99999846 41.22401477
Axis -0.16331011 0.48951511 -0.85656568
Axis point 5640.79054811 2950.03367223 0.00000000
Rotation angle (degrees) 0.19474769
Shift along axis -35.25526796
> select subtract #2
2 models selected
> select add #4
3 models selected
> select subtract #4
Nothing selected
> volume #4 level 2.355
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
[Repeated 1 time(s)]
> ui mousemode right select
> select add #4.1.1
1 model selected
> select subtract #4.1.1
Nothing selected
> select add #4.1
2 models selected
> select subtract #4.1
Nothing selected
> ui mousemode right clip
[Repeated 1 time(s)]
> ui mousemode right select
> ui mousemode right "crop volume"
> volume #4 region 0,0,0,299,299,233
> volume #4 region 0,0,0,299,299,299
[Repeated 1 time(s)]
> select add #4
3 models selected
> ui mousemode right "crop volume"
> volume #4 region 0,0,0,299,299,299
> volume #4 region 0,204,0,299,299,299
> volume #4 region 0,0,0,299,299,299
> volume #4 region 41,0,0,299,299,299
[Repeated 1 time(s)]
> volume #4 region 62,0,0,299,299,299
> volume #4 region 103,0,0,299,299,299
> volume #4 region 111,0,0,299,299,299
> volume #4 region 88,0,0,299,299,299
> volume #4 region 129,0,0,299,299,299
> volume #4 region 140,0,0,299,299,299
> volume #4 region 0,0,0,299,299,299
> volume #4 region 0,0,0,299,299,275
> volume #4 region 42,0,0,299,299,275
> volume #4 region 74,0,0,299,299,275
> volume #4 region 0,0,0,299,299,275
> volume #4 region 25,0,0,299,299,275
[Repeated 1 time(s)]
> volume #4 region 134,0,0,299,299,275
[Repeated 1 time(s)]
> volume #4 region 0,0,0,299,299,275
> volume #4 region 55,0,0,299,299,275
> volume #4 region 0,0,0,299,299,275
> volume #4 region 0,0,0,299,299,279
> volume #4 region 0,0,0,299,176,279
> volume #4 region 0,0,0,299,129,279
> volume #4 region 0,0,0,299,123,279
> volume #4 region 0,0,0,299,106,279
> show #!1 models
> hide #!1 models
> volume #4 region 0,0,0,299,96,279
> show #!1 models
> view orient
> ui mousemode right select
> view orient
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> select add #2
6907 atoms, 7069 bonds, 870 residues, 3 models selected
> select subtract #4
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> combine #2 close false
> select subtract #2
Nothing selected
> select add #5
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.013862,0.66388,-0.74771,225.55,-0.0021535,0.7478,0.66392,245.1,0.9999,-0.0075932,0.011796,365.59
> view matrix models
> #5,0.013862,0.66388,-0.74771,256.62,-0.0021535,0.7478,0.66392,180.38,0.9999,-0.0075932,0.011796,352.18
> view matrix models
> #5,0.013862,0.66388,-0.74771,255.2,-0.0021535,0.7478,0.66392,180.29,0.9999,-0.0075932,0.011796,359.72
> view matrix models
> #5,0.013862,0.66388,-0.74771,256.7,-0.0021535,0.7478,0.66392,180.63,0.9999,-0.0075932,0.011796,364.04
> fitmap #5 inMap #1
Fit molecule copy of 1tub (#5) to map
cryosparc_P45_J170_007_volume_map_sharp.mrc (#1) using 6907 atoms
average map value = 0.1767, steps = 84
shifted from previous position = 4.74
rotated from previous position = 21.5 degrees
atoms outside contour = 2355, contour level = 0.13968
Position of copy of 1tub (#5) relative to
cryosparc_P45_J170_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.02218036 0.35023506 -0.93639918 257.76795664
0.05767667 0.93551792 0.34853928 167.51233971
0.99808889 -0.04627766 -0.04095052 364.86525025
Axis -0.19781155 -0.96921902 -0.14657788
Axis point -45.85861309 0.00000000 268.96895234
Rotation angle (degrees) 93.65832741
Shift along axis -266.82680069
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.057936,0.97189,-0.22819,261.57,0.16374,0.21623,0.96251,222.97,0.9848,-0.093129,-0.14661,362.4
> view matrix models
> #5,0.13864,0.9847,-0.10561,270.04,-0.2575,0.13881,0.95626,200.3,0.95628,-0.10539,0.27281,375.14
> view matrix models
> #5,-0.44933,-0.56238,0.69414,322.45,0.23778,-0.82425,-0.51388,219.51,0.86114,-0.065848,0.50409,375.52
> hide #!1 models
> hide #!4 models
> view matrix models
> #5,-0.22161,-0.97101,-0.089628,326.33,0.19405,0.04616,-0.9799,166.78,0.95563,-0.23455,0.1782,377.07
> view matrix models
> #5,0.12842,0.25543,-0.95826,269.92,-0.17931,0.95632,0.23089,148.42,0.97538,0.14218,0.16861,363
> view matrix models
> #5,0.26345,0.95385,0.14412,287.16,-0.55794,0.028787,0.82938,182.23,0.78695,-0.29892,0.53977,381.46
> view matrix models
> #5,-0.10197,0.19376,0.97573,322.89,-0.22608,-0.9597,0.16695,219.47,0.96876,-0.20357,0.14166,375.42
> view matrix models
> #5,-0.09316,0.20524,0.97427,322.92,-0.055985,-0.97806,0.20068,231.63,0.99408,-0.035849,0.10261,369
> view matrix models
> #5,-0.088195,0.11924,0.98894,327.13,-0.05523,-0.99187,0.11467,229.36,0.99457,-0.044506,0.094064,369.09
> show #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.088195,0.11924,0.98894,330.49,-0.05523,-0.99187,0.11467,230.01,0.99457,-0.044506,0.094064,361.68
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.089153,0.15413,0.98402,328.88,-0.041663,-0.98767,0.15092,231.88,0.99515,-0.027542,0.094474,361.05
> fitmap #5 inMap #1
Fit molecule copy of 1tub (#5) to map
cryosparc_P45_J170_007_volume_map_sharp.mrc (#1) using 6907 atoms
average map value = 0.2143, steps = 124
shifted from previous position = 8.25
rotated from previous position = 51.4 degrees
atoms outside contour = 1236, contour level = 0.13968
Position of copy of 1tub (#5) relative to
cryosparc_P45_J170_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.00246368 0.86607568 0.49990682 289.84772147
-0.01332690 -0.49983550 0.86601781 245.28751605
0.99990815 -0.00879580 0.01031067 357.65785305
Axis -0.65411327 -0.37385964 -0.65754453
Axis point -17.74843521 34.96109828 -0.00000000
Rotation angle (degrees) 138.03304181
Shift along axis -516.47230592
> show #!4 models
> view orient
> hide #!1 models
> hide #2 models
> hide #5 models
> select subtract #5
Nothing selected
> select add #4
2 models selected
> ui mousemode right "crop volume"
> volume #4 region 0,0,0,299,246,279
> ui mousemode right select
> show #2 models
> show #!1 models
> show #!3 models
> show #5 models
> hide #!3 models
> select subtract #4
Nothing selected
> select add #3
6702 atoms, 6858 bonds, 2 pseudobonds, 843 residues, 3 models selected
> close #4
> rename #1 helical14
> open C:/Users/2803976/Downloads/nonhelical0.mrc
Opened nonhelical0.mrc as #4, grid size 300,300,300, pixel 2.08, shown at
level 0.224, step 2, values float32
> open C:/Users/2803976/Downloads/nonhelical14.mrc
Opened nonhelical14.mrc as #6, grid size 300,300,300, pixel 2.08, shown at
level 0.23, step 2, values float32
> open C:/Users/2803976/Downloads/helical0.mrc
Opened helical0.mrc as #7, grid size 300,300,300, pixel 2.08, shown at level
0.258, step 2, values float32
> color #4 #ff5500ff models
> select subtract #3
Nothing selected
> select add #4
2 models selected
> select add #6
4 models selected
> select add #7
6 models selected
> transparency sel 50
> color #4 lime models
> color #4 #00aa00ff models
> color #4 #005500ff models
> color #4 #00aa00ff models
> transparency sel 0
> select subtract #4
4 models selected
> select add #4
6 models selected
> select subtract #4
4 models selected
> color #6 magenta models
> color #7 red models
> color #7 yellow models
> transparency sel 50
> select subtract #7
2 models selected
> select subtract #6
Nothing selected
> hide #!1 models
> volume #4 level 0.08471
> volume #4 step 1
> volume #6 level 0.08668
> volume #6 step 1
> volume #7 step 1
> volume #7 level 0.1395
> color #4 #aa0000ff models
> color #4 #ff5500ff models
> color #4 magenta models
> color #6 #00ff0080 models
> color #6 #00aa0080 models
> select add #6
2 models selected
> select add #4
4 models selected
> transparency sel 0
> select subtract #4
2 models selected
> select subtract #6
Nothing selected
> hide #5 models
> hide #!6 models
> select add #4
2 models selected
> transparency sel 50
> select add #7
4 models selected
> select subtract #4
2 models selected
> hide #!4 models
> select add #4
4 models selected
> select subtract #4
2 models selected
> select subtract #7
Nothing selected
> show #!4 models
> hide #!4 models
> color #7 #55557f80 models
> show #!4 models
> hide #!7 models
> volume #4 level 0.1393
> select add #3
6702 atoms, 6858 bonds, 2 pseudobonds, 843 residues, 3 models selected
> close #3
> open C:/Users/2803976/Downloads/cryosparc_P45_14pf_3_r1.mrc
Opened cryosparc_P45_14pf_3_r1.mrc as #3, grid size 300,300,300, pixel 2.09,
shown at level 3.4, step 2, values float32
> color #3 #55557fff models
> transparency #3.1#4.1 0
> select add #3
3 models selected
> transparency sel 50
> hide #!4 models
> show #5 models
> select subtract #3
Nothing selected
> show #!7 models
> color #7 #ffaaff80 models
> color #7 #ffaa0080 models
> color #7 #55ff0080 models
> color #7 #00ffff80 models
> color #7 #00aaff80 models
> color #7 #aaaaff80 models
> color #7 #aaaa7f80 models
> color #7 #ff557f80 models
[Repeated 1 time(s)]
> hide #!3 models
> hide #!7 models
> show #!6 models
> select add #6
3 models selected
> transparency sel 50
> select subtract #6
Nothing selected
> show #!4 models
> hide #!6 models
> select add #4
3 models selected
> transparency sel 50
> select subtract #4
Nothing selected
> show #!1 models
> hide #!4 models
> hide #2 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> fitmap #1 inMap #3
Fit map helical14 in map cryosparc_P45_14pf_3_r1.mrc using 905685 points
correlation = 0.739, correlation about mean = 0.3911, overlap = 4.483e+05
steps = 52, shift = 2.68, angle = 0.114 degrees
Position of helical14 (#1) relative to cryosparc_P45_14pf_3_r1.mrc (#3)
coordinates:
Matrix rotation and translation
0.99999802 0.00105857 -0.00168210 1.70087036
-0.00105938 0.99999932 -0.00047848 2.08093788
0.00168159 0.00048026 0.99999847 0.86577141
Axis 0.23447421 -0.82263399 -0.51797216
Axis point 28.87193801 0.00000000 1256.66763127
Rotation angle (degrees) 0.11713904
Shift along axis -1.76148550
> fitmap #5 inMap #3
Fit molecule copy of 1tub (#5) to map cryosparc_P45_14pf_3_r1.mrc (#3) using
6907 atoms
average map value = 3.419, steps = 56
shifted from previous position = 4.32
rotated from previous position = 1.21 degrees
atoms outside contour = 4008, contour level = 3.3972
Position of copy of 1tub (#5) relative to cryosparc_P45_14pf_3_r1.mrc (#3)
coordinates:
Matrix rotation and translation
-0.00363480 0.87470419 0.48464354 290.13127986
-0.00332959 -0.48465463 0.87469925 249.12467971
0.99998784 0.00156570 0.00467402 358.87113511
Axis -0.65099694 -0.38423396 -0.65465048
Axis point -18.81182871 33.38521668 0.00000000
Rotation angle (degrees) 137.88563324
Shift along axis -519.53189778
> hide #!1 models
> show #!1 models
> hide #5 models
> show #5 models
> hide #!3 models
> volume #1 level 0.1285
> volume #3 step 1
> volume #1 level 0.1553
> show #!3 models
> hide #!1 models
> volume #3 level 2.603
> show #!1 models
> hide #!3 models
> volume #1 level 0.1341
> show #!3 models
> hide #!3 models
> volume #1 level 0.1307
> show #2 models
> select #1
3 models selected
> select subtract #1
Nothing selected
> fitmap #2 inMap #1
Fit molecule 1tub (#2) to map helical14 (#1) using 6907 atoms
average map value = 0.2165, steps = 48
shifted from previous position = 2.7
rotated from previous position = 0.139 degrees
atoms outside contour = 1145, contour level = 0.13075
Position of 1tub (#2) relative to helical14 (#1) coordinates:
Matrix rotation and translation
0.01370965 0.66397175 -0.74763196 372.44178360
-0.00273046 0.74772431 0.66400369 274.11715001
0.99990229 -0.00706188 0.01206399 372.13908656
Axis -0.33770544 -0.87942499 -0.33550964
Axis point 28.46548507 0.00000000 238.50997472
Rotation angle (degrees) 96.50275710
Shift along axis -491.69734073
> show #!3 models
> hide #!1 models
> show #!1 models
> select add #3
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,1.3483,0,1,0,-1.8971,0,0,1,-40.731
> hide #!1 models
> show #!1 models
> fitmap #3 inMap #1
Fit map cryosparc_P45_14pf_3_r1.mrc in map helical14 using 385345 points
correlation = 0.9334, correlation about mean = 0.3758, overlap = 3.905e+05
steps = 64, shift = 2.71, angle = 0.159 degrees
Position of cryosparc_P45_14pf_3_r1.mrc (#3) relative to helical14 (#1)
coordinates:
Matrix rotation and translation
0.99999137 -0.00381972 0.00163398 -0.88124881
0.00381857 0.99999246 0.00070259 -3.01659038
-0.00163665 -0.00069634 0.99999842 -42.88878816
Axis -0.16602554 0.38815979 0.90651392
Axis point -3270.13443707 -1957.76001418 0.00000000
Rotation angle (degrees) 0.24138807
Shift along axis -39.90389292
> select subtract #3
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!7 models
> hide #!1 models
> undo
> hide #!1 models
> show #!1 models
> hide #!7 models
> fitmap #7 inMap #1
Fit map helical0.mrc in map helical14 using 898836 points
correlation = 0.998, correlation about mean = 0.9732, overlap = 5.011e+04
steps = 64, shift = 2.67, angle = 0.116 degrees
Position of helical0.mrc (#7) relative to helical14 (#1) coordinates:
Matrix rotation and translation
0.99999990 -0.00039743 -0.00018180 0.17644136
0.00039744 0.99999992 0.00006536 -0.13169407
0.00018178 -0.00006543 0.99999998 -0.07516223
Axis -0.14799025 -0.41137878 0.89937000
Axis point 372.36330940 429.14626513 0.00000000
Rotation angle (degrees) 0.02531921
Shift along axis -0.03953411
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> hide #!7 models
> show #!6 models
> show #!4 models
> hide #!6 models
> show #!3 models
> hide #5 models
> show #5 models
> hide #!4 models
> show #!1 models
> save "C:/Users/2803976/Downloads/chimerax session of mt /mt with fited
> tubulin.cxs"
[Errno 20] Not a directory: 'C:/Users/2803976/Downloads/chimerax session of mt
'
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/session.cxs
——— End of log from Mon Mar 24 11:21:24 2025 ———
opened ChimeraX session
> volume #6 level 0.07657
> volume #4 level 0.09189
> close #6
> close #4
> color #7 #0055ff80 models
> volume #7 level 0.1381
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> rename #3 reference
> rename #7 bestrefinedstructure
> hide #5 models
> hide #!3 models
> hide #2 models
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> ui tool show "Side View"
> transparency #7.1 0
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting flat
> lighting full
> transparency #7.1 50
> volume #!7 style image
> volume #!7 style surface
> volume #!7 style mesh
> volume #!7 style surface
> surface dust #7 size 20.8
> color #7 #c2f5ffff models
> color #7 #66ffdeff models
> color #7 #ccddbbff models
> color #7 #cdb4daff models
> color #7 #ca7ddaff models
> transparency #7.1 50
> transparency #7.1 0
> transparency #7.1 50
> transparency #7.1 0
> color #7 #554433ff models
> color #7 #543884ff models
> transparency #7.1 50
> transparency #7.1 0
> color #7 #99aa77ff models
> color #7 #9a77cfff models
> transparency #7.1 50
> color #7 #554433ff models
> color #7 #543884ff models
> transparency #7.1 50
> show #!3 models
> hide #!7 models
> color #3 #ffffaa80 models
> color #3 #ffa45e80 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> turn x 90
[Repeated 3 time(s)]
> turn y 90
[Repeated 3 time(s)]
> turn z 90
> color #7 #0055ff80 models
> show #2 models
> split #1
> split #2
Split 1tub (#2) into 2 models
Chain information for 1tub A #2.1
---
Chain | Description
A | No description available
Chain information for 1tub B #2.2
---
Chain | Description
B | No description available
> color #2.2 #ff5500ff
> color #2.2 #ff007fff
> color #2.2 magenta
> color #2.2 #ff55ffff
> color #2.2 lime
> color #2.2 #55ff00ff
> color #2.2 lime
> hide #!7 models
> show #!3 models
> color #3 hot pink
> hide #!3 models
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> show #!7 models
> hide #!7 models
> show #!7 models
> volume #7 change image level -0.03383,0 level 0.2587,0.8 level 0.5823,1
> volume #7 level 0.07479
> volume #7 level 0.1271
> volume #7 level 0.1326
> volume #7 style mesh
> volume #7 style image
> volume #7 style surface
> volume #7 level 0.1299
> ui tool show "Show Sequence Viewer"
> sequence chain #2.1/A
Alignment identifier is 2.1/A
> hide #!7 models
> select #2.1/A:356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.1/A:356-380
184 atoms, 187 bonds, 25 residues, 1 model selected
> select #2.1/A:380
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.1/A:380-381
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2.1/A:382
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2.1/A:356-382
198 atoms, 201 bonds, 27 residues, 1 model selected
> select #2.1/A:377
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.1/A:356-377
162 atoms, 165 bonds, 22 residues, 1 model selected
> select #2.1/A:372
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2.1/A:356-372
125 atoms, 128 bonds, 17 residues, 1 model selected
> select #2.1/A:357-358
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #2.1/A:357-372
117 atoms, 120 bonds, 16 residues, 1 model selected
> color sel hot pink
> show #!3 models
> hide #!3 models
> select
> #2.1/A:12-23,74-79,111-127,146-161,182-193,206-215,225-239,252-259,288-295,325-337,385-397,418-433
1150 atoms, 1154 bonds, 146 residues, 1 model selected
> select #2.1/A:282
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2.1/A:282-283
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #2.1/A:357-358
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #2.1/A:357-372
117 atoms, 120 bonds, 16 residues, 1 model selected
> color sel pink
> color sel purple
> color sel hot pink
> ui tool show "Show Sequence Viewer"
> sequence chain #2.2/B
Alignment identifier is 2.2/B
> select #2.2/B:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:357-372
62 atoms, 63 bonds, 8 residues, 1 model selected
> color sel hot pink
> select add #2
6907 atoms, 7069 bonds, 870 residues, 3 models selected
> select subtract #2
Nothing selected
> show #!7 models
> color #7 #00ffff80 models
> color #7 #00aaff80 models
> color #7 #0055ff80 models
> hide #!2 models
> lighting flat
> lighting simple
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
> volume #7 color #a6a6a680
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/presentationgrey4ish.png
> width 1339 height 803 supersample 3
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/whatever.png
> width 1339 height 803 supersample 4 transparentBackground true
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> view orient
> turn x 90
[Repeated 1 time(s)]
> turn y 90
> ui mousemode right clip
> view orient
> turn y 90
> color #7 #6a6a6a80 models
> color #7 #88888880 models
> transparency #7.1 0
> color #7 #93939380 models
> color #7 #84848480 models
> color #7 #8484841c models
> color #7 #848484ff models
> color #7 #c7c7c7ff models
> lighting simple
> lighting flat
> lighting simple
> volume #7 color #939393
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 4
> graphics silhouettes width 3
> color #7 #b9b9b9ff models
> color #7 #55ffffff models
> color #7 black models
> color #7 #eaeaeaff models
> color #7 #b6b6b6ff models
> lighting shadows true
> lighting gentle
> lighting gentle intensity 0.2
> lighting gentle intensity 0.1
> view orient
> turn y 90
> lighting gentle intensity 0.1
> lighting gentle
> lighting gentle intensity 0.1
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> turn y 90
> graphics silhouettes width 2
> graphics silhouettes width 2.5
> lighting gentle intensity 0.1
> volume #7 level 0.07341
> volume #7 level 0.1051
> lighting flat
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting gentle intensity 0.1
> lighting simple
> lighting gentle intensity 0.1
> surface dust #7 size 20.8
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/frontview.png
> width 1339 height 803 supersample 3
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/frontview.png
> width 1339 height 803 supersample 4 transparentBackground true
> turn y 90
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/sideview.png
> width 1339 height 803 supersample 3
> turn z 90
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/90turn.png
> width 1339 height 803 supersample 4 transparentBackground true
> turn z 90
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/sideview.png
> width 1339 height 803 supersample 4 transparentBackground true
> show #!2 models
> transparency #7.1 50
> lighting flat
> lighting full
> lighting soft
> lighting simple
> color #2.1 #0055ffff
> ui tool show "Show Sequence Viewer"
> sequence chain #2.1/A
Alignment identifier is 2.1/A
> select #2.1/A:357-358
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #2.1/A:357-372
117 atoms, 120 bonds, 16 residues, 1 model selected
> color sel hot pink
> select add #2.1
3462 atoms, 3542 bonds, 441 residues, 1 model selected
> select subtract #2.1
Nothing selected
> hide #!7 models
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/alphabetaloop.png
> width 1339 height 803 supersample 4 transparentBackground true
> show #!7 models
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/densitywithalphabeta.png
> width 1339 height 803 supersample 4 transparentBackground true
> ui mousemode right clip
[Repeated 1 time(s)]
> select add #7
4 models selected
> select add #7
4 models selected
> select add #7
4 models selected
> select add #3
6 models selected
> select add #7
6 models selected
> select add #7
6 models selected
> select subtract #3
4 models selected
> ui mousemode right clip
> ui mousemode right rotate
[Repeated 1 time(s)]
> ui mousemode right select
> select #7
4 models selected
> select clear
> ui mousemode right clip
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/zoomoutdensityalphabeta.png
> width 1339 height 803 supersample 4 transparentBackground true
> volume #7 level 0.11
> volume #7 level 0.09
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/zoomindensityyalphabeta.png
> width 1339 height 803 supersample 4 transparentBackground true
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/zoomindensityyalphabetaNT.png
> width 1339 height 803 supersample 4
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/zoomoutdensityalphabetaNT.png
> width 1339 height 803 supersample 4
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/zoomoutdensityalphabeta.png
> width 1339 height 803 supersample 3 transparentBackground true
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/session.cxs
——— End of log from Fri Apr 4 14:33:48 2025 ———
opened ChimeraX session
> ui tool show "Side View"
> hide #2.1 models
> hide #!2 models
> show #!3 models
> ui mousemode right clip
> ui mousemode right select
> hide #!7 models
> show #!7 models
> hide #!3 models
> select clear
> view orient
> turn y 90
[Repeated 3 time(s)]
> turn z 90
[Repeated 3 time(s)]
> turn x 90
> show #!3 models
> hide #!7 models
> turn y 10
[Repeated 18 time(s)]
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> transparency #7.1 0
> lighting simple
> lighting soft
> lighting full
> transparency #7.1 50
> transparency #7.1 0
> lighting simple
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/seammtsideview.png
> width 1339 height 803 supersample 4 transparentBackground true
> lighting soft
> lighting full
> lighting soft
> lighting simple
> transparency #7.1 50
> lighting shadows true
> lighting shadows false
> lighting simple
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> transparency #7.1 0
> lighting simple
> lighting soft
> transparency #7.1 50
> transparency #7.1 0
> lighting simple
> lighting simple gentle
Expected a keyword
> lighting gentle simple
Expected a keyword
> lighting gentle
[Repeated 1 time(s)]
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/seammtsideview.png
> width 1339 height 803 supersample 4 transparentBackground true
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/session.cxs
——— End of log from Tue Apr 8 11:30:02 2025 ———
opened ChimeraX session
> show #!7 models
> hide #!3 models
> show #!2 models
> transparency #7.1 50
> show #2.1 models
> ui mousemode right clip
> ui tool show "Side View"
> copy #2
Unknown command: copy #2
> duplicate #2
Unknown command: duplicate #2
> select add #2
6907 atoms, 7069 bonds, 870 residues, 3 models selected
> help help:user
> combine #2 [close false]
Expected a keyword
> combine #2
> view orient
> hide #!2 models
> select subtract #2
Nothing selected
> select add #1
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.012025,0.66477,-0.74695,381.5,-0.0032234,0.74702,0.66479,270.64,0.99992,-0.0055862,0.011126,460.11
> view matrix models
> #1,0.012025,0.66477,-0.74695,382.04,-0.0032234,0.74702,0.66479,274.48,0.99992,-0.0055862,0.011126,457.95
> fitmap #1 inMap #7
Fit molecule combination (#1) to map bestrefinedstructure (#7) using 6907
atoms
average map value = 0.2185, steps = 72
shifted from previous position = 8.31
rotated from previous position = 0.449 degrees
atoms outside contour = 540, contour level = 0.09
Position of combination (#1) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
0.01395596 0.67008548 -0.74215273 372.47299636
-0.00355975 0.74225361 0.67010962 273.77184279
0.99989627 -0.00671015 0.01274420 456.74746220
Axis -0.34069088 -0.87689550 -0.33909291
Axis point -9.00331240 0.00000000 274.28592572
Rotation angle (degrees) 96.63379840
Shift along axis -521.84727730
> ui tool show "Fit in Map"
> fitmap #1 inMap #7
Fit molecule combination (#1) to map bestrefinedstructure (#7) using 6907
atoms
average map value = 0.2185, steps = 44
shifted from previous position = 0.0374
rotated from previous position = 0.0369 degrees
atoms outside contour = 538, contour level = 0.09
Position of combination (#1) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
0.01375469 0.66985802 -0.74236179 372.47384500
-0.00408323 0.74246347 0.66987411 273.75832468
0.99989706 -0.00618267 0.01294754 456.73369286
Axis -0.34030260 -0.87699026 -0.33923772
Axis point -8.90030918 0.00000000 274.37990004
Rotation angle (degrees) 96.62768614
Shift along axis -521.77849565
> combine #2
> select subtract #1
Nothing selected
> rename #1 tub
> select add #4
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> view matrix models
> #4,0.012025,0.66477,-0.74695,364.88,-0.0032234,0.74702,0.66479,275.22,0.99992,-0.0055862,0.011126,543.97
> fitmap #4 inMap #7
Fit molecule combination (#4) to map bestrefinedstructure (#7) using 6907
atoms
average map value = 0.2126, steps = 64
shifted from previous position = 8.88
rotated from previous position = 0.8 degrees
atoms outside contour = 463, contour level = 0.09
Position of combination (#4) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
0.01514401 0.67435269 -0.73825408 372.55135359
-0.00594896 0.73838646 0.67435158 273.22181787
0.99986763 -0.00582054 0.01519383 541.37643042
Axis -0.34238296 -0.87493038 -0.34244816
Axis point -46.45828752 0.00000000 310.61276128
Rotation angle (degrees) 96.64041681
Shift along axis -551.99866577
> rename #4 tub
> rename #5 tub
> show #5 models
> hide #5 models
> combine #1
> select subtract #4
Nothing selected
> select add #6
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> view matrix models
> #6,0.011888,0.67036,-0.74194,382.53,-0.0045052,0.74202,0.67036,274.87,0.99992,-0.0046268,0.011842,286.68
> rename #6 tub
> fitmap #6 inMap #7
Fit molecule tub (#6) to map bestrefinedstructure (#7) using 6907 atoms
average map value = 0.2181, steps = 80
shifted from previous position = 9.2
rotated from previous position = 0.791 degrees
atoms outside contour = 522, contour level = 0.09
Position of tub (#6) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.01563198 0.65968848 -0.75137656 372.55380032
-0.00227559 0.75148991 0.65974066 274.50361350
0.99987522 -0.00860323 0.01324846 287.57224775
Axis -0.33620529 -0.88095385 -0.33299597
Axis point 66.06277994 0.00000000 202.18152930
Rotation angle (degrees) 96.30464124
Shift along axis -462.83997478
> show #!2 models
> combine #1
> select add #8
13814 atoms, 14138 bonds, 1740 residues, 2 models selected
> select subtract #6
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> view matrix models
> #8,0.011888,0.67036,-0.74194,386.39,-0.0045052,0.74202,0.67036,272.43,0.99992,-0.0046268,0.011842,204.07
> fitmap #8 inMap #7
Fit molecule copy of tub (#8) to map bestrefinedstructure (#7) using 6907
atoms
average map value = 0.2111, steps = 68
shifted from previous position = 13.5
rotated from previous position = 1.03 degrees
atoms outside contour = 474, contour level = 0.09
Position of copy of tub (#8) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
0.01452221 0.65652219 -0.75416689 372.41072939
-0.00109761 0.75425645 0.65657902 274.95667371
0.99989394 -0.00870719 0.01167407 202.95101948
Axis -0.33466562 -0.88236288 -0.33080911
Axis point 103.98970597 0.00000000 165.16004006
Rotation angle (degrees) 96.30226684
Shift along axis -434.38267721
> select subtract #8
Nothing selected
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/session.cxs
> rename #8 tub
> combine #1,#2,#4,#5,#6,#8
Expected a keyword
> combine #1 ,#2,#4,#5,#6,#8
Expected a keyword
> combine #1
> combine #1 #2,#4,#5,#6,#8
Expected a keyword
> delete #9
> combine #1#2#4#6#8
Remapping chain ID 'A' in 1tub A #2.1 to 'C'
Remapping chain ID 'B' in 1tub B #2.2 to 'D'
Remapping chain ID 'A' in tub #4 to 'E'
Remapping chain ID 'B' in tub #4 to 'F'
Remapping chain ID 'A' in tub #6 to 'G'
Remapping chain ID 'B' in tub #6 to 'H'
Remapping chain ID 'A' in tub #8 to 'I'
Remapping chain ID 'B' in tub #8 to 'J'
> hide #1 models
> hide #4 models
> hide #9 models
> show #9 models
> hide #8 models
> hide #6 models
> rename #9 1PF
> fitmap #9 inMap #7
Fit molecule 1PF (#9) to map bestrefinedstructure (#7) using 34535 atoms
average map value = 0.2159, steps = 48
shifted from previous position = 0.0521
rotated from previous position = 0.109 degrees
atoms outside contour = 2587, contour level = 0.09
Position of 1PF (#9) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.01379999 0.66844615 -0.74363250 372.50972303
-0.00394414 0.74373392 0.66846413 273.71662759
0.99989700 -0.00629181 0.01289996 456.71650046
Axis -0.33962268 -0.87756494 -0.33843198
Axis point -9.02132849 0.00000000 274.82200205
Rotation angle (degrees) 96.59111253
Shift along axis -521.28433851
> fitmap #9 inMap #7
Fit molecule 1PF (#9) to map bestrefinedstructure (#7) using 34535 atoms
average map value = 0.2159, steps = 44
shifted from previous position = 0.0641
rotated from previous position = 0.294 degrees
atoms outside contour = 2571, contour level = 0.09
Position of 1PF (#9) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.01378849 0.67225667 -0.74018973 372.44328341
-0.00399471 0.74029123 0.67227445 273.94190168
0.99989695 -0.00631280 0.01289297 456.72669186
Axis -0.34162037 -0.87600977 -0.34044443
Axis point -8.73523055 0.00000000 273.56915819
Rotation angle (degrees) 96.69093806
Shift along axis -522.70005298
> fitmap #9 inMap #7
Fit molecule 1PF (#9) to map bestrefinedstructure (#7) using 34535 atoms
average map value = 0.2159, steps = 40
shifted from previous position = 0.00616
rotated from previous position = 0.221 degrees
atoms outside contour = 2575, contour level = 0.09
Position of 1PF (#9) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.01378623 0.66940085 -0.74277347 372.47863597
-0.00394893 0.74287473 0.66941881 273.73139338
0.99989717 -0.00629561 0.01288486 456.72064549
Axis -0.34012271 -0.87717805 -0.33893246
Axis point -8.95566189 0.00000000 274.51684039
Rotation angle (degrees) 96.61672330
Shift along axis -521.59706334
> fitmap #9 inMap #7
Fit molecule 1PF (#9) to map bestrefinedstructure (#7) using 34535 atoms
average map value = 0.2159, steps = 44
shifted from previous position = 0.0141
rotated from previous position = 0.0623 degrees
atoms outside contour = 2566, contour level = 0.09
Position of 1PF (#9) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.01374080 0.66860478 -0.74349097 372.48606333
-0.00411645 0.74359270 0.66862019 273.65909876
0.99989712 -0.00612684 0.01296984 456.71509921
Axis -0.33962077 -0.87750043 -0.33860113
Axis point -8.98121145 0.00000000 274.79138443
Rotation angle (degrees) 96.59487694
Shift along axis -521.28422865
> view orient
> turn y 90
> turn z 90
[Repeated 2 time(s)]
> turn y 90
[Repeated 1 time(s)]
> combine #9
> select add #10
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #10,0.011874,0.66911,-0.74307,381.37,-0.0045384,0.74315,0.66911,330.78,0.99992,-0.0045729,0.011861,458.59
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.020823,0.67598,-0.73662,382.61,-0.038566,0.73678,0.67504,326.3,0.99904,0.014352,0.041412,458.69
> view matrix models
> #10,0.064272,0.67244,-0.73735,389.04,-0.012193,0.73936,0.6732,329.96,0.99786,-0.034277,0.055719,460.98
> view matrix models
> #10,0.020647,0.67257,-0.73974,382.61,-0.01274,0.74002,0.67247,329.83,0.99971,-0.0044606,0.023848,458.96
> view matrix models
> #10,0.030377,0.46187,-0.88643,387.61,-0.035981,0.88677,0.46081,313.31,0.99889,0.017896,0.043556,458.6
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.030377,0.46187,-0.88643,379.18,-0.035981,0.88677,0.46081,314.54,0.99889,0.017896,0.043556,459.55
> fitmap #10 inMap #7
Fit molecule copy of 1PF (#10) to map bestrefinedstructure (#7) using 34535
atoms
average map value = 0.2166, steps = 200
shifted from previous position = 11.7
rotated from previous position = 10.1 degrees
atoms outside contour = 2619, contour level = 0.09
Position of copy of 1PF (#10) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
0.01482195 0.30287220 -0.95291591 382.24487541
0.00080745 0.95301667 0.30291679 304.47253201
0.99988982 -0.00525925 0.01388102 447.65884501
Axis -0.15409446 -0.97644366 -0.15103869
Axis point -27.56558377 0.00000000 361.09608229
Rotation angle (degrees) 90.52370120
Shift along axis -423.81589335
> select subtract #10
Nothing selected
> select add #10
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> select subtract #10
Nothing selected
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/session.cxs
> combine #9
> select add #11
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #11,0.011874,0.66911,-0.74307,351.87,-0.0045384,0.74315,0.66911,378.74,0.99992,-0.0045729,0.011861,452.09
> view matrix models
> #11,0.011874,0.66911,-0.74307,350.66,-0.0045384,0.74315,0.66911,386.68,0.99992,-0.0045729,0.011861,452.76
> view matrix models
> #11,0.011874,0.66911,-0.74307,352.27,-0.0045384,0.74315,0.66911,377,0.99992,-0.0045729,0.011861,453.21
> fitmap #11 inMap #7
Fit molecule copy of 1PF (#11) to map bestrefinedstructure (#7) using 34535
atoms
average map value = 0.2174, steps = 564
shifted from previous position = 13
rotated from previous position = 49.5 degrees
atoms outside contour = 2520, contour level = 0.09
Position of copy of 1PF (#11) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
0.01398918 -0.13048110 -0.99135210 378.56024493
0.00617055 0.99144150 -0.13040578 335.98221625
0.99988311 -0.00429292 0.01467459 438.62983544
Axis 0.06305962 -0.99566791 0.06832928
Axis point -32.30348678 0.00000000 431.84619574
Rotation angle (degrees) 89.42401688
Shift along axis -280.68358813
> select subtract #11
Nothing selected
> combine #9
> select add #12
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #12,0.011874,0.66911,-0.74307,295.44,-0.0045384,0.74315,0.66911,397.29,0.99992,-0.0045729,0.011861,437.42
> fitmap #12 inMap #7
Fit molecule copy of 1PF (#12) to map bestrefinedstructure (#7) using 34535
atoms
average map value = 0.169, steps = 240
shifted from previous position = 27.1
rotated from previous position = 1.22 degrees
atoms outside contour = 7995, contour level = 0.09
Position of copy of 1PF (#12) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
0.02659317 0.68025806 -0.73249011 314.41030341
0.00146583 0.73272193 0.68052658 412.76601818
0.99964526 -0.01917106 0.01848826 424.21001426
Axis -0.35202808 -0.87146255 -0.34151027
Axis point -36.03133625 0.00000000 181.42694104
Rotation angle (degrees) 96.37863291
Shift along axis -615.26345511
> select subtract #12
Nothing selected
> show #5 models
> hide #5 models
> select add #12
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> hide #!7 models
> show #!7 models
> delete #4
> delete #6
> delete #8
> select subtract #12
Nothing selected
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/session.cxs
——— End of log from Wed Apr 16 14:14:18 2025 ———
opened ChimeraX session
> ui tool show "Side View"
> select add #12
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> select subtract #12
Nothing selected
> ui mousemode right "rotate selected models"
> select add #12
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #12,0.052465,-0.40493,-0.91284,357.77,-0.0014598,0.91407,-0.40555,369.71,0.99862,0.02261,0.047365,424.98
> ui tool show "Fit in Map"
> fitmap #12 inMap #7
Fit molecule copy of 1PF (#12) to map bestrefinedstructure (#7) using 34535
atoms
average map value = 0.2178, steps = 216
shifted from previous position = 8.82
rotated from previous position = 9.52 degrees
atoms outside contour = 2370, contour level = 0.09
Position of copy of 1PF (#12) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
0.01025832 -0.54666159 -0.83729079 361.75985417
0.01038509 0.83734793 -0.54657166 362.43976505
0.99989345 -0.00308844 0.01426691 429.65584836
Axis 0.27239201 -0.92079072 0.27918997
Axis point 0.47182913 0.00000000 468.99115801
Rotation angle (degrees) 93.96019509
Shift along axis -115.23507511
> select subtract #12
Nothing selected
> combine #12
> rename #12 1PF
> rename #4 1PF
> select add #4
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #4,0.019486,-0.46126,-0.88705,359.56,0.034412,0.887,-0.46048,368.42,0.99922,-0.021552,0.033157,432.59
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.019486,-0.46126,-0.88705,323.97,0.034412,0.887,-0.46048,386.89,0.99922,-0.021552,0.033157,432.41
> graphics quality low
Expected a number or a keyword
> graphics quality 8
> graphics quality 6
> set silhouettes false
> lighting soft
> hide H,OXT
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide HOXT
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide H and O X T
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide H
> hide O
> view matrix models
> #4,0.019486,-0.46126,-0.88705,313.26,0.034412,0.887,-0.46048,392.99,0.99922,-0.021552,0.033157,436.71
> view matrix models
> #4,0.019486,-0.46126,-0.88705,309.15,0.034412,0.887,-0.46048,388.28,0.99922,-0.021552,0.033157,436.23
> fitmap #4 inMap #7
Fit molecule 1PF (#4) to map bestrefinedstructure (#7) using 34535 atoms
average map value = 0.217, steps = 312
shifted from previous position = 14.2
rotated from previous position = 31.5 degrees
atoms outside contour = 2461, contour level = 0.09
Position of 1PF (#4) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.00520955 -0.85699378 -0.51530041 335.19709042
0.01247886 0.51532298 -0.85690518 378.86135540
0.99990856 -0.00196627 0.01337891 420.77860939
Axis 0.43957259 -0.77905489 0.44704521
Axis point 70.61481887 0.00000000 479.79159932
Rotation angle (degrees) 103.47636779
Shift along axis 40.29672572
> mousemode rotate scale 0.5
Expected a keyword
> mousemode setting rotate scale 0.5
Expected a keyword
> mousemode setting rotate 0.5
Expected a keyword
> mousemode setting rotate speed 0.5
> select subtract #4
Nothing selected
> show #5 models
> hide #5 models
> combine #4
> hide #!7 models
> show #!7 models
> select add #6
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #6,0.0033541,-0.85665,-0.51589,286.02,0.012063,0.51589,-0.85657,381.15,0.99992,-0.0033499,0.012064,429.27
> surface dust #7 size 20.8
> view matrix models
> #6,0.0033541,-0.85665,-0.51589,284.78,0.012063,0.51589,-0.85657,352.96,0.99992,-0.0033499,0.012064,424.13
> fitmap #6 inMap #7
Fit molecule copy of 1PF (#6) to map bestrefinedstructure (#7) using 34535
atoms
average map value = 0.2139, steps = 296
shifted from previous position = 20.3
rotated from previous position = 25.6 degrees
atoms outside contour = 2747, contour level = 0.09
Position of copy of 1PF (#6) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
-0.00036554 -0.99549695 -0.09479278 303.82915800
0.01267517 0.09478055 -0.99541749 382.25728897
0.99991960 -0.00156538 0.01258345 411.88985634
Axis 0.55535914 -0.61171931 0.56336109
Axis point 164.72981589 0.00000000 488.70693642
Rotation angle (degrees) 116.51939776
Shift along axis 166.94285437
> combine #6
> rename #6 1PF
> rename #10 1PF
> rename #11 1PF
> select subtract #6
Nothing selected
> select add #8
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #8,-0.0022208,-0.99543,-0.095474,255.81,0.012263,0.09544,-0.99536,347.72,0.99992,-0.0033813,0.011995,407.46
> fitmap #8 inMap #7
Fit molecule copy of copy of 1PF (#8) to map bestrefinedstructure (#7) using
34535 atoms
average map value = 0.211, steps = 320
shifted from previous position = 8.66
rotated from previous position = 26.5 degrees
atoms outside contour = 3251, contour level = 0.09
Position of copy of copy of 1PF (#8) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
-0.00526576 -0.93339295 0.35881731 274.74732011
0.00989560 -0.35885336 -0.93334149 371.91332081
0.99993717 -0.00136404 0.01112612 402.96770321
Axis 0.63275355 -0.43527971 0.64043307
Axis point -229.55382244 358.52466647 0.00000000
Rotation angle (degrees) 132.57047032
Shift along axis 270.03486636
> show #5 models
> hide #5 models
> rename #8 1PF
> combine #8
> select add #13
69070 atoms, 70690 bonds, 8700 residues, 2 models selected
> select subtract #8
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #13,-0.0071229,-0.93363,0.35818,245.41,0.0094862,-0.35823,-0.93358,312.84,0.99993,-0.0032521,0.011408,393.75
> fitmap #13 inMap #7
Fit molecule copy of 1PF (#13) to map bestrefinedstructure (#7) using 34535
atoms
average map value = 0.2062, steps = 352
shifted from previous position = 15.1
rotated from previous position = 25.8 degrees
atoms outside contour = 4146, contour level = 0.09
Position of copy of 1PF (#13) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
-0.00845469 -0.68444683 0.72901374 253.01908871
0.00541193 -0.72906044 -0.68442792 349.42555675
0.99994961 -0.00184126 0.00986816 394.08939601
Axis 0.67744542 -0.26889518 0.68466275
Axis point -155.86644494 255.60714444 0.00000000
Rotation angle (degrees) 149.74863343
Shift along axis 347.26610407
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/session.cxs
> combine #13
> select subtract #13
Nothing selected
> select add #14
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #14,-0.010315,-0.68492,0.72854,263.28,0.0050046,-0.72861,-0.68491,291.58,0.99993,-0.0034187,0.010943,384.51
> view matrix models
> #14,-0.010315,-0.68492,0.72854,233.88,0.0050046,-0.72861,-0.68491,302.93,0.99993,-0.0034187,0.010943,386.98
> view matrix models
> #14,-0.010315,-0.68492,0.72854,254.13,0.0050046,-0.72861,-0.68491,301.79,0.99993,-0.0034187,0.010943,386.5
> fitmap #14 inMap #7
Fit molecule copy of copy of 1PF (#14) to map bestrefinedstructure (#7) using
34535 atoms
average map value = 0.1989, steps = 332
shifted from previous position = 3.66
rotated from previous position = 25.7 degrees
atoms outside contour = 4925, contour level = 0.09
Position of copy of copy of 1PF (#14) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
-0.00972510 -0.30017818 0.95383356 243.16808017
-0.00001236 -0.95387864 -0.30019250 319.81062982
0.99995271 -0.00293119 0.00927286 385.18458388
Axis 0.69950463 -0.10852591 0.70633943
Axis point -96.83761344 186.31241633 -0.00000000
Rotation angle (degrees) 167.73228098
Shift along axis 407.46052013
> select subtract #14
Nothing selected
> lighting flat
> select add #8
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #8,-0.0071229,-0.93363,0.35818,278.74,0.0094862,-0.35823,-0.93358,373.57,0.99993,-0.0032521,0.011408,489.79
> fitmap #8 inMap #7
Fit molecule 1PF (#8) to map bestrefinedstructure (#7) using 34535 atoms
average map value = 0.2185, steps = 52
shifted from previous position = 2.39
rotated from previous position = 0.527 degrees
atoms outside contour = 2448, contour level = 0.09
Position of 1PF (#8) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
-0.00480327 -0.93006056 0.36737482 275.59751478
0.00944412 -0.36740487 -0.93001315 372.95239024
0.99994386 -0.00099757 0.01054835 487.39743734
Axis 0.63419092 -0.43182219 0.64135129
Axis point -277.75090453 373.87886664 0.00000000
Rotation angle (degrees) 132.90852823
Shift along axis 326.32529840
> select subtract #8
Nothing selected
> select add #13
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #13,-0.010315,-0.68492,0.72854,256.93,0.0050046,-0.72861,-0.68491,351.12,0.99993,-0.0034187,0.010943,477.99
> fitmap #13 inMap #7
Fit molecule copy of 1PF (#13) to map bestrefinedstructure (#7) using 34535
atoms
average map value = 0.2186, steps = 68
shifted from previous position = 3.13
rotated from previous position = 0.584 degrees
atoms outside contour = 2578, contour level = 0.09
Position of copy of 1PF (#13) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
-0.00801740 -0.67698834 0.73595006 253.32902857
0.00532329 -0.73599219 -0.67696910 350.73018455
0.99995369 -0.00150986 0.00950456 478.50975691
Axis 0.67835102 -0.26513388 0.68523275
Axis point -199.40532396 263.54431120 0.00000000
Rotation angle (degrees) 150.14091746
Shift along axis 406.74610721
> select add #14
69070 atoms, 70690 bonds, 8700 residues, 2 models selected
> select subtract #13
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #14,-0.011589,-0.3008,0.95362,246.94,-0.00041883,-0.95368,-0.30083,320.81,0.99993,-0.0038856,0.010926,470.49
> fitmap #14 inMap #7
Fit molecule copy of copy of 1PF (#14) to map bestrefinedstructure (#7) using
34535 atoms
average map value = 0.2162, steps = 56
shifted from previous position = 2.93
rotated from previous position = 0.572 degrees
atoms outside contour = 2641, contour level = 0.09
Position of copy of copy of 1PF (#14) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
-0.00895941 -0.29067210 0.95678077 242.95956246
0.00001846 -0.95681922 -0.29068361 321.02332356
0.99995986 -0.00258669 0.00857790 469.58191470
Axis 0.70004577 -0.10492072 0.70634804
Axis point -138.46439137 189.15033606 0.00000000
Rotation angle (degrees) 168.12541861
Shift along axis 468.08908140
> select subtract #14
Nothing selected
> combine #14
> select add #15
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #15,-0.010823,-0.2913,0.95657,278.21,-0.00038852,-0.95663,-0.29132,287.26,0.99994,-0.0035247,0.010241,458.35
> fitmap #15 inMap #7
Fit molecule copy of copy of copy of 1PF (#15) to map bestrefinedstructure
(#7) using 34535 atoms
average map value = 0.2144, steps = 236
shifted from previous position = 18.3
rotated from previous position = 24.3 degrees
atoms outside contour = 2593, contour level = 0.09
Position of copy of copy of copy of 1PF (#15) relative to bestrefinedstructure
(#7) coordinates:
Matrix rotation and translation
-0.00776964 0.12943683 0.99155722 247.14304562
-0.00472063 -0.99158085 0.12940292 289.02552555
0.99995867 -0.00367536 0.00831525 460.51550344
Axis -0.70355051 -0.04441627 -0.70925586
Axis point -95.93908087 133.90259470 0.00000000
Rotation angle (degrees) 174.57307159
Shift along axis -513.33837038
> select subtract #15
Nothing selected
> show #5 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> combine #15
> select add #16
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #16,-0.0096365,0.12879,0.99163,290.83,-0.0051284,-0.99166,0.12874,262.28,0.99994,-0.0038448,0.010217,458.03
> fitmap #16 inMap #7
Fit molecule copy of copy of copy of copy of 1PF (#16) to map
bestrefinedstructure (#7) using 34535 atoms
average map value = 0.2145, steps = 252
shifted from previous position = 8.1
rotated from previous position = 25.8 degrees
atoms outside contour = 2551, contour level = 0.09
Position of copy of copy of copy of copy of 1PF (#16) relative to
bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
-0.00457206 0.54763038 0.83670787 263.73798220
-0.00877848 -0.83670635 0.54758142 262.70709805
0.99995101 -0.00484145 0.00863284 451.37896150
Axis -0.68976909 -0.20382949 -0.69474610
Axis point -69.52630560 82.43174297 0.00000000
Rotation angle (degrees) 156.39428451
Shift along axis -549.05953580
> select subtract #16
Nothing selected
> hide #5 models
> combine #16
> select add #17
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #17,-0.0064416,0.54709,0.83705,313.13,-0.0091884,-0.83707,0.54702,273.85,0.99994,-0.0041674,0.010419,443.31
> fitmap #17 inMap #7
Fit molecule copy of copy of copy of copy of copy of 1PF (#17) to map
bestrefinedstructure (#7) using 34535 atoms
average map value = 0.2132, steps = 268
shifted from previous position = 23.3
rotated from previous position = 25.6 degrees
atoms outside contour = 2325, contour level = 0.09
Position of copy of copy of copy of copy of copy of 1PF (#17) relative to
bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.00034685 0.85531131 0.51811430 290.30712899
-0.01107934 -0.51807924 0.85526086 245.88931286
0.99993856 -0.00603701 0.00929659 442.20271369
Axis -0.65585297 -0.36689499 -0.65973097
Axis point -64.46460229 24.11698629 0.00000000
Rotation angle (degrees) 138.95707893
Shift along axis -572.34917401
> show #5 models
> select subtract #17
Nothing selected
> select add #17
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> select subtract #17
Nothing selected
> combine #17
> select add #18
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #18,-0.0015242,0.85498,0.51866,341.05,-0.011492,-0.51864,0.85491,261.55,0.99993,-0.0046576,0.010616,478.25
> fitmap #18 inMap #7
Fit molecule copy of copy of copy of copy of copy of copy of 1PF (#18) to map
bestrefinedstructure (#7) using 34535 atoms
average map value = 0.2134, steps = 244
shifted from previous position = 5.06
rotated from previous position = 26.9 degrees
atoms outside contour = 2377, contour level = 0.09
Position of copy of copy of copy of copy of copy of copy of 1PF (#18) relative
to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.00555460 0.99710231 0.07586912 320.62744070
-0.01057397 -0.07580747 0.99706640 241.47387792
0.99992866 -0.00634054 0.01012225 475.05637272
Axis -0.59166159 -0.54487418 -0.59417901
Axis point -116.95905204 -80.07485945 0.00000000
Rotation angle (degrees) 122.00986824
Shift along axis -603.54434625
> hide #5 models
> select subtract #18
Nothing selected
> show #5 models
> hide #5 models
> show #5 models
> show #!3 models
> hide #!3 models
> hide #5 models
> combine #18
> select add #19
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> view matrix models
> #19,0.0036839,0.99706,0.076509,364.21,-0.010991,-0.076465,0.99701,280.8,0.99993,-0.0045138,0.010677,466.63
> fitmap #18 inMap #7
Fit molecule copy of copy of copy of copy of copy of copy of 1PF (#18) to map
bestrefinedstructure (#7) using 34535 atoms
average map value = 0.2134, steps = 60
shifted from previous position = 0.00893
rotated from previous position = 0.32 degrees
atoms outside contour = 2388, contour level = 0.09
Position of copy of copy of copy of copy of copy of copy of 1PF (#18) relative
to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.00558608 0.99751048 0.07029672 320.40294595
-0.01050401 -0.07023540 0.99747513 241.25067728
0.99992922 -0.00631037 0.01008552 475.04874226
Axis -0.59067720 -0.54704190 -0.59316575
Axis point -117.88650267 -81.64899446 0.00000000
Rotation angle (degrees) 121.82198712
Shift along axis -603.01158648
> fitmap #19 inMap #7
Fit molecule copy of copy of copy of copy of copy of copy of copy of 1PF (#19)
to map bestrefinedstructure (#7) using 34535 atoms
average map value = 0.2171, steps = 260
shifted from previous position = 5.41
rotated from previous position = 25.9 degrees
atoms outside contour = 2460, contour level = 0.09
Position of copy of copy of copy of copy of copy of copy of copy of 1PF (#19)
relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.01056526 0.93026102 -0.36674622 350.26545549
-0.00851179 0.36683707 0.93024626 252.08403406
0.99990795 -0.00670663 0.01179392 465.93257285
Axis -0.49198158 -0.71761204 -0.49293720
Axis point -2.05248935 0.00000000 178.65511623
Rotation angle (degrees) 107.78234331
Shift along axis -582.89818787
> select subtract #19
Nothing selected
> combine #1.1
No structures specified
> show #1 models
> hide #1 models
> select add #1
6907 atoms, 7069 bonds, 870 residues, 1 model selected
> show #1 models
> view matrix models
> #1,0.011888,0.67036,-0.74194,469.04,-0.0045052,0.74202,0.67036,583.65,0.99992,-0.0046268,0.011842,461.96
> combine #2.1
> delete #1
> combine #2.2
> rename #20 id #2
> rename #1 id #2
> rename #3 id #1
> select add #2
13814 atoms, 14138 bonds, 1740 residues, 5 models selected
> view matrix models #2,1,0,0,69.363,0,1,0,222.35,0,0,1,83.957
> view matrix models #2,1,0,0,37.669,0,1,0,201.94,0,0,1,46.655
> view matrix models #2,1,0,0,7.3292,0,1,0,-86.752,0,0,1,95.12
> view matrix models #2,1,0,0,-269.52,0,1,0,-182.53,0,0,1,82.404
> view matrix models #2,1,0,0,-328.47,0,1,0,171.29,0,0,1,54.653
> view matrix models #2,1,0,0,-463.26,0,1,0,-30.886,0,0,1,19.548
> select subtract #2.2
10369 atoms, 10611 bonds, 1311 residues, 4 models selected
> select subtract #2.3
6907 atoms, 7069 bonds, 870 residues, 3 models selected
> select subtract #2.4
3462 atoms, 3542 bonds, 441 residues, 2 models selected
> view matrix models #2,1,0,0,-482.41,0,1,0,-59.874,0,0,1,12.063
> select subtract #2.1
1 model selected
> select add #2.1
3462 atoms, 3542 bonds, 441 residues, 2 models selected
> view matrix models #2,1,0,0,-483.49,0,1,0,-60.79,0,0,1,18.566
> select add #2
13814 atoms, 14138 bonds, 1740 residues, 5 models selected
> select subtract #2
Nothing selected
> select add #2.4
3445 atoms, 3527 bonds, 429 residues, 1 model selected
> view matrix models
> #2.4,0.012025,0.66477,-0.74695,551.63,-0.0032234,0.74702,0.66479,556.44,0.99992,-0.0055862,0.011126,557.62
> select subtract #2.4
Nothing selected
> select add #2.2
3445 atoms, 3527 bonds, 429 residues, 1 model selected
> view matrix models
> #2.2,0.012025,0.66477,-0.74695,774.59,-0.0032234,0.74702,0.66479,450.24,0.99992,-0.0055862,0.011126,596.35
> select subtract #2.2
Nothing selected
> select add #2.4
3445 atoms, 3527 bonds, 429 residues, 1 model selected
> view matrix models
> #2.4,0.012025,0.66477,-0.74695,631.29,-0.0032234,0.74702,0.66479,590.59,0.99992,-0.0055862,0.011126,581.13
> view matrix models
> #2.4,0.012025,0.66477,-0.74695,683.79,-0.0032234,0.74702,0.66479,514.69,0.99992,-0.0055862,0.011126,647.1
> view matrix models
> #2.4,0.012025,0.66477,-0.74695,752.71,-0.0032234,0.74702,0.66479,496.28,0.99992,-0.0055862,0.011126,611.98
> view matrix models
> #2.4,0.012025,0.66477,-0.74695,747.44,-0.0032234,0.74702,0.66479,487.57,0.99992,-0.0055862,0.011126,609.68
> select subtract #2.4
Nothing selected
> select add #2.2
3445 atoms, 3527 bonds, 429 residues, 1 model selected
> view matrix models
> #2.2,0.012025,0.66477,-0.74695,797.4,-0.0032234,0.74702,0.66479,474.24,0.99992,-0.0055862,0.011126,602.2
> fitmap #2.2 inMap #7
Fit molecule 1tub B (#2.2) to map bestrefinedstructure (#7) using 3445 atoms
average map value = 0.1755, steps = 172
shifted from previous position = 18.4
rotated from previous position = 51.1 degrees
atoms outside contour = 504, contour level = 0.09
Position of 1tub B (#2.2) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.69573112 0.68406269 -0.21912653 872.93610845
-0.17623664 0.45829924 0.87115008 476.54947482
0.69634679 -0.56746809 0.43940995 597.36150237
Axis -0.75323125 -0.47932324 -0.45043525
Axis point 0.00000000 30.02206140 107.14552338
Rotation angle (degrees) 72.73928582
Shift along axis -1155.01667305
> fitmap #2.2 inMap #7
Fit molecule 1tub B (#2.2) to map bestrefinedstructure (#7) using 3445 atoms
average map value = 0.1806, steps = 104
shifted from previous position = 6.28
rotated from previous position = 16.3 degrees
atoms outside contour = 537, contour level = 0.09
Position of 1tub B (#2.2) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.74636922 0.63325408 -0.20474922 880.44069977
-0.33131598 0.62035433 0.71090803 450.73556688
0.57720248 -0.46276318 0.67282058 585.39218155
Axis -0.68691582 -0.45765372 -0.56453497
Axis point 0.00000000 -144.38858524 23.74386449
Rotation angle (degrees) 58.68303639
Shift along axis -1141.54380970
> fitmap #2.2 inMap #7
Fit molecule 1tub B (#2.2) to map bestrefinedstructure (#7) using 3445 atoms
average map value = 0.1806, steps = 40
shifted from previous position = 0.0131
rotated from previous position = 0.057 degrees
atoms outside contour = 537, contour level = 0.09
Position of 1tub B (#2.2) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.74572960 0.63394119 -0.20495346 880.35628728
-0.33183112 0.62015987 0.71083743 450.69219119
0.57773304 -0.46208257 0.67283299 585.41501646
Axis -0.68627547 -0.45794986 -0.56507336
Axis point 0.00000000 -145.50880297 23.52873654
Rotation angle (degrees) 58.71058624
Shift along axis -1141.36378267
> fitmap #2.2 inMap #7
Fit molecule 1tub B (#2.2) to map bestrefinedstructure (#7) using 3445 atoms
average map value = 0.1806, steps = 40
shifted from previous position = 0.00374
rotated from previous position = 0.0204 degrees
atoms outside contour = 535, contour level = 0.09
Position of 1tub B (#2.2) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.74592359 0.63373526 -0.20488440 880.38058142
-0.33184203 0.62034458 0.71067114 450.67858227
0.57747629 -0.46211711 0.67302965 585.40516004
Axis -0.68633886 -0.45785293 -0.56507491
Axis point 0.00000000 -145.48585918 23.45934069
Rotation angle (degrees) 58.69129612
Shift along axis -1141.38168762
> fitmap #2.2 inMap #7
Fit molecule 1tub B (#2.2) to map bestrefinedstructure (#7) using 3445 atoms
average map value = 0.1806, steps = 40
shifted from previous position = 0.00655
rotated from previous position = 0.0282 degrees
atoms outside contour = 537, contour level = 0.09
Position of 1tub B (#2.2) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.74578348 0.63388312 -0.20493703 880.36467997
-0.33217465 0.62048654 0.71039176 450.63166132
0.57746602 -0.46172355 0.67330851 585.40082172
Axis -0.68601360 -0.45792349 -0.56541261
Axis point 0.00000000 -146.17810953 23.24810738
Rotation angle (degrees) 58.68188308
Shift along axis -1141.28997249
> ui mousemode right "rotate selected models"
> view matrix models
> #2.2,-0.81575,0.55332,0.16853,772.88,-0.38121,-0.73343,0.56281,497.34,0.43501,0.39486,0.80923,546.77
> fitmap #2.2 inMap #7
Fit molecule 1tub B (#2.2) to map bestrefinedstructure (#7) using 3445 atoms
average map value = 0.1871, steps = 156
shifted from previous position = 8.36
rotated from previous position = 50.8 degrees
atoms outside contour = 403, contour level = 0.09
Position of 1tub B (#2.2) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
-0.16212028 0.97945264 0.11995639 799.69377991
-0.92310911 -0.19349319 0.33231002 427.94764530
0.34869268 -0.05685864 0.93551083 559.85424910
Axis -0.19902450 -0.11697788 -0.97298789
Axis point 483.65382713 -89.41243620 0.00000000
Rotation angle (degrees) 102.12535994
Shift along axis -753.95046100
> view matrix models
> #2.2,0.49144,0.80768,0.32579,867.48,-0.87086,0.45159,0.19411,402.43,0.0096606,-0.37911,0.9253,547.91
> view matrix models
> #2.2,0.69814,-0.68599,0.20497,940.08,0.41443,0.62065,0.66561,515.14,-0.58382,-0.37975,0.7176,493.09
> view matrix models
> #2.2,-0.435,-0.82749,-0.35502,835.35,0.54789,-0.55613,0.62492,571.89,-0.71456,0.077328,0.69529,463.39
> view matrix models
> #2.2,-0.74992,0.19543,-0.632,759.11,-0.43189,-0.86831,0.24396,492.62,-0.50109,0.4559,0.73557,466.63
> view matrix models
> #2.2,-0.22577,0.95213,-0.20611,785.52,-0.85021,-0.29587,-0.43543,412.15,-0.47557,0.076932,0.87631,488.91
> view matrix models
> #2.2,-0.63167,0.75985,0.15368,773.39,-0.67297,-0.43905,-0.59527,426.52,-0.38485,-0.47944,0.78869,515.55
> view matrix models
> #2.2,-0.53952,0.83885,0.07242,774.73,-0.72305,-0.41753,-0.55034,423.22,-0.43141,-0.34928,0.8318,508.08
> view matrix models
> #2.2,0.35514,0.75009,-0.55788,827.87,-0.024228,0.60397,0.79664,485.27,0.9345,-0.26941,0.23267,593.27
> view matrix models
> #2.2,0.79732,0.29235,0.52802,919.88,-0.58709,0.57862,0.56615,433.1,-0.14002,-0.7614,0.63298,541.08
> view matrix models
> #2.2,0.59111,-0.79664,-0.12634,924.34,0.51267,0.25015,0.82133,543.43,-0.6227,-0.55027,0.55628,491.2
> view matrix models
> #2.2,-0.47809,-0.63855,-0.60307,815.56,-0.18649,-0.59717,0.78014,520.16,-0.85829,0.48544,0.16641,416.84
> view matrix models
> #2.2,-0.86464,-0.44325,-0.23649,789.58,0.087349,-0.59619,0.79808,542.69,-0.49474,0.6694,0.5542,452.16
> view matrix models
> #2.2,-0.52,0.75229,-0.40456,763.05,-0.83625,-0.54487,0.061666,440.77,-0.17404,0.37038,0.91243,502.49
> view matrix models
> #2.2,0.12219,0.98862,-0.087799,816.08,-0.98648,0.11123,-0.12037,395.87,-0.10923,0.10132,0.98884,521.22
> view matrix models
> #2.2,0.074354,0.98835,-0.13283,810.68,-0.99035,0.05756,-0.12607,397.52,-0.11696,0.14093,0.98309,518.8
> view matrix models
> #2.2,0.0015108,0.98881,-0.1492,804.25,-0.99964,-0.0024885,-0.026614,402.69,-0.026688,0.14919,0.98845,525.89
> view matrix models
> #2.2,0.21758,0.97333,-0.072711,824.87,-0.97566,0.21899,0.011881,397.03,0.027487,0.068356,0.99728,533.8
> view matrix models
> #2.2,0.22418,0.97016,-0.092378,824.84,-0.97378,0.22675,0.01815,397.08,0.038555,0.085887,0.99556,533.92
> view matrix models
> #2.2,0.23924,0.96079,-0.14014,824.74,-0.96872,0.24598,0.0327,397.22,0.065891,0.12794,0.98959,534.21
> view matrix models
> #2.2,0.50296,0.8585,-0.10001,851.41,-0.86288,0.49209,-0.11527,390.58,-0.049747,0.14428,0.98829,524.24
> view matrix models
> #2.2,0.77717,0.62523,0.071359,888.81,-0.57449,0.7512,-0.32505,395.87,-0.25684,0.21163,0.943,503.34
> view matrix models
> #2.2,0.62997,-0.033414,-0.7759,873.86,-0.13553,0.97901,-0.1522,427.91,0.7647,0.20105,0.61222,574
> view matrix models
> #2.2,-0.21409,-0.33169,-0.91878,813.25,0.2314,0.89659,-0.3776,452.72,0.94901,-0.29345,-0.11519,583.19
> fitmap #2.2 inMap #7
Fit molecule 1tub B (#2.2) to map bestrefinedstructure (#7) using 3445 atoms
average map value = 0.2127, steps = 80
shifted from previous position = 8.71
rotated from previous position = 21.9 degrees
atoms outside contour = 158, contour level = 0.09
Position of 1tub B (#2.2) relative to bestrefinedstructure (#7) coordinates:
Matrix rotation and translation
0.02476996 -0.55702096 -0.83012897 848.99644080
0.03848343 0.83029955 -0.55598712 425.51523856
0.99895219 -0.01817445 0.04200257 580.03663425
Axis 0.26926315 -0.91575409 0.29814728
Axis point 188.09300463 0.00000000 797.90694090
Rotation angle (degrees) 92.94997110
Shift along axis 11.87248339
> select subtract #2.2
Nothing selected
> select add #2.4
3445 atoms, 3527 bonds, 429 residues, 1 model selected
> view matrix models
> #2.4,-0.96233,0.091608,-0.256,709.74,0.061165,0.99034,0.12446,463.94,0.26493,0.10412,-0.95863,512.33
> ui mousemode right "translate selected models"
> view matrix models
> #2.4,-0.96233,0.091608,-0.256,717.52,0.061165,0.99034,0.12446,445.54,0.26493,0.10412,-0.95863,470.98
> view matrix models
> #2.4,-0.96233,0.091608,-0.256,718.28,0.061165,0.99034,0.12446,447.01,0.26493,0.10412,-0.95863,475.58
> ui mousemode right "rotate selected models"
> view matrix models
> #2.4,-0.55612,-0.74793,-0.36238,780.97,0.30224,0.22417,-0.9265,460.36,0.7742,-0.62477,0.10139,583.01
> view matrix models
> #2.4,-0.55395,-0.54867,-0.62618,763.85,0.41491,0.47013,-0.77899,464.64,0.72179,-0.69133,-0.032776,576.78
> view matrix models
> #2.4,-0.5851,-0.39818,-0.70648,752.46,0.36267,0.65071,-0.66711,457.09,0.72534,-0.64655,-0.23633,568.12
> view matrix models
> #2.4,0.066731,-0.48013,-0.87465,802.09,0.22661,0.86099,-0.45535,445.14,0.9717,-0.16782,0.16626,582.67
> fitmap #2.4 inMap #7
Fit molecule copy of 1tub B (#2.4) to map bestrefinedstructure (#7) using 3445
atoms
average map value = 0.2161, steps = 84
shifted from previous position = 13.8
rotated from previous position = 33.2 degrees
atoms outside contour = 159, contour level = 0.09
Position of copy of 1tub B (#2.4) relative to bestrefinedstructure (#7)
coordinates:
Matrix rotation and translation
0.00507951 -0.86293951 -0.50528170 821.15462283
0.03818851 0.50508702 -0.86222312 442.72880617
0.99925763 -0.01491628 0.03551997 570.86049474
Axis 0.43502578 -0.77246325 0.46265874
Axis point 308.39410699 0.00000000 777.39724365
Rotation angle (degrees) 103.12973543
Shift along axis 279.34529420
> select subtract #2.4
Nothing selected
> rename #7 id #3
> delete 5
Missing or invalid "atoms" argument: invalid atoms specifier
> delete #5
> rename #4 id #3
> rename #6 id #3
> rename #8 id #3
> rename #9 id #3
> rename #10 id #3
> rename #11 id #3
> rename #12 id #3
> rename #13 id #3
> rename #14 id #3
> rename #15 id #3
> rename #16 id #3
> rename #17 id #3
> rename #18 id #3
> rename #19 id #3
> show #3.2 models
> hide #3.2 models
> rename #3.3 id #2
> rename #3.4 id #2
> rename #3.5 id #2
> rename #3.6 id #2
> rename #3.7 id #2
> rename #3.8 id #2
> rename #3.9 id #2
> rename #3.10 id #2
> rename #3.11 id #2
> rename #3.12 id #2
> rename #3.13 id #2
> rename #3.14 id #2
> rename #3.15 id #2
> rename #3.16 id #2
> select add #2.1
3462 atoms, 3542 bonds, 441 residues, 1 model selected
> view matrix models
> #2.1,0.47779,-0.87411,-0.08746,475.84,0.23761,0.032745,0.97081,323.98,-0.84573,-0.48462,0.22335,324.58
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,0.47779,-0.87411,-0.08746,773.41,0.23761,0.032745,0.97081,466.24,-0.84573,-0.48462,0.22335,83.038
> select subtract #2.1
Nothing selected
> select add #2.3
3462 atoms, 3542 bonds, 441 residues, 1 model selected
> view matrix models
> #2.3,0.012025,0.66477,-0.74695,620.18,-0.0032234,0.74702,0.66479,394.05,0.99992,-0.0055862,0.011126,122.2
> ui mousemode right "translate selected models"
> select subtract #2.3
Nothing selected
> select add #2.1
3462 atoms, 3542 bonds, 441 residues, 1 model selected
> view matrix models
> #2.1,0.47779,-0.87411,-0.08746,750.41,0.23761,0.032745,0.97081,493.74,-0.84573,-0.48462,0.22335,81.195
> view matrix models
> #2.1,0.47779,-0.87411,-0.08746,752.15,0.23761,0.032745,0.97081,494.05,-0.84573,-0.48462,0.22335,88.508
> ui mousemode right "rotate selected models"
> view matrix models
> #2.1,-0.3932,-0.82763,-0.40052,704.35,0.81723,-0.51421,0.26026,515.69,-0.42135,-0.22498,0.87855,117.36
> view matrix models
> #2.1,-0.96428,0.1573,-0.21313,648.24,-0.043493,-0.88769,-0.45838,471.45,-0.2613,-0.43274,0.86282,131.6
> view matrix models
> #2.1,-0.48715,0.68533,0.5413,671.91,-0.83585,-0.18628,-0.51639,409.38,-0.25306,-0.70401,0.66358,136.06
> view matrix models
> #2.1,0.42071,0.37402,0.82651,730.78,-0.7708,0.62782,0.10824,400.56,-0.47841,-0.68261,0.55242,122.31
> view matrix models
> #2.1,0.77294,-0.19258,0.60455,760.22,-0.21984,0.81251,0.53991,430.09,-0.59518,-0.55022,0.58568,113.41
> fitmap #2.1 inMap #3
Fit molecule 1tub A (#2.1) to map bestrefinedstructure (#3) using 3462 atoms
average map value = 0.1707, steps = 108
shifted from previous position = 7.51
rotated from previous position = 19.7 degrees
atoms outside contour = 647, contour level = 0.09
Position of 1tub A (#2.1) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.74807354 0.14224251 0.64819199 750.22566544
-0.43635508 0.84134104 0.31896594 406.74849860
-0.49998008 -0.52145196 0.69145325 119.85460953
Axis -0.54713774 0.74749510 -0.37668472
Axis point 613.63684699 -0.00000000 -790.96657420
Rotation angle (degrees) 50.17581033
Shift along axis -151.58166441
> view matrix models
> #2.1,0.15343,-0.58297,0.79787,761.73,0.45894,0.75711,0.46494,452.91,-0.87512,0.29484,0.38371,64.202
> fitmap #2.1 inMap #3
Fit molecule 1tub A (#2.1) to map bestrefinedstructure (#3) using 3462 atoms
average map value = 0.1806, steps = 128
shifted from previous position = 5.05
rotated from previous position = 39.2 degrees
atoms outside contour = 526, contour level = 0.09
Position of 1tub A (#2.1) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.18278380 -0.03367997 0.98257593 732.49607143
0.51012926 0.85110197 0.12407020 439.75519648
-0.84045112 0.52391882 -0.13838656 36.68669659
Axis 0.20568619 0.93778365 0.27974099
Axis point 266.11774153 0.00000000 -305.12835187
Rotation angle (degrees) 103.59363962
Shift along axis 573.32233224
> view matrix models
> #2.1,0.15905,-0.57653,0.80145,763.92,0.30575,0.80063,0.51527,447.91,-0.93873,0.16309,0.30361,64.022
> view matrix models
> #2.1,-0.72773,0.68263,0.066432,653.3,0.33693,0.27146,0.90155,483.05,0.59739,0.67847,-0.42755,81.837
> view matrix models
> #2.1,0.95349,0.28143,0.10791,739.16,-0.21245,0.37355,0.90296,456.65,0.21381,-0.88389,0.41597,156.3
> view matrix models
> #2.1,0.12791,-0.59205,0.79569,763.08,0.10679,0.80584,0.58243,441.83,-0.98602,0.010471,0.1663,63.57
> fitmap #2.1 inMap #3
Fit molecule 1tub A (#2.1) to map bestrefinedstructure (#3) using 3462 atoms
average map value = 0.1783, steps = 92
shifted from previous position = 2.59
rotated from previous position = 26.5 degrees
atoms outside contour = 532, contour level = 0.09
Position of 1tub A (#2.1) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.17282241 -0.27747815 0.94505982 742.20702629
0.11314699 0.94755251 0.29890105 424.19926814
-0.97843245 0.15858748 -0.13236251 46.28597851
Axis -0.07130606 0.97750109 0.19851211
Axis point 374.90093117 0.00000000 -348.08757321
Rotation angle (degrees) 100.30081545
Shift along axis 370.91971354
> flip#2.1 horizontaly
Unknown command: flip#2.1 horizontaly
> flip #2.1 horizontaly
Unknown command: flip #2.1 horizontaly
> view matrix models
> #2.1,0.18414,-0.87907,0.4397,765.77,-0.06294,-0.45698,-0.88725,434.63,0.98088,0.1357,-0.13947,129.14
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,0.18414,-0.87907,0.4397,763.84,-0.06294,-0.45698,-0.88725,433.36,0.98088,0.1357,-0.13947,122.8
> fitmap #2.1 inMap #3
Fit molecule 1tub A (#2.1) to map bestrefinedstructure (#3) using 3462 atoms
average map value = 0.2079, steps = 60
shifted from previous position = 4.04
rotated from previous position = 12.4 degrees
atoms outside contour = 221, contour level = 0.09
Position of 1tub A (#2.1) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.01070357 -0.92167207 0.38782206 756.63468559
-0.01118766 -0.38770959 -0.92171355 431.64809149
0.99988009 -0.01420444 -0.00616146 130.37941108
Axis 0.63739103 -0.42988030 0.63948073
Axis point 118.77243019 427.83635339 0.00000000
Rotation angle (degrees) 134.61080782
Shift along axis 380.09026642
> fitmap #2.1 inMap #3
Fit molecule 1tub A (#2.1) to map bestrefinedstructure (#3) using 3462 atoms
average map value = 0.2079, steps = 28
shifted from previous position = 0.0583
rotated from previous position = 0.11 degrees
atoms outside contour = 223, contour level = 0.09
Position of 1tub A (#2.1) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.01138684 -0.92211339 0.38675206 756.62463521
-0.01253864 -0.38661503 -0.92215582 431.57320782
0.99985651 -0.01534977 -0.00715971 130.40123506
Axis 0.63715646 -0.43079053 0.63910185
Axis point 118.73239331 428.07403445 0.00000000
Rotation angle (degrees) 134.63443253
Shift along axis 379.51029239
> select subtract #2.1
Nothing selected
> select add #2.3
3462 atoms, 3542 bonds, 441 residues, 1 model selected
> view matrix models
> #2.3,0.012025,0.66477,-0.74695,621.96,-0.0032234,0.74702,0.66479,396.21,0.99992,-0.0055862,0.011126,126.11
> ui mousemode right "rotate selected models"
> view matrix models
> #2.3,0.10331,-0.15252,-0.98289,650.24,-0.16121,0.97254,-0.16786,353.05,0.9815,0.17579,0.075884,120.32
> view matrix models
> #2.3,0.26197,-0.90407,-0.33767,708.03,-0.18764,0.2955,-0.93673,353.2,0.94666,0.30876,-0.092228,108.02
> view matrix models
> #2.3,0.12365,-0.92293,-0.36457,702.24,-0.47436,0.26772,-0.83864,345.88,0.8716,0.27663,-0.4047,95.813
> view matrix models
> #2.3,0.60329,-0.53115,0.59491,738.25,-0.24822,-0.83395,-0.49286,410.33,0.75791,0.14967,-0.63496,88.535
> fitmap #2.3 inMap #3
Fit molecule copy of 1tub A (#2.3) to map bestrefinedstructure (#3) using 3462
atoms
average map value = 0.1989, steps = 96
shifted from previous position = 13.5
rotated from previous position = 40.3 degrees
atoms outside contour = 228, contour level = 0.09
Position of copy of 1tub A (#2.3) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.00802821 -0.65705345 0.75380124 735.91631282
-0.02073453 -0.75377285 -0.65680787 409.07465080
0.99975279 -0.01035672 -0.01967514 121.05603244
Axis 0.68783348 -0.26169605 0.67705264
Axis point 0.00000000 381.66717405 -204.59857604
Rotation angle (degrees) 151.97100332
Shift along axis 481.09596835
> fitmap #2.3 inMap #3
Fit molecule copy of 1tub A (#2.3) to map bestrefinedstructure (#3) using 3462
atoms
average map value = 0.1989, steps = 36
shifted from previous position = 0.00844
rotated from previous position = 0.0102 degrees
atoms outside contour = 230, contour level = 0.09
Position of copy of 1tub A (#2.3) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.00804097 -0.65695044 0.75389087 735.91238062
-0.02061881 -0.75386389 -0.65670701 409.07917887
0.99975508 -0.01026377 -0.01960733 121.05413409
Axis 0.68783948 -0.26160859 0.67708035
Axis point 0.00000000 381.62695757 -204.61739868
Rotation angle (degrees) 151.97164218
Shift along axis 481.13433392
> select subtract #2.3
Nothing selected
> select add #2.2
3445 atoms, 3527 bonds, 429 residues, 1 model selected
> view matrix models
> #2.2,0.017841,-0.60503,-0.796,852.84,0.018053,0.79619,-0.60478,424.72,0.99968,-0.0035808,0.025128,581.49
> ui mousemode right "translate selected models"
> view matrix models
> #2.2,0.017841,-0.60503,-0.796,754.78,0.018053,0.79619,-0.60478,395.64,0.99968,-0.0035808,0.025128,571.24
> fitmap #2.2 inMap #3
Fit molecule 1tub B (#2.2) to map bestrefinedstructure (#3) using 3445 atoms
average map value = 0.2185, steps = 192
shifted from previous position = 35.1
rotated from previous position = 48.3 degrees
atoms outside contour = 167, contour level = 0.09
Position of 1tub B (#2.2) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.01169762 -0.99694607 -0.07721210 788.61000877
0.03875802 0.07670729 -0.99630006 447.23886250
0.99918016 -0.01464695 0.03774237 562.10049211
Axis 0.54919463 -0.60219729 0.57943393
Axis point 455.59139924 0.00000000 762.47799915
Rotation angle (degrees) 116.65543425
Shift along axis 489.47444831
> fitmap #2.2 inMap #3
Fit molecule 1tub B (#2.2) to map bestrefinedstructure (#3) using 3445 atoms
average map value = 0.2185, steps = 48
shifted from previous position = 0.0434
rotated from previous position = 0.0529 degrees
atoms outside contour = 167, contour level = 0.09
Position of 1tub B (#2.2) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.01134347 -0.99701437 -0.07637848 788.63330334
0.03891651 0.07588533 -0.99635682 447.26449808
0.99917808 -0.01427455 0.03793953 562.08989227
Axis 0.54947650 -0.60177550 0.57960488
Axis point 455.98296135 0.00000000 762.64177297
Rotation angle (degrees) 116.66411023
Shift along axis 489.97269614
> fitmap #2.2 inMap #3
Fit molecule 1tub B (#2.2) to map bestrefinedstructure (#3) using 3445 atoms
average map value = 0.2185, steps = 40
shifted from previous position = 0.0325
rotated from previous position = 0.0313 degrees
atoms outside contour = 166, contour level = 0.09
Position of 1tub B (#2.2) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.01155655 -0.99697439 -0.07686686 788.62545596
0.03881032 0.07636685 -0.99632417 447.25159805
0.99917977 -0.01449732 0.03781037 562.09590674
Axis 0.54931210 -0.60202614 0.57950042
Axis point 455.75753024 0.00000000 762.54233007
Rotation angle (degrees) 116.65964532
Shift along axis 489.67916639
> select subtract #2.2
Nothing selected
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/session.cxs
——— End of log from Wed Apr 16 17:09:40 2025 ———
opened ChimeraX session
> select add #2
497304 atoms, 508968 bonds, 62640 residues, 19 models selected
> select subtract #2.1
493842 atoms, 505426 bonds, 62199 residues, 18 models selected
> select subtract #2.2
490397 atoms, 501899 bonds, 61770 residues, 17 models selected
> select subtract #2.3
486935 atoms, 498357 bonds, 61329 residues, 16 models selected
> select subtract #2.4
483490 atoms, 494830 bonds, 60900 residues, 15 models selected
> view matrix models #2,1,0,0,-372.88,0,1,0,4.3785,0,0,1,14.086
> undo
> select add #2
497304 atoms, 508968 bonds, 62640 residues, 19 models selected
> select subtract #2
Nothing selected
> select add #2.5
34535 atoms, 35345 bonds, 4350 residues, 1 model selected
> select add #2.6
69070 atoms, 70690 bonds, 8700 residues, 2 models selected
> select add #2.7
103605 atoms, 106035 bonds, 13050 residues, 3 models selected
> select add #2.8
138140 atoms, 141380 bonds, 17400 residues, 4 models selected
> select add #2.9
172675 atoms, 176725 bonds, 21750 residues, 5 models selected
> select add #2.10
207210 atoms, 212070 bonds, 26100 residues, 6 models selected
> select add #2.11
241745 atoms, 247415 bonds, 30450 residues, 7 models selected
> select add #2.12
276280 atoms, 282760 bonds, 34800 residues, 8 models selected
> select add #2.13
310815 atoms, 318105 bonds, 39150 residues, 9 models selected
> select add #2.14
345350 atoms, 353450 bonds, 43500 residues, 10 models selected
> rename #2.12 1PF
> rename #2.13 " 1PF"
> rename #2.14 1PF
> rename #2.15 " 1PF"
> rename #2.16 1PF
> rename #2.17 1PF
> rename #2.18 " 1PF"
> select add #2.15
379885 atoms, 388795 bonds, 47850 residues, 11 models selected
> select add #2.16
414420 atoms, 424140 bonds, 52200 residues, 12 models selected
> select add #2.17
448955 atoms, 459485 bonds, 56550 residues, 13 models selected
> select add #2.18
483490 atoms, 494830 bonds, 60900 residues, 14 models selected
> view matrix models
> #2.5,0.0033541,-0.85665,-0.51589,730.75,0.012063,0.51589,-0.85657,612.15,0.99992,-0.0033499,0.012064,392.92,#2.6,-0.0022208,-0.99543,-0.095474,699.4,0.012263,0.09544,-0.99536,615.57,0.99992,-0.0033813,0.011995,383.98,#2.7,-0.0066607,-0.9303,0.36674,671.02,0.0090344,-0.36679,-0.93026,606.25,0.99994,-0.002883,0.010848,459.43,#2.8,0.011874,0.66911,-0.74307,767.9,-0.0045384,0.74315,0.66911,506.91,0.99992,-0.0045729,0.011861,428.88,#2.9,0.012959,0.30351,-0.95274,777.7,0.00038475,0.95282,0.30354,537.72,0.99992,-0.0043001,0.012231,419.86,#2.10,0.01213,-0.12982,-0.99146,774.05,0.0057484,0.99153,-0.12976,569.23,0.99991,-0.0041254,0.012773,410.84,#2.11,0.0084015,-0.5461,-0.83768,757.29,0.0099654,0.83771,-0.54602,595.7,0.99992,-0.0037604,0.01248,401.84,#2.12,-0.0098776,-0.67747,0.73548,648.76,0.0049157,-0.73554,-0.67746,584.05,0.99994,-0.0030763,0.010596,450.49,#2.13,-0.010823,-0.2913,0.95657,638.39,-0.00038852,-0.95663,-0.29132,554.35,0.99994,-0.0035247,0.010241,441.53,#2.14,-0.0096365,0.12879,0.99163,642.56,-0.0051284,-0.99166,0.12874,522.35,0.99994,-0.0038448,0.010217,432.46,#2.15,-0.0064416,0.54709,0.83705,659.16,-0.0091884,-0.83707,0.54702,496.03,0.99994,-0.0041674,0.010419,423.34,#2.16,-0.0015242,0.85498,0.51866,685.73,-0.011492,-0.51864,0.85491,479.2,0.99993,-0.0046576,0.010616,414.21,#2.17,0.0037154,0.99747,0.070937,715.77,-0.010921,-0.070893,0.99742,474.52,0.99993,-0.0044805,0.01063,447.11,#2.18,0.008696,0.93051,-0.36615,745.65,-0.0089317,0.36622,0.93048,485.34,0.99992,-0.0048211,0.011496,438.05
> view matrix models
> #2.5,0.0033541,-0.85665,-0.51589,873.23,0.012063,0.51589,-0.85657,522.84,0.99992,-0.0033499,0.012064,352.32,#2.6,-0.0022208,-0.99543,-0.095474,841.88,0.012263,0.09544,-0.99536,526.26,0.99992,-0.0033813,0.011995,343.38,#2.7,-0.0066607,-0.9303,0.36674,813.5,0.0090344,-0.36679,-0.93026,516.95,0.99994,-0.002883,0.010848,418.83,#2.8,0.011874,0.66911,-0.74307,910.38,-0.0045384,0.74315,0.66911,417.6,0.99992,-0.0045729,0.011861,388.28,#2.9,0.012959,0.30351,-0.95274,920.17,0.00038475,0.95282,0.30354,448.41,0.99992,-0.0043001,0.012231,379.26,#2.10,0.01213,-0.12982,-0.99146,916.53,0.0057484,0.99153,-0.12976,479.93,0.99991,-0.0041254,0.012773,370.24,#2.11,0.0084015,-0.5461,-0.83768,899.76,0.0099654,0.83771,-0.54602,506.4,0.99992,-0.0037604,0.01248,361.24,#2.12,-0.0098776,-0.67747,0.73548,791.23,0.0049157,-0.73554,-0.67746,494.74,0.99994,-0.0030763,0.010596,409.89,#2.13,-0.010823,-0.2913,0.95657,780.86,-0.00038852,-0.95663,-0.29132,465.05,0.99994,-0.0035247,0.010241,400.93,#2.14,-0.0096365,0.12879,0.99163,785.04,-0.0051284,-0.99166,0.12874,433.05,0.99994,-0.0038448,0.010217,391.86,#2.15,-0.0064416,0.54709,0.83705,801.63,-0.0091884,-0.83707,0.54702,406.72,0.99994,-0.0041674,0.010419,382.74,#2.16,-0.0015242,0.85498,0.51866,828.21,-0.011492,-0.51864,0.85491,389.89,0.99993,-0.0046576,0.010616,373.61,#2.17,0.0037154,0.99747,0.070937,858.24,-0.010921,-0.070893,0.99742,385.22,0.99993,-0.0044805,0.01063,406.51,#2.18,0.008696,0.93051,-0.36615,888.13,-0.0089317,0.36622,0.93048,396.04,0.99992,-0.0048211,0.011496,397.45
> view matrix models
> #2.5,0.0033541,-0.85665,-0.51589,798.01,0.012063,0.51589,-0.85657,475.4,0.99992,-0.0033499,0.012064,398.86,#2.6,-0.0022208,-0.99543,-0.095474,766.66,0.012263,0.09544,-0.99536,478.83,0.99992,-0.0033813,0.011995,389.91,#2.7,-0.0066607,-0.9303,0.36674,738.28,0.0090344,-0.36679,-0.93026,469.51,0.99994,-0.002883,0.010848,465.36,#2.8,0.011874,0.66911,-0.74307,835.16,-0.0045384,0.74315,0.66911,370.16,0.99992,-0.0045729,0.011861,434.82,#2.9,0.012959,0.30351,-0.95274,844.96,0.00038475,0.95282,0.30354,400.97,0.99992,-0.0043001,0.012231,425.79,#2.10,0.01213,-0.12982,-0.99146,841.31,0.0057484,0.99153,-0.12976,432.49,0.99991,-0.0041254,0.012773,416.77,#2.11,0.0084015,-0.5461,-0.83768,824.54,0.0099654,0.83771,-0.54602,458.96,0.99992,-0.0037604,0.01248,407.78,#2.12,-0.0098776,-0.67747,0.73548,716.01,0.0049157,-0.73554,-0.67746,447.3,0.99994,-0.0030763,0.010596,456.42,#2.13,-0.010823,-0.2913,0.95657,705.64,-0.00038852,-0.95663,-0.29132,417.61,0.99994,-0.0035247,0.010241,447.46,#2.14,-0.0096365,0.12879,0.99163,709.82,-0.0051284,-0.99166,0.12874,385.61,0.99994,-0.0038448,0.010217,438.39,#2.15,-0.0064416,0.54709,0.83705,726.42,-0.0091884,-0.83707,0.54702,359.29,0.99994,-0.0041674,0.010419,429.27,#2.16,-0.0015242,0.85498,0.51866,752.99,-0.011492,-0.51864,0.85491,342.45,0.99993,-0.0046576,0.010616,420.14,#2.17,0.0037154,0.99747,0.070937,783.02,-0.010921,-0.070893,0.99742,337.78,0.99993,-0.0044805,0.01063,453.04,#2.18,0.008696,0.93051,-0.36615,812.91,-0.0089317,0.36622,0.93048,348.6,0.99992,-0.0048211,0.011496,443.98
> view matrix models
> #2.5,0.0033541,-0.85665,-0.51589,806.71,0.012063,0.51589,-0.85657,445.69,0.99992,-0.0033499,0.012064,402.37,#2.6,-0.0022208,-0.99543,-0.095474,775.37,0.012263,0.09544,-0.99536,449.11,0.99992,-0.0033813,0.011995,393.42,#2.7,-0.0066607,-0.9303,0.36674,746.99,0.0090344,-0.36679,-0.93026,439.79,0.99994,-0.002883,0.010848,468.87,#2.8,0.011874,0.66911,-0.74307,843.87,-0.0045384,0.74315,0.66911,340.45,0.99992,-0.0045729,0.011861,438.33,#2.9,0.012959,0.30351,-0.95274,853.66,0.00038475,0.95282,0.30354,371.26,0.99992,-0.0043001,0.012231,429.3,#2.10,0.01213,-0.12982,-0.99146,850.02,0.0057484,0.99153,-0.12976,402.77,0.99991,-0.0041254,0.012773,420.28,#2.11,0.0084015,-0.5461,-0.83768,833.25,0.0099654,0.83771,-0.54602,429.25,0.99992,-0.0037604,0.01248,411.29,#2.12,-0.0098776,-0.67747,0.73548,724.72,0.0049157,-0.73554,-0.67746,417.59,0.99994,-0.0030763,0.010596,459.93,#2.13,-0.010823,-0.2913,0.95657,714.35,-0.00038852,-0.95663,-0.29132,387.89,0.99994,-0.0035247,0.010241,450.98,#2.14,-0.0096365,0.12879,0.99163,718.53,-0.0051284,-0.99166,0.12874,355.9,0.99994,-0.0038448,0.010217,441.9,#2.15,-0.0064416,0.54709,0.83705,735.12,-0.0091884,-0.83707,0.54702,329.57,0.99994,-0.0041674,0.010419,432.79,#2.16,-0.0015242,0.85498,0.51866,761.7,-0.011492,-0.51864,0.85491,312.74,0.99993,-0.0046576,0.010616,423.65,#2.17,0.0037154,0.99747,0.070937,791.73,-0.010921,-0.070893,0.99742,308.07,0.99993,-0.0044805,0.01063,456.55,#2.18,0.008696,0.93051,-0.36615,821.61,-0.0089317,0.36622,0.93048,318.88,0.99992,-0.0048211,0.011496,447.5
> view matrix models
> #2.5,0.0033541,-0.85665,-0.51589,813.76,0.012063,0.51589,-0.85657,450.2,0.99992,-0.0033499,0.012064,401.5,#2.6,-0.0022208,-0.99543,-0.095474,782.41,0.012263,0.09544,-0.99536,453.62,0.99992,-0.0033813,0.011995,392.55,#2.7,-0.0066607,-0.9303,0.36674,754.04,0.0090344,-0.36679,-0.93026,444.31,0.99994,-0.002883,0.010848,468.01,#2.8,0.011874,0.66911,-0.74307,850.91,-0.0045384,0.74315,0.66911,344.96,0.99992,-0.0045729,0.011861,437.46,#2.9,0.012959,0.30351,-0.95274,860.71,0.00038475,0.95282,0.30354,375.77,0.99992,-0.0043001,0.012231,428.44,#2.10,0.01213,-0.12982,-0.99146,857.06,0.0057484,0.99153,-0.12976,407.29,0.99991,-0.0041254,0.012773,419.41,#2.11,0.0084015,-0.5461,-0.83768,840.3,0.0099654,0.83771,-0.54602,433.76,0.99992,-0.0037604,0.01248,410.42,#2.12,-0.0098776,-0.67747,0.73548,731.77,0.0049157,-0.73554,-0.67746,422.1,0.99994,-0.0030763,0.010596,459.07,#2.13,-0.010823,-0.2913,0.95657,721.4,-0.00038852,-0.95663,-0.29132,392.41,0.99994,-0.0035247,0.010241,450.11,#2.14,-0.0096365,0.12879,0.99163,725.58,-0.0051284,-0.99166,0.12874,360.41,0.99994,-0.0038448,0.010217,441.04,#2.15,-0.0064416,0.54709,0.83705,742.17,-0.0091884,-0.83707,0.54702,334.08,0.99994,-0.0041674,0.010419,431.92,#2.16,-0.0015242,0.85498,0.51866,768.74,-0.011492,-0.51864,0.85491,317.25,0.99993,-0.0046576,0.010616,422.79,#2.17,0.0037154,0.99747,0.070937,798.78,-0.010921,-0.070893,0.99742,312.58,0.99993,-0.0044805,0.01063,455.69,#2.18,0.008696,0.93051,-0.36615,828.66,-0.0089317,0.36622,0.93048,323.4,0.99992,-0.0048211,0.011496,446.63
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!2 models
> ui tool show "Fit in Map"
> show #!3 models
> fitmap sel inMap #3
Fit molecules 1PF (#2.5), 1PF (#2.6), 1PF (#2.7), 1PF (#2.8), 1PF (#2.9), 1PF
(#2.10), 1PF (#2.11), 1PF (#2.12), 1PF (#2.13), 1PF (#2.14), 1PF (#2.15), 1PF
(#2.16), 1PF (#2.17), 1PF (#2.18) to map bestrefinedstructure (#3) using
483490 atoms
average map value = 0.216, steps = 80
shifted from previous position = 11.2
rotated from previous position = 0.00566 degrees
atoms outside contour = 35273, contour level = 0.09
Position of 1PF (#2.5) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.00520376 -0.85703973 -0.51522404 818.59839083
0.01252158 0.51524646 -0.85695057 439.95469028
0.99990806 -0.00199205 0.01341271 401.28346205
Axis 0.43958530 -0.77902002 0.44709347
Axis point 374.78066505 0.00000000 697.52183663
Rotation angle (degrees) 103.47779669
Shift along axis 196.52152473
Position of 1PF (#2.6) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.00037134 -0.99550540 -0.09470405 787.23019722
0.01271739 0.09469169 -0.99542541 443.34745052
0.99991906 -0.00157403 0.01262507 392.39441892
Axis 0.55536694 -0.61167847 0.56339773
Axis point 506.74579197 0.00000000 689.72153959
Rotation angle (degrees) 116.52109586
Shift along axis 387.08966099
Position of 1PF (#2.7) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.00480879 -0.93002779 0.36745772 758.99903091
0.00948595 -0.36748786 -0.92997994 434.04322475
0.99994344 -0.00098639 0.01058937 467.90226115
Axis 0.63419499 -0.43177832 0.64137680
Axis point -86.40323028 504.36950920 0.00000000
Rotation angle (degrees) 132.91038580
Shift along axis 594.04457843
Position of 1PF (#2.8) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.01373650 0.66853849 -0.74355066 855.89657838
-0.00407297 0.74365207 0.66855442 334.75727854
0.99989735 -0.00615514 0.01293811 437.22457183
Axis -0.33960145 -0.87752940 -0.33854541
Axis point 267.08471877 0.00000000 462.29776316
Rotation angle (degrees) 96.59420410
Shift along axis -732.44344959
Position of 1PF (#2.9) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.01481721 0.30278723 -0.95294299 865.65268458
0.00085103 0.95304345 0.30283239 365.57119931
0.99988986 -0.00529811 0.01386376 428.16706109
Axis -0.15407168 -0.97645719 -0.15097440
Axis point 229.24807931 0.00000000 581.66627871
Rotation angle (degrees) 90.52356414
Shift along axis -554.97945843
Position of 1PF (#2.10) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.01398395 -0.13056950 -0.99134053 861.96528602
0.00621405 0.99142968 -0.13049358 397.08017321
0.99988291 -0.00433542 0.01467547 419.13670273
Axis 0.06308226 -0.99566195 0.06839523
Axis point 220.11993382 0.00000000 670.43066561
Rotation angle (degrees) 89.42448018
Shift along axis -312.31595102
Position of 1PF (#2.11) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.01025271 -0.54673626 -0.83724211 845.16257758
0.01042826 0.83729904 -0.54664573 423.53584424
0.99989306 -0.00312638 0.01428610 410.16151908
Axis 0.27241045 -0.92076725 0.27924937
Axis point 270.99759068 -0.00000000 703.80953376
Rotation angle (degrees) 93.96120900
Shift along axis -45.20946952
Position of 1PF (#2.12) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.00802255 -0.67692268 0.73601039 736.73256831
0.00536484 -0.73605263 -0.67690305 411.81865748
0.99995342 -0.00148192 0.00953660 459.01541578
Axis 0.67835256 -0.26508858 0.68524875
Axis point 24.69032499 344.96336104 0.00000000
Rotation angle (degrees) 150.14284768
Shift along axis 705.13574076
Position of 1PF (#2.13) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.00896409 -0.29058675 0.95680665 726.36579351
0.00005992 -0.95684525 -0.29059792 382.11049452
0.99995982 -0.00254762 0.00859466 450.08878051
Axis 0.70004537 -0.10487464 0.70635529
Axis point 105.95425170 237.41465705 0.00000000
Rotation angle (degrees) 168.12736127
Shift along axis 786.33789934
Position of 1PF (#2.14) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.00777390 0.12952529 0.99154564 730.55217290
-0.00467906 -0.99156946 0.12949171 350.11268665
0.99995883 -0.00363285 0.00831442 441.02374100
Axis -0.70354843 -0.04446277 -0.70925501
Axis point 156.98849160 156.62279363 0.00000000
Rotation angle (degrees) 174.57116257
Shift along axis -842.34411132
Position of 1PF (#2.15) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
-0.00457595 0.54770503 0.83665898 747.14949944
-0.00873664 -0.83665770 0.54765641 323.79535326
0.99995136 -0.00480354 0.00861361 431.88838881
Axis -0.68976508 -0.20387610 -0.69473640
Axis point 180.84794030 77.59464571 0.00000000
Rotation angle (degrees) 156.39245899
Shift along axis -881.42035497
Position of 1PF (#2.16) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.00034316 0.85535755 0.51803798 773.72018899
-0.01103705 -0.51800321 0.85530746 306.97955005
0.99993903 -0.00601112 0.00926287 422.71297586
Axis -0.65584658 -0.36694107 -0.65971169
Axis point 170.24970340 -16.31260323 0.00000000
Rotation angle (degrees) 138.95539392
Shift along axis -898.95383629
Position of 1PF (#2.17) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.00558234 0.99751677 0.07020771 803.81626594
-0.01046126 -0.07014670 0.99748183 302.34498674
0.99992969 -0.00630274 0.01004370 455.55934105
Axis -0.59066735 -0.54708594 -0.59313495
Axis point 83.28158884 -183.70934210 0.00000000
Rotation angle (degrees) 121.82053273
Shift along axis -910.40487640
Position of 1PF (#2.18) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.01056135 0.93022833 -0.36682924 833.67785178
-0.00846859 0.36691976 0.93021405 313.18062163
0.99990836 -0.00671778 0.01175289 446.44285337
Axis -0.49196739 -0.71765129 -0.49289422
Axis point 296.76386286 0.00000000 325.60847334
Rotation angle (degrees) 107.78120784
Shift along axis -854.94589859
> hide #!1 models
> select add #2
497304 atoms, 508968 bonds, 62640 residues, 19 models selected
> select subtract #2
Nothing selected
> show #!1 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> open "C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/kinesin
> bound.pdb"
Summary of feedback from opening
C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/kinesin bound.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY I 10 HIS I 28 1 19
Start residue of secondary structure not found: HELIX 2 2 SER I 54 THR I 57 1
4
Start residue of secondary structure not found: HELIX 3 3 VAL I 80 THR I 86 1
7
Start residue of secondary structure not found: HELIX 4 4 ILE I 116 CYS I 135
1 20
Start residue of secondary structure not found: HELIX 5 5 GLY I 149 TYR I 167
1 19
49 messages similar to the above omitted
Chain information for kinesin bound.pdb
---
Chain | Description
4.1/I | No description available
4.2/Q | No description available
4.3/Y | No description available
Computing secondary structure
[Repeated 1 time(s)]
> view orient
> color #4.2 #0055ffff
> color #4.3 lime
> color #4.1 blue
> hide #!3 models
> color #4.1 #0055ffff
> color #4.2 lime
> color #4.3 #aa0000ff
> color #4.3 red
> show #!3 models
> ui mousemode right "translate selected models"
> select add #4
9343 atoms, 9539 bonds, 1 pseudobond, 1181 residues, 5 models selected
> view matrix models #4,1,0,0,-1.2811,0,1,0,-5.9896,0,0,1,47.609
> volume #3 level 0.07486
> view matrix models #4,1,0,0,19.513,0,1,0,-1.4268,0,0,1,43.07
> view matrix models #4,1,0,0,25.885,0,1,0,1.0893,0,0,1,32.412
> view matrix models #4,1,0,0,23.062,0,1,0,0.51186,0,0,1,32.68
> view matrix models #4,1,0,0,31.375,0,1,0,-1.2312,0,0,1,34.576
> hide #!3 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #2.2 models
> hide #2.4 models
> show #2.2 models
> show #2.4 models
> show #!4 models
> view matrix models #4,1,0,0,-189.72,0,1,0,-165.34,0,0,1,45.923
> view matrix models #4,1,0,0,70.997,0,1,0,-119.97,0,0,1,76.758
> view matrix models #4,1,0,0,119.4,0,1,0,-359.34,0,0,1,67.907
> view matrix models #4,1,0,0,85.686,0,1,0,-263.97,0,0,1,88.587
> view matrix models #4,1,0,0,-15.713,0,1,0,-206,0,0,1,94.016
> view matrix models #4,1,0,0,37.725,0,1,0,-236.48,0,0,1,82.799
> view matrix models #4,1,0,0,121.39,0,1,0,-204.19,0,0,1,69.826
> view matrix models #4,1,0,0,118.04,0,1,0,-205.67,0,0,1,74.779
> hide #!2 models
> show #!3 models
> view matrix models #4,1,0,0,112.56,0,1,0,-210.97,0,0,1,73.111
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.50871,0.84008,0.18836,92.575,-0.85952,-0.48304,-0.167,756.77,-0.049306,-0.24686,0.9678,209.1
> view matrix models
> #4,-0.9993,0.017717,0.032978,654.21,-0.02419,-0.9779,-0.20766,758.13,0.02857,-0.20831,0.97765,166.44
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.9993,0.017717,0.032978,660.68,-0.02419,-0.9779,-0.20766,765.26,0.02857,-0.20831,0.97765,161.9
> fitmap sel inMap #3
Fit molecules kinesin bound.pdb (#4.1), kinesin bound.pdb (#4.2), kinesin
bound.pdb (#4.3) to map bestrefinedstructure (#3) using 9343 atoms
average map value = 0.1674, steps = 176
shifted from previous position = 22.1
rotated from previous position = 27.4 degrees
atoms outside contour = 2667, contour level = 0.074856
Position of kinesin bound.pdb (#4.1) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.90837308 -0.41773948 0.01876384 190.27032849
0.41256137 0.88798830 -0.20314993 13.41735640
0.06820168 0.19227717 0.97896784 -94.95322148
Axis 0.42935419 -0.05367954 0.90153951
Axis point 87.80688017 440.97621455 0.00000000
Rotation angle (degrees) 27.41876641
Shift along axis -4.63095440
Position of kinesin bound.pdb (#4.2) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.90837308 -0.41773948 0.01876384 190.27032849
0.41256137 0.88798830 -0.20314993 13.41735640
0.06820168 0.19227717 0.97896784 -94.95322148
Axis 0.42935419 -0.05367954 0.90153951
Axis point 87.80688017 440.97621455 0.00000000
Rotation angle (degrees) 27.41876641
Shift along axis -4.63095440
Position of kinesin bound.pdb (#4.3) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.90837308 -0.41773948 0.01876384 190.27032849
0.41256137 0.88798830 -0.20314993 13.41735640
0.06820168 0.19227717 0.97896784 -94.95322148
Axis 0.42935419 -0.05367954 0.90153951
Axis point 87.80688017 440.97621455 0.00000000
Rotation angle (degrees) 27.41876641
Shift along axis -4.63095440
> select subtract #4
Nothing selected
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/kinesinmask.cxs
> combine #4
> select add #5
9343 atoms, 9539 bonds, 1 pseudobond, 1181 residues, 2 models selected
> rename #5 id #4
> view matrix models
> #4.4,-0.89827,0.43928,0.011883,217.98,-0.43936,-0.8983,-0.0046195,1033.4,0.0086449,-0.0093703,0.99992,20.395
> view matrix models
> #4.4,-0.89827,0.43928,0.011883,325.34,-0.43936,-0.8983,-0.0046195,1094.9,0.0086449,-0.0093703,0.99992,52.733
> view matrix models
> #4.4,-0.89827,0.43928,0.011883,372.73,-0.43936,-0.8983,-0.0046195,1032.7,0.0086449,-0.0093703,0.99992,24.878
> view matrix models
> #4.4,-0.89827,0.43928,0.011883,360.9,-0.43936,-0.8983,-0.0046195,1028.3,0.0086449,-0.0093703,0.99992,23.132
> view matrix models
> #4.4,-0.89827,0.43928,0.011883,371.93,-0.43936,-0.8983,-0.0046195,1015.9,0.0086449,-0.0093703,0.99992,2.2925
> view matrix models
> #4.4,-0.89827,0.43928,0.011883,385.68,-0.43936,-0.8983,-0.0046195,1019.7,0.0086449,-0.0093703,0.99992,3.4128
> ui mousemode right "rotate selected models"
> view matrix models
> #4.4,0.60501,0.7676,-0.21153,-109.71,-0.66691,0.34341,-0.66129,742.38,-0.43497,0.54116,0.71969,-27.015
> view matrix models
> #4.4,0.84256,0.46354,-0.27426,-17.813,-0.51678,0.83924,-0.16918,310.84,0.15175,0.28428,0.94666,-151.68
> view matrix models
> #4.4,0.88222,0.27821,-0.37987,90.319,-0.31827,0.9469,-0.045678,164.99,0.34699,0.1612,0.92391,-143.17
> view matrix models
> #4.4,0.97817,0.17517,-0.11176,20.005,-0.17934,0.98338,-0.028323,103.67,0.10494,0.047748,0.99333,-47.234
> ui mousemode right "translate selected models"
> view matrix models
> #4.4,0.97817,0.17517,-0.11176,-3.861,-0.17934,0.98338,-0.028323,99.728,0.10494,0.047748,0.99333,-48.591
> view matrix models
> #4.4,0.97817,0.17517,-0.11176,-16.173,-0.17934,0.98338,-0.028323,103.95,0.10494,0.047748,0.99333,-41.992
> view matrix models
> #4.4,0.97817,0.17517,-0.11176,-2.5527,-0.17934,0.98338,-0.028323,110.06,0.10494,0.047748,0.99333,-39.26
> fitmap sel inMap #3
Fit molecule combination (#4.4) to map bestrefinedstructure (#3) using 9343
atoms
average map value = 0.1617, steps = 96
shifted from previous position = 12.2
rotated from previous position = 15.3 degrees
atoms outside contour = 2685, contour level = 0.074856
Position of combination (#4.4) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.99958884 0.01659120 0.02338569 12.46138687
-0.01155222 0.97949655 -0.20112946 123.76417558
-0.02624318 0.20077661 0.97928548 -57.37280666
Axis 0.99007391 0.12225803 -0.06932980
Axis point 0.00000000 332.90864899 562.29360706
Rotation angle (degrees) 11.71055661
Shift along axis 31.44650321
> select add #4
18686 atoms, 19078 bonds, 2 pseudobonds, 2362 residues, 7 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> combine #4
Remapping chain ID 'I' in combination #4.4 to 'J'
Remapping chain ID 'Q' in combination #4.4 to 'R'
Remapping chain ID 'Y' in combination #4.4 to 'Z'
> select add #5
18686 atoms, 19078 bonds, 2 pseudobonds, 2362 residues, 2 models selected
> select subtract #5
Nothing selected
> select add #5
18686 atoms, 19078 bonds, 2 pseudobonds, 2362 residues, 2 models selected
> view matrix models
> #5,-0.89827,0.43928,0.011883,522.51,-0.43936,-0.8983,-0.0046195,847.59,0.0086449,-0.0093703,0.99992,56.148
> view matrix models
> #5,-0.89827,0.43928,0.011883,517.61,-0.43936,-0.8983,-0.0046195,849.89,0.0086449,-0.0093703,0.99992,54.388
> view matrix models
> #5,-0.89827,0.43928,0.011883,518.2,-0.43936,-0.8983,-0.0046195,856.18,0.0086449,-0.0093703,0.99992,64.373
> view matrix models
> #5,-0.89827,0.43928,0.011883,518.05,-0.43936,-0.8983,-0.0046195,853.94,0.0086449,-0.0093703,0.99992,64.28
> fitmap sel inMap #3
Fit molecule combination (#5) to map bestrefinedstructure (#3) using 18686
atoms
average map value = 0.1653, steps = 172
shifted from previous position = 15
rotated from previous position = 51.2 degrees
atoms outside contour = 5408, contour level = 0.074856
Position of combination (#5) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
-0.21909352 0.97560237 0.01407297 53.83410791
-0.97565692 -0.21920168 0.00664927 713.35509623
0.00957187 -0.01227358 0.99987886 53.57876733
Axis -0.00969728 0.00230666 -0.99995032
Axis point 312.15304269 335.40128732 0.00000000
Rotation angle (degrees) 102.66252904
Shift along axis -52.45268515
> select subtract #5
Nothing selected
> rename #5 id #4
> combine #4
Remapping chain ID 'I' in combination #4.4 to 'J'
Remapping chain ID 'Q' in combination #4.4 to 'R'
Remapping chain ID 'Y' in combination #4.4 to 'Z'
Remapping chain ID 'I' in combination #4.5 to 'K'
Remapping chain ID 'J' in combination #4.5 to 'L'
Remapping chain ID 'Q' in combination #4.5 to 'S'
Remapping chain ID 'R' in combination #4.5 to 'T'
Remapping chain ID 'Y' in combination #4.5 to 'a'
Remapping chain ID 'Z' in combination #4.5 to 'b'
> select add #5
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #5,-0.89827,0.43928,0.011883,393.5,-0.43936,-0.8983,-0.0046195,926.13,0.0086449,-0.0093703,0.99992,24.128
> view matrix models
> #5,-0.89827,0.43928,0.011883,632.54,-0.43936,-0.8983,-0.0046195,815.46,0.0086449,-0.0093703,0.99992,-37.107
> view matrix models
> #5,-0.89827,0.43928,0.011883,608.33,-0.43936,-0.8983,-0.0046195,824.47,0.0086449,-0.0093703,0.99992,-55.994
> select subtract #5.1
37372 atoms, 38156 bonds, 4724 residues, 1 model selected
> select add #5.1
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> select subtract #5
Nothing selected
> undo
[Repeated 9 time(s)]
> delete #5
> view matrix models
> #4.5,-0.89827,0.43928,0.011883,590.8,-0.43936,-0.8983,-0.0046195,970.46,0.0086449,-0.0093703,0.99992,-5.5356
> view matrix models
> #4.5,-0.89827,0.43928,0.011883,299.17,-0.43936,-0.8983,-0.0046195,866.7,0.0086449,-0.0093703,0.99992,-12.186
> view matrix models
> #4.5,-0.89827,0.43928,0.011883,351.72,-0.43936,-0.8983,-0.0046195,925.29,0.0086449,-0.0093703,0.99992,-11.322
> view matrix models
> #4.5,-0.89827,0.43928,0.011883,349.05,-0.43936,-0.8983,-0.0046195,951.82,0.0086449,-0.0093703,0.99992,6.3114
> ui mousemode right "rotate selected models"
> view matrix models
> #4.5,0.57689,-0.72848,-0.36948,572.39,0.77068,0.63532,-0.04931,-112.54,0.27066,-0.25631,0.92793,65.769
> ui mousemode right "translate selected models"
> view matrix models
> #4.5,0.57689,-0.72848,-0.36948,573.6,0.77068,0.63532,-0.04931,-120.23,0.27066,-0.25631,0.92793,25.545
> fitmap sel inMap #3
Fit molecule combination (#4.5) to map bestrefinedstructure (#3) using 18686
atoms
average map value = 0.1279, steps = 176
shifted from previous position = 46.9
rotated from previous position = 21.9 degrees
atoms outside contour = 6986, contour level = 0.074856
Position of combination (#4.5) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.35796088 -0.69227907 -0.62658893 663.40335344
0.75238173 0.61126200 -0.24552088 -36.20358392
0.55297897 -0.38354720 0.73966601 54.47286689
Axis -0.07380479 -0.63073298 0.77248221
Axis point 358.81364906 627.21565143 0.00000000
Rotation angle (degrees) 69.24060070
Shift along axis 15.95177244
> view matrix models
> #4.5,0.35743,-0.69116,-0.62813,664.57,0.75192,0.61188,-0.24541,-30.223,0.55396,-0.38458,0.7384,70.417
> ui mousemode right "rotate selected models"
> view matrix models
> #4.5,0.40639,-0.86233,-0.30204,618.27,0.82483,0.48844,-0.28473,18.275,0.39306,-0.13342,0.90978,-55.527
> ui mousemode right "translate selected models"
> view matrix models
> #4.5,0.40639,-0.86233,-0.30204,592.82,0.82483,0.48844,-0.28473,24.944,0.39306,-0.13342,0.90978,-54.486
> view matrix models
> #4.5,0.40639,-0.86233,-0.30204,601.12,0.82483,0.48844,-0.28473,4.1242,0.39306,-0.13342,0.90978,-67.05
> fitmap sel inMap #3
Fit molecule combination (#4.5) to map bestrefinedstructure (#3) using 18686
atoms
average map value = 0.1653, steps = 100
shifted from previous position = 12.5
rotated from previous position = 22.5 degrees
atoms outside contour = 5408, contour level = 0.074856
Position of combination (#4.5) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.24296730 -0.96986575 0.01809206 600.32089349
0.94856505 0.23364621 -0.21362070 58.89642650
0.20295625 0.06906434 0.97674913 -116.16260610
Axis 0.14512014 -0.09490250 0.98485210
Axis point 273.05421527 410.75846772 0.00000000
Rotation angle (degrees) 76.89823425
Shift along axis -32.87375054
> select add #4
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 9 models selected
> select subtract #4
Nothing selected
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/kinesinmask.cxs
> combine #4
Remapping chain ID 'I' in combination #4.4 to 'J'
Remapping chain ID 'Q' in combination #4.4 to 'R'
Remapping chain ID 'Y' in combination #4.4 to 'Z'
Remapping chain ID 'I' in combination #4.5 to 'K'
Remapping chain ID 'J' in combination #4.5 to 'L'
Remapping chain ID 'Q' in combination #4.5 to 'S'
Remapping chain ID 'R' in combination #4.5 to 'T'
Remapping chain ID 'Y' in combination #4.5 to 'a'
Remapping chain ID 'Z' in combination #4.5 to 'b'
> select add #5
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #5,-0.89827,0.43928,0.011883,360.38,-0.43936,-0.8983,-0.0046195,879.38,0.0086449,-0.0093703,0.99992,64.012
> view matrix models
> #5,-0.89827,0.43928,0.011883,636.78,-0.43936,-0.8983,-0.0046195,923.75,0.0086449,-0.0093703,0.99992,25.816
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.10308,0.98406,0.14488,96.681,-0.98529,0.12098,-0.12066,670.53,-0.13627,-0.13031,0.98206,121.49
> view matrix models
> #5,-0.3285,0.94245,0.062221,255.35,-0.93504,-0.3152,-0.16235,857.34,-0.1334,-0.11151,0.98477,111.82
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.3285,0.94245,0.062221,87.224,-0.93504,-0.3152,-0.16235,914.84,-0.1334,-0.11151,0.98477,129.59
> view matrix models
> #5,-0.3285,0.94245,0.062221,84.724,-0.93504,-0.3152,-0.16235,917.06,-0.1334,-0.11151,0.98477,132.73
> view matrix models
> #5,-0.3285,0.94245,0.062221,94.531,-0.93504,-0.3152,-0.16235,905.71,-0.1334,-0.11151,0.98477,126.99
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.17828,0.7787,0.60154,-147.25,-0.89987,-0.11828,0.41981,619.83,0.39806,-0.61615,0.67964,303.56
> view matrix models
> #5,0.17696,0.79137,0.58516,-146.9,-0.92936,-0.061362,0.36404,621.73,0.324,-0.60825,0.72461,304.79
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.17696,0.79137,0.58516,-173.57,-0.92936,-0.061362,0.36404,589.56,0.324,-0.60825,0.72461,275.35
> view matrix models
> #5,0.17696,0.79137,0.58516,-165.71,-0.92936,-0.061362,0.36404,571.77,0.324,-0.60825,0.72461,273.94
> view matrix models
> #5,0.17696,0.79137,0.58516,-163,-0.92936,-0.061362,0.36404,561.22,0.324,-0.60825,0.72461,309.57
> fitmap sel inMap #3
Fit molecule combination (#5) to map bestrefinedstructure (#3) using 37372
atoms
average map value = 0.1676, steps = 224
shifted from previous position = 28.5
rotated from previous position = 43.7 degrees
atoms outside contour = 10809, contour level = 0.074856
Position of combination (#5) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.22181171 0.97502808 0.01094527 -94.08859046
-0.97506609 0.22171460 0.00942128 564.50617442
0.00675928 -0.01276211 0.99989571 45.63039026
Axis -0.01137478 0.00214641 -0.99993300
Axis point 306.41091844 341.55634063 0.00000000
Rotation angle (degrees) 77.19045141
Shift along axis -43.34543311
> combine #4
Remapping chain ID 'I' in combination #4.4 to 'J'
Remapping chain ID 'Q' in combination #4.4 to 'R'
Remapping chain ID 'Y' in combination #4.4 to 'Z'
Remapping chain ID 'I' in combination #4.5 to 'K'
Remapping chain ID 'J' in combination #4.5 to 'L'
Remapping chain ID 'Q' in combination #4.5 to 'S'
Remapping chain ID 'R' in combination #4.5 to 'T'
Remapping chain ID 'Y' in combination #4.5 to 'a'
Remapping chain ID 'Z' in combination #4.5 to 'b'
> select subtract #5
Nothing selected
> select add #6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #6,-0.89827,0.43928,0.011883,479.23,-0.43936,-0.8983,-0.0046195,1078.1,0.0086449,-0.0093703,0.99992,73.334
> view matrix models
> #6,-0.89827,0.43928,0.011883,302.64,-0.43936,-0.8983,-0.0046195,866.46,0.0086449,-0.0093703,0.99992,43.375
> view matrix models
> #6,-0.89827,0.43928,0.011883,274.97,-0.43936,-0.8983,-0.0046195,864.77,0.0086449,-0.0093703,0.99992,38.704
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99254,0.0063464,0.12179,-74.027,-0.046862,0.94182,0.33283,-135.86,-0.11259,-0.33605,0.93509,231.54
> view matrix models
> #6,0.98908,0.14054,0.044389,-104.82,-0.14656,0.90595,0.39722,-115.6,0.015611,-0.39939,0.91665,230.95
> view matrix models
> #6,0.9843,0.15397,-0.086316,-66.071,-0.12382,0.95079,0.28403,-103.3,0.1258,-0.26889,0.95492,133.58
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.9843,0.15397,-0.086316,-61.595,-0.12382,0.95079,0.28403,-102.01,0.1258,-0.26889,0.95492,121.81
> view matrix models
> #6,0.9843,0.15397,-0.086316,-95.551,-0.12382,0.95079,0.28403,-121.03,0.1258,-0.26889,0.95492,115.54
> fitmap sel inMap #3
Fit molecule combination (#6) to map bestrefinedstructure (#3) using 37372
atoms
average map value = 0.1687, steps = 236
shifted from previous position = 24.4
rotated from previous position = 38.2 degrees
atoms outside contour = 10797, contour level = 0.074856
Position of combination (#6) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.89616651 -0.44366416 -0.00690504 161.35971004
0.44370394 0.89615322 0.00601714 -140.08915264
0.00351839 -0.00845615 0.99995804 9.12835951
Axis -0.01630705 -0.01174408 0.99979806
Axis point 379.89420535 275.08806476 0.00000000
Rotation angle (degrees) 26.34490562
Shift along axis 8.14043340
> combine #4
Remapping chain ID 'I' in combination #4.4 to 'J'
Remapping chain ID 'Q' in combination #4.4 to 'R'
Remapping chain ID 'Y' in combination #4.4 to 'Z'
Remapping chain ID 'I' in combination #4.5 to 'K'
Remapping chain ID 'J' in combination #4.5 to 'L'
Remapping chain ID 'Q' in combination #4.5 to 'S'
Remapping chain ID 'R' in combination #4.5 to 'T'
Remapping chain ID 'Y' in combination #4.5 to 'a'
Remapping chain ID 'Z' in combination #4.5 to 'b'
> select add #7
74744 atoms, 76312 bonds, 8 pseudobonds, 9448 residues, 4 models selected
> select subtract #6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #7,-0.89827,0.43928,0.011883,311.7,-0.43936,-0.8983,-0.0046195,799.32,0.0086449,-0.0093703,0.99992,18.099
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.050537,-0.93227,-0.35822,796.71,0.8974,0.11503,-0.42596,154.23,0.43831,-0.343,0.83081,103.44
> view matrix models
> #7,-0.1924,-0.94889,-0.25017,805.4,0.96261,-0.23204,0.13979,98.17,-0.19069,-0.21392,0.95806,171.74
> view matrix models
> #7,-0.26411,-0.96013,0.091578,716.05,0.96344,-0.25821,0.071481,131.72,-0.044986,0.10711,0.99323,-15.315
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.26411,-0.96013,0.091578,705.83,0.96344,-0.25821,0.071481,11.497,-0.044986,0.10711,0.99323,-12.97
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.40169,-0.91199,0.083141,724.26,0.91419,-0.39401,0.094891,74.702,-0.053782,0.11412,0.99201,-13.247
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.40169,-0.91199,0.083141,735.4,0.91419,-0.39401,0.094891,82.06,-0.053782,0.11412,0.99201,-12.622
> view matrix models
> #7,-0.40169,-0.91199,0.083141,736.73,0.91419,-0.39401,0.094891,81.706,-0.053782,0.11412,0.99201,-15.381
> view matrix models
> #7,-0.40169,-0.91199,0.083141,742.16,0.91419,-0.39401,0.094891,82.457,-0.053782,0.11412,0.99201,-58.151
> fitmap sel inMap #3
Fit molecule combination (#7) to map bestrefinedstructure (#3) using 37372
atoms
average map value = 0.1625, steps = 124
shifted from previous position = 19.6
rotated from previous position = 17 degrees
atoms outside contour = 10919, contour level = 0.074856
Position of combination (#7) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
-0.62556724 -0.78016846 0.00168565 786.16083104
0.78010626 -0.62554213 -0.01145855 262.50533716
0.00999405 -0.00585310 0.99993295 -30.14947887
Axis 0.00359253 -0.00532485 0.99997937
Axis point 330.17910022 319.84848193 0.00000000
Rotation angle (degrees) 128.72537300
Shift along axis -28.72235227
> select subtract #7
Nothing selected
> split #7
Split combination (#7) into 12 models
Chain information for combination I #7.1
---
Chain | Description
I | No description available
Chain information for combination J #7.2
---
Chain | Description
J | No description available
Chain information for combination K #7.3
---
Chain | Description
K | No description available
Chain information for combination L #7.4
---
Chain | Description
L | No description available
Chain information for combination Q #7.5
---
Chain | Description
Q | No description available
Chain information for combination R #7.6
---
Chain | Description
R | No description available
Chain information for combination S #7.7
---
Chain | Description
S | No description available
Chain information for combination T #7.8
---
Chain | Description
T | No description available
Chain information for combination Y #7.9
---
Chain | Description
Y | No description available
Chain information for combination Z #7.10
---
Chain | Description
Z | No description available
Chain information for combination a #7.11
---
Chain | Description
a | No description available
Chain information for combination b #7.12
---
Chain | Description
b | No description available
> select add #7.12
2575 atoms, 2616 bonds, 326 residues, 1 model selected
> select subtract #7.12
Nothing selected
> select add #7.11
2575 atoms, 2616 bonds, 326 residues, 1 model selected
> select add #7.7
5993 atoms, 6113 bonds, 754 residues, 2 models selected
> select add #7.3
9343 atoms, 9539 bonds, 1 pseudobond, 1181 residues, 4 models selected
> close sel
> combine #7
> close #7
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/kinesinmask.cxs
> rename #5 id #4
> undo
Undo failed, probably because structures have been modified.
> select add #4
74744 atoms, 76312 bonds, 8 pseudobonds, 9448 residues, 11 models selected
> select subtract #4
Nothing selected
> select add #4.1
3350 atoms, 3426 bonds, 1 pseudobond, 427 residues, 2 models selected
> select subtract #4.1
Nothing selected
> select add #4.2
3418 atoms, 3497 bonds, 428 residues, 1 model selected
> select subtract #4.2
Nothing selected
> select add #4.3
2575 atoms, 2616 bonds, 326 residues, 1 model selected
> select subtract #4.3
Nothing selected
> select add #4.4
9343 atoms, 9539 bonds, 1 pseudobond, 1181 residues, 2 models selected
> select subtract #4.4
Nothing selected
> select add #4.5
18686 atoms, 19078 bonds, 2 pseudobonds, 2362 residues, 2 models selected
> select subtract #4.5
Nothing selected
> select add #4.6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> select subtract #4.6.1
37372 atoms, 38156 bonds, 4724 residues, 1 model selected
> select add #4.6.1
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> select subtract #4.6
Nothing selected
> select add #4.6.1
4 pseudobonds, 1 model selected
> select subtract #4.6.1
Nothing selected
> rename #6 id #4.7
> rename #8 id #4.8
> select add #4
140145 atoms, 143085 bonds, 15 pseudobonds, 17715 residues, 15 models selected
> view matrix models
> #4,-0.9993,0.017717,0.032978,605.47,-0.02419,-0.9779,-0.20766,755.85,0.02857,-0.20831,0.97765,48.63
> view matrix models
> #4,-0.9993,0.017717,0.032978,625.35,-0.02419,-0.9779,-0.20766,695.27,0.02857,-0.20831,0.97765,48.1
> select subtract #4.1
136795 atoms, 139659 bonds, 14 pseudobonds, 17288 residues, 13 models selected
> select subtract #4.2
133377 atoms, 136162 bonds, 14 pseudobonds, 16860 residues, 12 models selected
> select subtract #4.3
130802 atoms, 133546 bonds, 14 pseudobonds, 16534 residues, 11 models selected
> select subtract #4.4
121459 atoms, 124007 bonds, 13 pseudobonds, 15353 residues, 9 models selected
> select subtract #4.5
102773 atoms, 104929 bonds, 11 pseudobonds, 12991 residues, 7 models selected
> select subtract #4.6
65401 atoms, 66773 bonds, 7 pseudobonds, 8267 residues, 5 models selected
> select subtract #4.8
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 3 models selected
> select subtract #4.7
1 model selected
> select add #4.7
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 3 models selected
> view matrix models
> #4,-0.9993,0.017717,0.032978,624.04,-0.02419,-0.9779,-0.20766,702.67,0.02857,-0.20831,0.97765,48.203
> select add #4
140145 atoms, 143085 bonds, 15 pseudobonds, 17715 residues, 15 models selected
> select subtract #4
Nothing selected
> select add #4.6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #4.6,0.22115,0.9752,0.0090878,-81.094,-0.97522,0.22107,0.0090011,576.77,0.0067688,-0.010853,0.99992,47.776
> select add #4.7
74744 atoms, 76312 bonds, 8 pseudobonds, 9448 residues, 4 models selected
> select subtract #4.6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #4.7,0.89645,-0.44305,-0.0087648,379.41,0.44311,0.89645,0.0056088,-270.23,0.0053722,-0.0089118,0.99995,-29.138
> ui mousemode right "rotate selected models"
> view matrix models
> #4.7,-0.88872,-0.26086,0.37699,643.75,-0.4582,0.53212,-0.71197,359.83,-0.01488,-0.80549,-0.59243,842.97
> view matrix models
> #4.7,-0.87578,0.43069,0.218,397.63,-0.48138,-0.81284,-0.32797,813.24,0.035948,-0.39217,0.91919,153.18
> view matrix models
> #4.7,-0.97347,0.15548,0.16786,557.44,-0.20815,-0.90642,-0.36754,794.39,0.095004,-0.39273,0.91473,139.35
> ui mousemode right "translate selected models"
> view matrix models
> #4.7,-0.97347,0.15548,0.16786,753.15,-0.20815,-0.90642,-0.36754,791.65,0.095004,-0.39273,0.91473,126.35
> select subtract #4.7
Nothing selected
> select add #4.8
28029 atoms, 28617 bonds, 3 pseudobonds, 3543 residues, 2 models selected
> view matrix models
> #4.8,-0.62507,-0.78057,-0.00018563,729.91,0.78052,-0.62502,-0.011873,302.76,0.0091513,-0.0075661,0.99993,-16.561
> view matrix models
> #4.8,-0.62507,-0.78057,-0.00018563,730.24,0.78052,-0.62502,-0.011873,290.88,0.0091513,-0.0075661,0.99993,-18.88
> ui mousemode right "rotate selected models"
> view matrix models
> #4.8,-0.32433,-0.94373,0.064652,698.26,0.94569,-0.32507,-0.00096241,107.08,0.021925,0.060828,0.99791,-52.38
> ui mousemode right "translate selected models"
> view matrix models
> #4.8,-0.32433,-0.94373,0.064652,665.88,0.94569,-0.32507,-0.00096241,115.79,0.021925,0.060828,0.99791,-48.634
> view matrix models
> #4.8,-0.32433,-0.94373,0.064652,708.54,0.94569,-0.32507,-0.00096241,107.7,0.021925,0.060828,0.99791,-52.916
> select subtract #4.8
Nothing selected
> select add #4.7
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #4.7,-0.97347,0.15548,0.16786,526.69,-0.20815,-0.90642,-0.36754,785.71,0.095004,-0.39273,0.91473,139.63
> view matrix models
> #4.7,-0.97347,0.15548,0.16786,538.44,-0.20815,-0.90642,-0.36754,782.61,0.095004,-0.39273,0.91473,138.29
> ui mousemode right "rotate selected models"
> view matrix models
> #4.7,-0.99015,-0.067604,0.12262,653.05,0.014999,-0.92189,-0.38716,737,0.13921,-0.3815,0.91382,122.16
> select subtract #4.7
Nothing selected
> select add #4.6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #4.6,0.21337,0.97644,-0.032185,-65.927,-0.97659,0.21409,0.020827,576.21,0.027227,0.026988,0.99926,26.45
> ui mousemode right "translate selected models"
> select subtract #4.6
Nothing selected
> select add #4.5
18686 atoms, 19078 bonds, 2 pseudobonds, 2362 residues, 2 models selected
> view matrix models
> #4.5,0.24322,-0.96984,0.01613,552.54,0.94832,0.23426,-0.21404,53.712,0.2038,0.067354,0.97669,-112.36
> ui mousemode right "rotate selected models"
> view matrix models
> #4.5,0.46727,-0.88404,0.011575,446.17,0.86687,0.45554,-0.20253,-28.151,0.17377,0.10467,0.97921,-121.41
> select subtract #4.5
Nothing selected
> select add #4.4
9343 atoms, 9539 bonds, 1 pseudobond, 1181 residues, 2 models selected
> select add #4.3
11918 atoms, 12155 bonds, 1 pseudobond, 1507 residues, 3 models selected
> select add #4.2
15336 atoms, 15652 bonds, 1 pseudobond, 1935 residues, 4 models selected
> select add #4.1
18686 atoms, 19078 bonds, 2 pseudobonds, 2362 residues, 6 models selected
> view matrix models
> #4.1,0.90219,-0.41621,0.11325,160.28,0.42915,0.89255,-0.1385,-14.324,-0.043435,0.17355,0.98387,-52.892,#4.2,0.90219,-0.41621,0.11325,160.28,0.42915,0.89255,-0.1385,-14.324,-0.043435,0.17355,0.98387,-52.892,#4.3,0.90219,-0.41621,0.11325,160.28,0.42915,0.89255,-0.1385,-14.324,-0.043435,0.17355,0.98387,-52.892,#4.4,0.99292,0.015094,0.11784,-15.512,0.0011266,0.99065,-0.13639,95.674,-0.11879,0.13556,0.98362,-5.9564
> ui mousemode right "translate selected models"
> view matrix models
> #4.1,0.90219,-0.41621,0.11325,114.45,0.42915,0.89255,-0.1385,52.602,-0.043435,0.17355,0.98387,-37.031,#4.2,0.90219,-0.41621,0.11325,114.45,0.42915,0.89255,-0.1385,52.602,-0.043435,0.17355,0.98387,-37.031,#4.3,0.90219,-0.41621,0.11325,114.45,0.42915,0.89255,-0.1385,52.602,-0.043435,0.17355,0.98387,-37.031,#4.4,0.99292,0.015094,0.11784,-61.343,0.0011266,0.99065,-0.13639,162.6,-0.11879,0.13556,0.98362,9.9046
> ui mousemode right "translate selected models"
> select subtract #4.4
9343 atoms, 9539 bonds, 1 pseudobond, 1181 residues, 4 models selected
> select subtract #4.3
6768 atoms, 6923 bonds, 1 pseudobond, 855 residues, 3 models selected
> select subtract #4.2
3350 atoms, 3426 bonds, 1 pseudobond, 427 residues, 2 models selected
> select subtract #4.1
Nothing selected
> select add #4.5
18686 atoms, 19078 bonds, 2 pseudobonds, 2362 residues, 2 models selected
> select subtract #4.5
Nothing selected
> select add #4.6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #4.6,0.21337,0.97644,-0.032185,-48.439,-0.97659,0.21409,0.020827,557.66,0.027227,0.026988,0.99926,24.253
> view matrix models
> #4.6,0.21337,0.97644,-0.032185,-46.909,-0.97659,0.21409,0.020827,555.35,0.027227,0.026988,0.99926,34.476
> view matrix models
> #4.6,0.21337,0.97644,-0.032185,-54.759,-0.97659,0.21409,0.020827,558.56,0.027227,0.026988,0.99926,35.073
> select subtract #4.6
Nothing selected
> select add #4.1
3350 atoms, 3426 bonds, 1 pseudobond, 427 residues, 2 models selected
> select add #4.2
6768 atoms, 6923 bonds, 1 pseudobond, 855 residues, 3 models selected
> select add #4.3
9343 atoms, 9539 bonds, 1 pseudobond, 1181 residues, 4 models selected
> view matrix models
> #4.1,0.90219,-0.41621,0.11325,153.93,0.42915,0.89255,-0.1385,-32.059,-0.043435,0.17355,0.98387,-63.418,#4.2,0.90219,-0.41621,0.11325,153.93,0.42915,0.89255,-0.1385,-32.059,-0.043435,0.17355,0.98387,-63.418,#4.3,0.90219,-0.41621,0.11325,153.93,0.42915,0.89255,-0.1385,-32.059,-0.043435,0.17355,0.98387,-63.418
> view matrix models
> #4.1,0.90219,-0.41621,0.11325,168.84,0.42915,0.89255,-0.1385,-44.408,-0.043435,0.17355,0.98387,-19.821,#4.2,0.90219,-0.41621,0.11325,168.84,0.42915,0.89255,-0.1385,-44.408,-0.043435,0.17355,0.98387,-19.821,#4.3,0.90219,-0.41621,0.11325,168.84,0.42915,0.89255,-0.1385,-44.408,-0.043435,0.17355,0.98387,-19.821
> view matrix models
> #4.1,0.90219,-0.41621,0.11325,168.05,0.42915,0.89255,-0.1385,-45.444,-0.043435,0.17355,0.98387,-17.858,#4.2,0.90219,-0.41621,0.11325,168.05,0.42915,0.89255,-0.1385,-45.444,-0.043435,0.17355,0.98387,-17.858,#4.3,0.90219,-0.41621,0.11325,168.05,0.42915,0.89255,-0.1385,-45.444,-0.043435,0.17355,0.98387,-17.858
> fitmap sel inMap #3
Fit molecules kinesin bound.pdb (#4.1), kinesin bound.pdb (#4.2), kinesin
bound.pdb (#4.3) to map bestrefinedstructure (#3) using 9343 atoms
average map value = 0.1636, steps = 112
shifted from previous position = 6.25
rotated from previous position = 26 degrees
atoms outside contour = 2693, contour level = 0.074856
Position of kinesin bound.pdb (#4.1) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.99968542 0.01113694 0.02247264 -22.63903418
-0.00640436 0.97965252 -0.20059891 55.06730471
-0.02424944 0.20039188 0.97941567 -41.13963586
Axis 0.99234396 0.11562453 -0.04341000
Axis point 0.00000000 234.99359976 258.92801619
Rotation angle (degrees) 11.65640901
Shift along axis -14.31270595
Position of kinesin bound.pdb (#4.2) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.99968542 0.01113694 0.02247264 -22.63903418
-0.00640436 0.97965252 -0.20059891 55.06730471
-0.02424944 0.20039188 0.97941567 -41.13963586
Axis 0.99234396 0.11562453 -0.04341000
Axis point 0.00000000 234.99359976 258.92801619
Rotation angle (degrees) 11.65640901
Shift along axis -14.31270595
Position of kinesin bound.pdb (#4.3) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.99968542 0.01113694 0.02247264 -22.63903418
-0.00640436 0.97965252 -0.20059891 55.06730471
-0.02424944 0.20039188 0.97941567 -41.13963586
Axis 0.99234396 0.11562453 -0.04341000
Axis point 0.00000000 234.99359976 258.92801619
Rotation angle (degrees) 11.65640901
Shift along axis -14.31270595
> select subtract #4.1
5993 atoms, 6113 bonds, 754 residues, 2 models selected
> select subtract #4.2
2575 atoms, 2616 bonds, 326 residues, 1 model selected
> select subtract #4.3
Nothing selected
> select add #4.3
2575 atoms, 2616 bonds, 326 residues, 1 model selected
> select subtract #4.3
Nothing selected
> select add #4.5
18686 atoms, 19078 bonds, 2 pseudobonds, 2362 residues, 2 models selected
> view matrix models
> #4.5,0.46727,-0.88404,0.011575,454.24,0.86687,0.45554,-0.20253,-19.587,0.17377,0.10467,0.97921,-79.107
> fitmap sel inMap #3
Fit molecule combination (#4.5) to map bestrefinedstructure (#3) using 18686
atoms
average map value = 0.1674, steps = 88
shifted from previous position = 24.6
rotated from previous position = 11.4 degrees
atoms outside contour = 5411, contour level = 0.074856
Position of combination (#4.5) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.63245015 -0.77441749 0.01686277 366.56089864
0.75972591 0.61591199 -0.20849211 -75.60946849
0.15107395 0.14467195 0.97787866 -98.77216406
Axis 0.22352454 -0.08494492 0.97098977
Axis point 274.82531106 345.08031584 -0.00000000
Rotation angle (degrees) 52.18452789
Shift along axis -7.54876644
> select subtract #4.5
Nothing selected
> select add #4.6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> select subtract #4.6
Nothing selected
> select add #4.7
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #4.7,-0.99015,-0.067604,0.12262,655.27,0.014999,-0.92189,-0.38716,746.02,0.13921,-0.3815,0.91382,122.37
> select subtract #4.7
Nothing selected
> select add #4.8
28029 atoms, 28617 bonds, 3 pseudobonds, 3543 residues, 2 models selected
> view matrix models
> #4.8,-0.32433,-0.94373,0.064652,713.63,0.94569,-0.32507,-0.00096241,126.47,0.021925,0.060828,0.99791,-48.963
> fitmap sel inMap #3
Fit molecule combination (#4.8) to map bestrefinedstructure (#3) using 28029
atoms
average map value = 0.1678, steps = 108
shifted from previous position = 22.2
rotated from previous position = 14.4 degrees
atoms outside contour = 8110, contour level = 0.074856
Position of combination (#4.8) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
-0.20227751 -0.97910219 0.02104153 715.78244666
0.95509578 -0.20197684 -0.21678895 138.78560235
0.21650843 -0.02375485 0.97599173 -81.60334901
Axis 0.09880893 -0.10005422 0.99006361
Axis point 306.54811107 357.05498321 0.00000000
Rotation angle (degrees) 102.36456820
Shift along axis -23.95289231
> select subtract #4.8
Nothing selected
> select add #1
2 models selected
> select add #3
7 models selected
> select subtract #3
2 models selected
> select subtract #1
Nothing selected
> hide #!3 models
> show #!1 models
> hide #!4.4 models
> select add #4.1
3350 atoms, 3426 bonds, 1 pseudobond, 427 residues, 2 models selected
> select subtract #4.1
Nothing selected
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #4.1
3350 atoms, 3426 bonds, 1 pseudobond, 427 residues, 2 models selected
> select subtract #4.1
Nothing selected
> color #4.1 #aa55ffff
> color #4.3 #ffaa00ff
> color #4.3 #ff5500ff
> color #4.3 #ffaa00ff
> color #4.2 magenta
> select add #4.6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> select subtract #4.6
Nothing selected
> select add #4.7
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #4.7,-0.99015,-0.067604,0.12262,642.93,0.014999,-0.92189,-0.38716,764.87,0.13921,-0.3815,0.91382,82.548
> fitmap sel inMap #3
Fit molecule combination (#4.7) to map bestrefinedstructure (#3) using 37372
atoms
average map value = 0.1692, steps = 84
shifted from previous position = 8.75
rotated from previous position = 11.8 degrees
atoms outside contour = 10734, contour level = 0.074856
Position of combination (#4.7) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
-0.99930926 -0.01130803 0.03539948 653.55457850
0.00336639 -0.97620823 -0.21680902 726.42120216
0.03700895 -0.21654008 0.97557200 17.48124053
Axis 0.01821478 -0.10900671 0.99387412
Axis point 325.27823096 365.38460493 0.00000000
Rotation angle (degrees) 179.57701390
Shift along axis -49.90628121
> select subtract #4.7
Nothing selected
> select add #4.8
28029 atoms, 28617 bonds, 3 pseudobonds, 3543 residues, 2 models selected
> select subtract #4.8
Nothing selected
> select add #4.6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> view matrix models
> #4.6,0.21337,0.97644,-0.032185,-77.162,-0.97659,0.21409,0.020827,565.58,0.027227,0.026988,0.99926,-121.07
> fitmap sel inMap #3
Fit molecule combination (#4.6) to map bestrefinedstructure (#3) using 37372
atoms
average map value = 0.1536, steps = 196
shifted from previous position = 33.7
rotated from previous position = 13.1 degrees
atoms outside contour = 11379, contour level = 0.074856
Position of combination (#4.6) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.20988522 0.97696887 0.03847095 -91.02214721
-0.95733380 0.21334280 -0.19492781 660.97335616
-0.19864590 0.00408293 0.98006282 -54.59601077
Axis 0.10159221 0.12104486 -0.98743464
Axis point 352.92158006 391.55416597 0.00000000
Rotation angle (degrees) 78.36680461
Shift along axis 124.67027760
> view matrix models
> #4.6,0.20962,0.9771,0.036515,-80.778,-0.95739,0.21269,-0.19536,659.57,-0.19865,0.0059919,0.98005,-12.963
> fitmap sel inMap #3
Fit molecule combination (#4.6) to map bestrefinedstructure (#3) using 37372
atoms
average map value = 0.1632, steps = 60
shifted from previous position = 8.51
rotated from previous position = 0.194 degrees
atoms outside contour = 10772, contour level = 0.074856
Position of combination (#4.6) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.20810932 0.97739136 0.03737168 -88.82405016
-0.95722797 0.21137069 -0.19757794 653.62022656
-0.20101025 0.00534460 0.97957455 -12.99787811
Axis 0.10354329 0.12163680 -0.98715920
Axis point 353.90204873 386.42062317 0.00000000
Rotation angle (degrees) 78.49068292
Shift along axis 83.13811358
> select subtract #4.6
Nothing selected
> close #4.4
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> select add #3
3 models selected
> select subtract #3
Nothing selected
> select add #3
3 models selected
> view matrix models
> #3,1,0.00066125,-0.0018638,4.6076,-0.00066202,1,-0.00041293,0.36893,0.0018636,0.00041416,1,-43.297
> select subtract #3
Nothing selected
> select add #4
130802 atoms, 133546 bonds, 14 pseudobonds, 16534 residues, 13 models selected
> fitmap sel inMap #3
Fit molecules kinesin bound.pdb (#4.1), kinesin bound.pdb (#4.2), kinesin
bound.pdb (#4.3), combination (#4.5), combination (#4.6), combination (#4.7),
combination (#4.8) to map bestrefinedstructure (#3) using 130802 atoms
average map value = 0.1569, steps = 52
shifted from previous position = 3.64
rotated from previous position = 0.204 degrees
atoms outside contour = 40548, contour level = 0.074856
Position of kinesin bound.pdb (#4.1) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.99963963 0.01469296 0.02246620 -29.25419419
-0.00989037 0.97962292 -0.20060185 59.80111080
-0.02495585 0.20030736 0.97941522 1.93667627
Axis 0.99124062 0.11725014 -0.06078183
Axis point 0.00000000 28.70225223 308.11249465
Rotation angle (degrees) 11.66715852
Shift along axis -22.10397160
Position of kinesin bound.pdb (#4.2) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.99963963 0.01469296 0.02246620 -29.25419419
-0.00989037 0.97962292 -0.20060185 59.80111080
-0.02495585 0.20030736 0.97941522 1.93667627
Axis 0.99124062 0.11725014 -0.06078183
Axis point 0.00000000 28.70225223 308.11249465
Rotation angle (degrees) 11.66715852
Shift along axis -22.10397160
Position of kinesin bound.pdb (#4.3) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.99963963 0.01469296 0.02246620 -29.25419419
-0.00989037 0.97962292 -0.20060185 59.80111080
-0.02495585 0.20030736 0.97941522 1.93667627
Axis 0.99124062 0.11725014 -0.06078183
Axis point 0.00000000 28.70225223 308.11249465
Rotation angle (degrees) 11.66715852
Shift along axis -22.10397160
Position of combination (#4.5) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.63520086 -0.77216365 0.01682777 359.44706706
0.75752846 0.61861828 -0.20847557 -72.23571150
0.15056729 0.14517138 0.97788279 -55.96083780
Axis 0.22443438 -0.08487489 0.97078600
Axis point 259.58485417 333.42895301 0.00000000
Rotation angle (degrees) 51.98622096
Shift along axis 32.47728135
Position of combination (#4.6) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.20462963 0.97812564 0.03737579 -93.33277908
-0.95796270 0.20796330 -0.19763281 658.58320119
-0.20108251 0.00463692 0.97956333 30.07843039
Axis 0.10313693 0.12158941 -0.98720757
Axis point 358.70335220 391.39997653 0.00000000
Rotation angle (degrees) 78.69228807
Shift along axis 40.75703266
Position of combination (#4.7) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
-0.99926503 -0.01486347 0.03533375 649.31644548
0.00685207 -0.97617928 -0.21685721 728.79862881
0.03771533 -0.21645570 0.97556367 60.02688618
Axis 0.01837599 -0.10899955 0.99387193
Axis point 322.10283436 369.47572053 0.00000000
Rotation angle (degrees) 179.37404759
Shift along axis -7.84785228
Position of combination (#4.8) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
-0.19879433 -0.97981674 0.02097626 709.42577184
0.95581136 -0.19856495 -0.21678706 140.94221414
0.21657674 -0.02304669 0.97599355 -39.05573711
Axis 0.09909441 -0.10004582 0.99003592
Axis point 298.47826958 357.08138148 0.00000000
Rotation angle (degrees) 102.16237255
Shift along axis 17.53286601
> select subtract #4
Nothing selected
> hide #!3 models
> show #!1 models
> select add #4
130802 atoms, 133546 bonds, 14 pseudobonds, 16534 residues, 13 models selected
> fitmap sel inMap #1
Fit molecules kinesin bound.pdb (#4.1), kinesin bound.pdb (#4.2), kinesin
bound.pdb (#4.3), combination (#4.5), combination (#4.6), combination (#4.7),
combination (#4.8) to map reference (#1) using 130802 atoms
average map value = 2.229, steps = 52
shifted from previous position = 3.67
rotated from previous position = 0.27 degrees
atoms outside contour = 68621, contour level = 2.6029
Position of kinesin bound.pdb (#4.1) relative to reference (#1) coordinates:
Matrix rotation and translation
0.99975599 0.01459046 0.01658567 -20.61938328
-0.01093661 0.97927656 -0.20223204 58.78191821
-0.01919261 0.20200130 0.97919718 0.44395275
Axis 0.99414106 0.08799040 -0.06277935
Axis point 0.00000000 32.84923707 293.98008367
Rotation angle (degrees) 11.73045943
Shift along axis -15.35420183
Position of kinesin bound.pdb (#4.2) relative to reference (#1) coordinates:
Matrix rotation and translation
0.99975599 0.01459046 0.01658567 -20.61938328
-0.01093661 0.97927656 -0.20223204 58.78191821
-0.01919261 0.20200130 0.97919718 0.44395275
Axis 0.99414106 0.08799040 -0.06277935
Axis point 0.00000000 32.84923707 293.98008367
Rotation angle (degrees) 11.73045943
Shift along axis -15.35420183
Position of kinesin bound.pdb (#4.3) relative to reference (#1) coordinates:
Matrix rotation and translation
0.99975599 0.01459046 0.01658567 -20.61938328
-0.01093661 0.97927656 -0.20223204 58.78191821
-0.01919261 0.20200130 0.97919718 0.44395275
Axis 0.99414106 0.08799040 -0.06277935
Axis point 0.00000000 32.84923707 293.98008367
Rotation angle (degrees) 11.73045943
Shift along axis -15.35420183
Position of combination (#4.5) relative to reference (#1) coordinates:
Matrix rotation and translation
0.63513582 -0.77232288 0.01094770 368.26762342
0.75658924 0.61921880 -0.21009710 -73.58244573
0.15548377 0.14172311 0.97761923 -55.42273004
Axis 0.22330521 -0.09173907 0.97042193
Axis point 264.87021752 341.52160368 0.00000000
Rotation angle (degrees) 51.97633273
Shift along axis 35.20303090
Position of combination (#4.6) relative to reference (#1) coordinates:
Matrix rotation and translation
0.20475618 0.97830610 0.03149733 -84.21406679
-0.95785364 0.20689151 -0.19927946 657.58639021
-0.20147285 0.01063387 0.97943637 29.20044204
Axis 0.10702271 0.11877806 -0.98713622
Axis point 362.56957226 385.21174400 0.00000000
Rotation angle (degrees) 78.72361090
Shift along axis 40.26920682
Position of combination (#4.7) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.99945846 -0.01466386 0.02945773 658.32481622
0.00787698 -0.97580626 -0.21849504 726.94487968
0.03194903 -0.21814467 0.97539334 63.55730689
Axis 0.01544806 -0.10984139 0.99382907
Axis point 326.59665692 368.86307885 0.00000000
Rotation angle (degrees) 179.35022890
Shift along axis -6.51369437
Position of combination (#4.8) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.19901290 -0.97988058 0.01509808 718.37233442
0.95567055 -0.19746114 -0.21840999 139.18671501
0.21699699 -0.02903761 0.97574032 -36.14373142
Axis 0.09685352 -0.10326015 0.98992764
Axis point 303.35298302 360.01004108 0.00000000
Rotation angle (degrees) 102.14385179
Shift along axis 19.42477237
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #3
130802 atoms, 133546 bonds, 14 pseudobonds, 16534 residues, 17 models selected
> view matrix models
> #3,1,0.00066125,-0.0018638,4.0537,-0.00066202,1,-0.00041293,2.1475,0.0018636,0.00041416,1,-81.927,#4,-0.9993,0.017717,0.032978,623.49,-0.02419,-0.9779,-0.20766,704.45,0.02857,-0.20831,0.97765,9.5718
> view matrix models
> #3,1,0.00066125,-0.0018638,5.7874,-0.00066202,1,-0.00041293,0.67717,0.0018636,0.00041416,1,-0.054168,#4,-0.9993,0.017717,0.032978,625.22,-0.02419,-0.9779,-0.20766,702.98,0.02857,-0.20831,0.97765,91.445
> show #!4 models
> select subtract #4
4 models selected
> select subtract #3
Nothing selected
> ui tool show "Fit to Segments"
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> fitmap #1 inMap #3
Fit map reference in map bestrefinedstructure using 385345 points
correlation = 0.9319, correlation about mean = 0.3836, overlap = 3.96e+05
steps = 68, shift = 4.19, angle = 0.00808 degrees
Position of reference (#1) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.99999200 -0.00356337 0.00181494 -1.03703563
0.00356221 0.99999345 0.00063920 -2.93143083
-0.00181721 -0.00063273 0.99999815 -42.81740627
Axis -0.15705911 0.44850156 0.87987430
Axis point -4069.11930600 -1993.18517665 0.00000000
Rotation angle (degrees) 0.23200276
Shift along axis -38.82581091
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.04457
> volume #3 level 0.1162
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!4 models
> select add #4
130802 atoms, 133546 bonds, 14 pseudobonds, 16534 residues, 13 models selected
> view matrix models
> #4,-0.9993,0.017717,0.032978,627.98,-0.02419,-0.9779,-0.20766,703.39,0.02857,-0.20831,0.97765,76.793
> view matrix models
> #4,-0.9993,0.017717,0.032978,625.18,-0.02419,-0.9779,-0.20766,702.77,0.02857,-0.20831,0.97765,48.298
> fitmap #1 inMap #3
Fit map reference in map bestrefinedstructure using 385345 points
correlation = 0.9319, correlation about mean = 0.3835, overlap = 3.959e+05
steps = 40, shift = 0.0295, angle = 0.00651 degrees
Position of reference (#1) relative to bestrefinedstructure (#3) coordinates:
Matrix rotation and translation
0.99999169 -0.00367037 0.00177677 -1.01221171
0.00366924 0.99999307 0.00063540 -2.94375518
-0.00177909 -0.00062887 0.99999822 -42.83631828
Axis -0.15318821 0.43085483 0.88932418
Axis point -3805.32821763 -1903.58989781 0.00000000
Rotation angle (degrees) 0.23643233
Shift along axis -39.20864569
> fitmap sel inMap #3
Fit molecules kinesin bound.pdb (#4.1), kinesin bound.pdb (#4.2), kinesin
bound.pdb (#4.3), combination (#4.5), combination (#4.6), combination (#4.7),
combination (#4.8) to map bestrefinedstructure (#3) using 130802 atoms
average map value = 0.1665, steps = 68
shifted from previous position = 3.24
rotated from previous position = 0.202 degrees
atoms outside contour = 43983, contour level = 0.11616
Position of kinesin bound.pdb (#4.1) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.99968543 0.01123837 0.02242191 -29.33959878
-0.00651464 0.97965766 -0.20057027 57.94939859
-0.02421988 0.20036110 0.97942270 -40.81863389
Axis 0.99234179 0.11544269 -0.04394031
Axis point 0.00000000 236.67695162 276.79371611
Rotation angle (degrees) 11.65468345
Shift along axis -20.63149188
Position of kinesin bound.pdb (#4.2) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.99968543 0.01123837 0.02242191 -29.33959878
-0.00651464 0.97965766 -0.20057027 57.94939859
-0.02421988 0.20036110 0.97942270 -40.81863389
Axis 0.99234179 0.11544269 -0.04394031
Axis point 0.00000000 236.67695162 276.79371611
Rotation angle (degrees) 11.65468345
Shift along axis -20.63149188
Position of kinesin bound.pdb (#4.3) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.99968543 0.01123837 0.02242191 -29.33959878
-0.00651464 0.97965766 -0.20057027 57.94939859
-0.02421988 0.20036110 0.97942270 -40.81863389
Axis 0.99234179 0.11544269 -0.04394031
Axis point 0.00000000 236.67695162 276.79371611
Rotation angle (degrees) 11.65468345
Shift along axis -20.63149188
Position of combination (#4.5) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.63252893 -0.77435427 0.01681122 359.84770953
0.75966143 0.61600141 -0.20846291 -72.77183585
0.15106840 0.14462965 0.97788578 -98.43558440
Axis 0.22349853 -0.08498135 0.97099257
Axis point 268.58288425 339.83950722 0.00000000
Rotation angle (degrees) 52.17817020
Shift along axis -8.97053805
Position of combination (#4.6) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
0.20801037 0.97741435 0.03732127 -95.45987590
-0.95725714 0.21126379 -0.19755092 656.51045990
-0.20097374 0.00536659 0.97958192 -12.69782370
Axis 0.10353859 0.12158995 -0.98716546
Axis point 352.40029828 391.94914946 0.00000000
Rotation angle (degrees) 78.49648546
Shift along axis 82.47614478
Position of combination (#4.7) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
-0.99930997 -0.01140860 0.03534709 646.92582760
0.00347703 -0.97621386 -0.21678192 729.23108435
0.03697950 -0.21650942 0.97557992 17.80078304
Axis 0.01819415 -0.10899200 0.99387611
Axis point 321.93657530 366.81193922 0.00000000
Rotation angle (degrees) 179.57092652
Shift along axis -50.01831748
Position of combination (#4.8) relative to bestrefinedstructure (#3)
coordinates:
Matrix rotation and translation
-0.20217925 -0.97912361 0.02098913 709.09223576
0.95512480 -0.20187035 -0.21676026 141.58552582
0.21647217 -0.02377719 0.97599923 -81.26332170
Axis 0.09878046 -0.10006010 0.99006586
Axis point 302.06658321 355.80998546 0.00000000
Rotation angle (degrees) 102.35834308
Shift along axis -24.57864361
> select subtract #4
Nothing selected
> select add #4
130802 atoms, 133546 bonds, 14 pseudobonds, 16534 residues, 13 models selected
> select subtract #4
Nothing selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> select add #2
497304 atoms, 508968 bonds, 62640 residues, 19 models selected
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!3 models
> fitmap sel inMap #1
Fit molecules 1tub A (#2.1), 1tub B (#2.2), copy of 1tub A (#2.3), copy of
1tub B (#2.4), 1PF (#2.5), 1PF (#2.6), 1PF (#2.7), 1PF (#2.8), 1PF (#2.9), 1PF
(#2.10), 1PF (#2.11), 1PF (#2.12), 1PF (#2.13), 1PF (#2.14), 1PF (#2.15), 1PF
(#2.16), 1PF (#2.17), 1PF (#2.18) to map reference (#1) using 497304 atoms
average map value = 2.184, steps = 52
shifted from previous position = 4.22
rotated from previous position = 0.0747 degrees
atoms outside contour = 302036, contour level = 2.6029
Position of 1tub A (#2.1) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.01361727 -0.92396020 0.38224606 759.03015211
-0.01330655 -0.38208017 -0.92403324 431.72105920
0.99981869 -0.01766917 -0.00709181 174.65152710
Axis 0.63580128 -0.43321826 0.63881036
Axis point 93.20395639 439.09021575 0.00000000
Rotation angle (degrees) 134.53900568
Shift along axis 407.13209878
Position of 1tub B (#2.2) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.01353404 -0.99655465 -0.08182699 790.17073262
0.03804317 0.08126204 -0.99596646 446.88678358
0.99918444 -0.01659243 0.03681230 606.42741694
Axis 0.54764490 -0.60447834 0.57852485
Axis point 439.45653763 0.00000000 777.09864062
Rotation angle (degrees) 116.59812671
Shift along axis 513.43291525
Position of copy of 1tub A (#2.3) relative to reference (#1) coordinates:
Matrix rotation and translation
0.00577091 -0.66061058 0.75070657 738.22831531
-0.02148171 -0.75062773 -0.66037607 409.33647885
0.99975259 -0.01231548 -0.01852285 165.24082715
Axis 0.68675299 -0.26391530 0.67728801
Axis point 0.00000000 379.51680499 -182.06415945
Rotation angle (degrees) 151.84688368
Shift along axis 510.86597465
Position of copy of 1tub B (#2.4) relative to reference (#1) coordinates:
Matrix rotation and translation
0.00309857 -0.86042125 -0.50957400 822.65826907
0.03733980 0.50932062 -0.85976638 442.19746538
0.99929781 -0.01636335 0.03370612 615.25864660
Axis 0.43299873 -0.77464694 0.46090586
Axis point 289.88141635 0.00000000 794.72420852
Rotation angle (degrees) 103.11682736
Shift along axis 297.23938617
Position of 1PF (#2.5) relative to reference (#1) coordinates:
Matrix rotation and translation
0.00309571 -0.85449985 -0.51944241 820.45638564
0.01167205 0.51944038 -0.85442696 439.57563185
0.99992708 -0.00341790 0.01158180 445.67421997
Axis 0.43754091 -0.78117418 0.44533678
Axis point 356.46269691 0.00000000 715.05790023
Rotation angle (degrees) 103.47028609
Shift along axis 214.07322033
Position of 1PF (#2.6) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.00247838 -0.99502398 -0.09960489 789.12454182
0.01189516 0.09956880 -0.99495957 443.12934730
0.99992617 -0.00365071 0.01158920 436.72010644
Axis 0.55367874 -0.61412441 0.56239759
Axis point 490.50522444 0.00000000 704.54896407
Rotation angle (degrees) 116.46558529
Shift along axis 410.39527017
Position of 1PF (#2.7) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.00693164 -0.93181197 0.36287517 760.68440154
0.00868548 -0.36292631 -0.93177736 433.90132522
0.99993825 -0.00330701 0.01060891 512.15884738
Axis 0.63285223 -0.43422688 0.64104998
Axis point -112.17082708 515.59352026 0.00000000
Rotation angle (degrees) 132.81430900
Shift along axis 621.30861476
Position of 1PF (#2.8) relative to reference (#1) coordinates:
Matrix rotation and translation
0.01154708 0.67218407 -0.74029402 857.16089074
-0.00496409 0.74037279 0.67217817 334.16718021
0.99992101 -0.00408680 0.01188593 481.60820430
Axis -0.34051540 -0.87623939 -0.34096010
Axis point 248.98418782 0.00000000 480.94551214
Rotation angle (degrees) 96.78229372
Shift along axis -748.89610957
Position of 1PF (#2.9) relative to reference (#1) coordinates:
Matrix rotation and translation
0.01265190 0.30746163 -0.95147636 867.08740931
-0.00004545 0.95155270 0.30748570 364.94038862
0.99991996 -0.00384704 0.01205292 472.59756084
Axis -0.15567734 -0.97576692 -0.15376437
Axis point 209.01710506 0.00000000 602.17099352
Rotation angle (degrees) 90.68018780
Shift along axis -563.75128611
Position of 1PF (#2.10) relative to reference (#1) coordinates:
Matrix rotation and translation
0.01184493 -0.12570299 -0.99199720 863.57396089
0.00532160 0.99206067 -0.12564748 396.47447896
0.99991569 -0.00379072 0.01241984 463.58553871
Axis 0.06093041 -0.99598963 0.06551448
Axis point 198.93867450 0.00000000 691.52976134
Rotation angle (degrees) 89.53230527
Shift along axis -311.89498932
Position of 1PF (#2.11) relative to reference (#1) coordinates:
Matrix rotation and translation
0.00813437 -0.54262121 -0.83993813 846.92052395
0.00955403 0.83996974 -0.54254910 423.01953525
0.99992127 -0.00361150 0.01201684 454.59607336
Axis 0.27013029 -0.92218792 0.27676535
Axis point 250.64739350 0.00000000 723.74833521
Rotation angle (degrees) 94.01051362
Shift along axis -35.50817860
Position of 1PF (#2.12) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.01016557 -0.68051436 0.73266421 738.32870012
0.00458015 -0.73272608 -0.68050827 411.79343806
0.99993784 -0.00356204 0.01056543 503.20526114
Axis 0.67726941 -0.26740122 0.68542157
Axis point 1.72130874 351.06456826 0.00000000
Rotation angle (degrees) 150.01578353
Shift along axis 734.84111794
Position of 1PF (#2.13) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.01113308 -0.29526292 0.95535116 727.83595343
-0.00072010 -0.95540776 -0.29528881 382.14378375
0.99993776 -0.00397542 0.01042401 494.23140748
Axis 0.69916055 -0.10700912 0.70691129
Axis point 84.52882028 240.12781321 0.00000000
Rotation angle (degrees) 167.97544778
Shift along axis 817.35907851
Position of 1PF (#2.14) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.00996611 0.12467539 0.99214753 731.88523956
-0.00546485 -0.99218877 0.12462567 350.13333089
0.99993540 -0.00417990 0.01056959 485.14875303
Axis -0.70281744 -0.04249391 -0.71009993
Axis point 135.97519530 156.74246559 0.00000000
Rotation angle (degrees) 174.74231640
Shift along axis -873.76434307
Position of 1PF (#2.15) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.00678807 0.54361031 0.83931028 748.37326581
-0.00953803 -0.83932663 0.54354376 323.74253911
0.99993147 -0.00431576 0.01088238 476.02740201
Axis -0.68918746 -0.20205564 -0.69584061
Axis point 159.20774619 74.95343940 0.00000000
Rotation angle (degrees) 156.58003229
Shift along axis -912.42267779
Position of 1PF (#2.16) relative to reference (#1) coordinates:
Matrix rotation and translation
-0.00188026 0.85282155 0.52219906 774.88112985
-0.01186251 -0.52218226 0.85275140 306.80433376
0.99992787 -0.00459119 0.01109844 466.89551683
Axis -0.65544621 -0.36522801 -0.66105882
Axis point 146.86609455 -22.39259875 0.00000000
Rotation angle (degrees) 139.15503659
Shift along axis -928.59183585
Position of 1PF (#2.17) relative to reference (#1) coordinates:
Matrix rotation and translation
0.00336168 0.99717261 0.07506978 804.88281850
-0.01131238 -0.07502747 0.99711729 301.99532272
0.99993036 -0.00420121 0.01102818 499.80309684
Axis -0.59054052 -0.54544848 -0.59476705
Axis point 56.85884356 -195.25044404 0.00000000
Rotation angle (degrees) 122.02699804
Shift along axis -937.30522619
Position of 1PF (#2.18) relative to reference (#1) coordinates:
Matrix rotation and translation
0.00835042 0.93202644 -0.36229402 834.81681851
-0.00934412 0.36236357 0.93198998 312.69204360
0.99992147 -0.00439719 0.01173485 490.76034031
Axis -0.49224729 -0.71610004 -0.49486700
Axis point 281.31342756 0.00000000 341.70880129
Rotation angle (degrees) 107.98545663
Shift along axis -877.71619606
> hide #!1 models
> show #!3 models
> select subtract #2
Nothing selected
> hide #!2 models
> show #!4 models
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/kinesinmask.cxs
> molmap
Missing or invalid "atoms" argument: empty atom specifier
> select add #4.6
37372 atoms, 38156 bonds, 4 pseudobonds, 4724 residues, 2 models selected
> select subtract #4.6
Nothing selected
> molmap #4.6/a resolution 8
Missing or invalid "resolution" argument: Expected a number
> molmap #4.6/a 8
Opened combination map 8 as #5, grid size 37,35,43, pixel 2.67, shown at level
0.0811, step 1, values float32
> hide #!5 models
> show #!5 models
> hide #!4.6 models
> show #!4.6 models
> view orient
> hide #!5 models
> show #!5 models
> molmap #4.6/Y 8
Opened combination map 8 as #6, grid size 37,36,43, pixel 2.67, shown at level
0.0791, step 1, values float32
> view orient
> close #5
> close #6
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/kinesinboundaligned.pdb
> models #4 relModel #3
> save C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/backup.cxs
——— End of log from Thu Apr 17 15:54:33 2025 ———
opened ChimeraX session
> show #!2 models
> hide #!4 models
> hide #!3 models
> close session
> open
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/14pf_pdbstructure1.pdb
Summary of feedback from opening
C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/14pf_pdbstructure1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 49 49 CYS F 12 VAL F 23 1 12
Start residue of secondary structure not found: HELIX 50 50 THR F 74 ARG F 79
1 6
Start residue of secondary structure not found: HELIX 51 51 GLY F 111 GLU F
127 1 17
Start residue of secondary structure not found: HELIX 52 52 GLY F 146 TYR F
161 1 16
Start residue of secondary structure not found: HELIX 53 53 VAL F 182 GLN F
193 1 12
259 messages similar to the above omitted
Chain information for 14pf_pdbstructure1.pdb
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.1/C 1.2/C 1.3/C 1.4/C 1.5/C 1.6/C 1.7/C 1.8/C 1.9/C 1.10/C 1.11/C 1.12/C 1.13/C 1.14/C 1.2/E 1.4/E 1.5/E 1.6/E 1.7/E 1.13/E 1.14/E 1.1/G 1.2/G 1.3/G 1.4/G 1.5/G 1.6/G 1.7/G 1.8/G 1.9/G 1.10/G 1.11/G 1.12/G 1.13/G 1.14/G 1.3/I 1.8/I 1.9/I 1.10/I 1.11/I 1.12/I | No description available
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B 1.13/B 1.14/B 1.1/D 1.2/D 1.3/D 1.4/D 1.5/D 1.6/D 1.7/D 1.8/D 1.9/D 1.10/D 1.11/D 1.12/D 1.13/D 1.14/D 1.1/F 1.2/F 1.4/F 1.5/F 1.6/F 1.7/F 1.13/F 1.14/F 1.1/H 1.2/H 1.3/H 1.4/H 1.5/H 1.6/H 1.7/H 1.8/H 1.9/H 1.10/H 1.11/H 1.12/H 1.13/H 1.14/H 1.3/J 1.8/J 1.9/J 1.10/J 1.11/J 1.12/J | No description available
> open
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/cryosparc_J217_map.mrc
Opened cryosparc_J217_map.mrc as #2, grid size 600,600,600, pixel 1.04, shown
at level 0.0922, step 4, values float32
> ui mousemode right "translate selected models"
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right select
> select #1.15/A:500@PA
1 atom, 1 residue, 1 model selected
> select #1.15/A:80
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 89 atoms, 440 residues, 80 bonds
> ui mousemode right "translate selected models"
> view matrix models #1.15,1,0,0,348.57,0,1,0,192.54,0,0,1,-19.871
> view matrix models #1.15,1,0,0,504.89,0,1,0,268.24,0,0,1,-58.262
> view matrix models #1.15,1,0,0,474.16,0,1,0,243.95,0,0,1,11.76
> view matrix models #1.15,1,0,0,493.2,0,1,0,298.74,0,0,1,47.677
> view matrix models #1.15,1,0,0,491.41,0,1,0,299.48,0,0,1,45.623
> ui tool show "Fit in Map"
> fitmap sel inMap #2
Fit molecule 14pf_pdbstructure1.pdb (#1.15) to map cryosparc_J217_map.mrc (#2)
using 3462 atoms
average map value = 0.06782, steps = 248
shifted from previous position = 10.4
rotated from previous position = 62.2 degrees
atoms outside contour = 2934, contour level = 0.09216
Position of 14pf_pdbstructure1.pdb (#1.15) relative to cryosparc_J217_map.mrc
(#2) coordinates:
Matrix rotation and translation
0.80151499 -0.21847039 0.55663670 248.95316495
0.57057487 0.55796629 -0.60259268 718.25238338
-0.17893586 0.80058998 0.57187206 79.26328213
Axis 0.79279893 0.41559888 0.44581098
Axis point 0.00000000 458.44703542 489.27343600
Rotation angle (degrees) 62.24597649
Shift along axis 531.21112745
> ui tool show "Side View"
> show sel cartoons
> hide sel atoms
> ui mousemode right select
> select clear
> show cartoons
> hide atoms
> lighting flat
> volume #2 level 0.05455
> transparency 50
> volume #2 step 1
> volume #2 level 0.03156
> volume #2 level 0.03826
> select #2
4 models selected
> select #2
4 models selected
> select subtract #2
Nothing selected
> hide #!2 models
Drag select of 519 residues
> select clear
> ui mousemode right "translate selected models"
> select add #1.1
24166 atoms, 24734 bonds, 3039 residues, 1 model selected
> select subtract #1.1
Nothing selected
> select add #1.15
3462 atoms, 3542 bonds, 441 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1.15,0.75466,0.47076,-0.45703,580.42,-0.60242,0.22113,-0.76694,620.75,-0.25998,0.8541,0.45047,109.17
> view matrix models
> #1.15,-0.46052,0.2814,-0.84186,549.54,-0.82919,-0.47486,0.29487,220.13,-0.31679,0.83386,0.45202,100.92
> view matrix models
> #1.15,-0.80833,0.032245,-0.58785,411.56,-0.51241,-0.53019,0.67552,122.71,-0.28989,0.84726,0.44509,106.96
> view matrix models
> #1.15,-0.84197,0.3907,-0.37207,265.79,-0.53212,-0.48752,0.69222,106.35,0.089055,0.78082,0.61838,110.61
> view matrix models
> #1.15,0.012495,0.25537,-0.96676,691.87,-0.83422,0.53571,0.13072,154.48,0.55129,0.80486,0.21973,360.92
> view matrix models
> #1.15,-0.15083,0.98797,0.03421,138.29,0.37294,0.024819,0.92752,101.73,0.91551,0.15266,-0.3722,765.92
> view matrix models
> #1.15,0.031828,0.79082,0.61122,-48.155,0.050826,-0.61202,0.7892,187.18,0.9982,0.0059471,-0.059673,667.31
> view matrix models
> #1.15,-0.52912,-0.82276,0.20759,237.22,0.49213,-0.098254,0.86496,166.36,-0.69126,0.55983,0.4569,67.553
> view matrix models
> #1.15,0.073268,-0.46904,-0.88013,762.49,-0.88217,-0.44213,0.16219,262.69,-0.46521,0.76454,-0.44617,465.88
> view matrix models
> #1.15,0.58863,-0.43837,-0.67923,766.15,-0.80712,-0.27139,-0.52431,545.96,0.045511,0.85684,-0.51356,574.77
> view matrix models
> #1.15,0.5766,-0.03678,-0.8162,768.8,-0.79944,-0.23158,-0.55432,554.82,-0.16862,0.97212,-0.16293,371.28
> view matrix models
> #1.15,0.73728,-0.037911,-0.67453,737.7,-0.6735,0.03733,-0.73825,620.14,0.053168,0.99858,0.00199,337.66
> view matrix models
> #1.15,-0.59157,-0.61956,-0.51594,507.03,-0.093374,-0.58297,0.80711,149.57,-0.80083,0.52563,0.28702,124.63
> view matrix models
> #1.15,0.41539,-0.1962,-0.88823,791.54,-0.89758,-0.24692,-0.36522,458.55,-0.14767,0.94897,-0.27867,427.46
> view matrix models
> #1.15,0.89092,-0.19851,-0.40848,673.59,-0.418,-0.00671,-0.90842,744.76,0.17759,0.98008,-0.088957,401.4
> view matrix models
> #1.15,0.89243,0.2424,-0.38054,603.21,-0.40169,0.042788,-0.91477,743.83,-0.20546,0.96923,0.13555,237.85
> view matrix models
> #1.15,0.86981,0.34567,-0.35206,573.22,-0.020271,-0.68791,-0.72551,829.64,-0.49297,0.63819,-0.59134,539.53
> view matrix models
> #1.15,0.71127,0.53952,-0.45057,560.65,0.70231,-0.5722,0.4235,455.61,-0.029323,-0.61766,-0.7859,873.7
> view matrix models
> #1.15,0.70618,0.50205,-0.49926,585.46,0.64826,-0.17487,0.74107,257.61,0.28474,-0.84698,-0.44895,817.6
> view matrix models
> #1.15,0.80693,0.45975,-0.37079,554.62,0.53319,-0.29695,0.79216,231.28,0.25409,-0.83693,-0.48476,825.96
> view matrix models
> #1.15,0.43217,0.9006,0.046438,250.29,0.46978,-0.26879,0.84087,195.3,0.76976,-0.34158,-0.53925,876.54
> view matrix models
> #1.15,0.70852,0.43992,-0.55179,616.54,-0.2243,0.88175,0.41497,97.728,0.66909,-0.17025,0.72341,297.63
> view matrix models
> #1.15,0.899,-0.097465,0.42696,305.72,-0.15771,0.83746,0.52324,69.568,-0.40856,-0.53773,0.73751,145.46
> view matrix models
> #1.15,0.80362,0.14647,0.57684,192.1,-0.30381,0.9344,0.18599,173.85,-0.51175,-0.32471,0.7954,73.727
> view matrix models
> #1.15,0.15849,0.92581,0.34317,70.975,-0.81407,0.3192,-0.48518,449.33,-0.55873,-0.20247,0.80426,45.161
> view matrix models
> #1.15,0.42066,0.89835,-0.12656,322.2,-0.78963,0.29386,-0.53864,479.91,-0.44669,0.32652,0.83298,-17.273
> view matrix models
> #1.15,0.35161,0.91633,-0.19157,334.99,-0.90888,0.28512,-0.30437,359.69,-0.22428,0.28114,0.93309,-13.599
> fitmap sel inMap #2
Fit molecule 14pf_pdbstructure1.pdb (#1.15) to map cryosparc_J217_map.mrc (#2)
using 3462 atoms
average map value = 0.06112, steps = 128
shifted from previous position = 10.3
rotated from previous position = 28.1 degrees
atoms outside contour = 1002, contour level = 0.038262
Position of 14pf_pdbstructure1.pdb (#1.15) relative to cryosparc_J217_map.mrc
(#2) coordinates:
Matrix rotation and translation
0.47045098 0.76752227 -0.43541410 487.93387298
-0.77640089 0.12552229 -0.61761300 542.74209203
-0.41937756 0.62861254 0.65495705 18.78809480
Axis 0.62807581 -0.00808214 -0.77811018
Axis point 648.88290826 47.19624827 0.00000000
Rotation angle (degrees) 82.79238092
Shift along axis 287.45373758
> fitmap sel inMap #2
Fit molecule 14pf_pdbstructure1.pdb (#1.15) to map cryosparc_J217_map.mrc (#2)
using 3462 atoms
average map value = 0.06112, steps = 44
shifted from previous position = 0.00277
rotated from previous position = 0.00793 degrees
atoms outside contour = 1002, contour level = 0.038262
Position of 14pf_pdbstructure1.pdb (#1.15) relative to cryosparc_J217_map.mrc
(#2) coordinates:
Matrix rotation and translation
0.47042071 0.76759820 -0.43531296 487.87767487
-0.77636723 0.12551519 -0.61765676 542.76706530
-0.41947382 0.62852124 0.65498302 18.77301879
Axis 0.62805139 -0.00798264 -0.77813092
Axis point 648.83279765 47.26134468 0.00000000
Rotation angle (degrees) 82.79271043
Shift along axis 287.47167029
> ui mousemode right "translate selected models"
> view matrix models
> #1.15,0.47042,0.7676,-0.43531,482.78,-0.77637,0.12552,-0.61766,541.83,-0.41947,0.62852,0.65498,27.542
> ui mousemode right "rotate selected models"
> view matrix models
> #1.15,-0.8872,-0.33602,-0.31617,333.26,0.45666,-0.73724,-0.49793,829.06,-0.065776,-0.58615,0.80753,188.46
> view matrix models
> #1.15,-0.65092,-0.57034,-0.50101,486,0.6927,-0.71624,-0.084614,692.94,-0.31059,-0.40213,0.86129,96.71
> fitmap sel inMap #2
Fit molecule 14pf_pdbstructure1.pdb (#1.15) to map cryosparc_J217_map.mrc (#2)
using 3462 atoms
average map value = 0.0802, steps = 120
shifted from previous position = 8.73
rotated from previous position = 14.1 degrees
atoms outside contour = 340, contour level = 0.038262
Position of 14pf_pdbstructure1.pdb (#1.15) relative to cryosparc_J217_map.mrc
(#2) coordinates:
Matrix rotation and translation
-0.76408819 -0.41644167 -0.49269221 447.57925454
0.50131479 -0.86397692 -0.04719523 656.29691185
-0.40602062 -0.28305521 0.86892291 59.56319081
Axis -0.24787315 -0.09108607 0.96450102
Axis point 146.67734693 386.00842347 0.00000000
Rotation angle (degrees) 151.59066728
Shift along axis -113.27363235
> select subtract #1.15
Nothing selected
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/14pf_pdbstructure1.pdb
> relModel #2.1
> view orient
> turn x 180
[Repeated 1 time(s)]
> turn y 180
[Repeated 1 time(s)]
> turn z 180
[Repeated 1 time(s)]
> turn x 180
[Repeated 1 time(s)]
> view orient
> select ~sel & ##selected
Nothing selected
> turn x 90
> turn y 90
[Repeated 1 time(s)]
> molmap #1
Missing or invalid "resolution" argument: Expected a number
> molmap #1 4
Opened map 4 as #3, grid size 238,240,370, pixel 1.33, shown at level 0.114,
step 1, values float32
> vop resample #3 onGrid #2
Opened map 4 resampled as #4, grid size 600,600,600, pixel 1.04, shown at step
1, values float32
> info #4
2 models
#4, map 4 resampled, shown size 600,600,600, step 1, voxel size 1.04, level
0.1138, value range 0 - 2.103, value type float32, 0 symmetry operators
#4.1, surface, shown, 6637468 triangles
> vop copy #4
Opened map 4 resampled copy as #5, grid size 600,600,600, pixel 1.04, shown at
step 1, values float32
> vop copy #4
Opened map 4 resampled copy as #6, grid size 600,600,600, pixel 1.04, shown at
step 1, values float32
> show #!4 models
> show #!2 models
> hide #!1 models
> move y 84.66 models #5
[Repeated 2 time(s)]
> color #5 #00aa7fff models
> color #6 magenta models
> transparency #2.1#4.1#5.1#6.1 0
> hide #!6 models
> show #!6 models
> fitmap #5 inMap #2
Fit map map 4 resampled copy in map cryosparc_J217_map.mrc using 5117114
points
correlation = 0.6256, correlation about mean = 0.1073, overlap = 8.208e+04
steps = 76, shift = 3.11, angle = 1.12 degrees
Position of map 4 resampled copy (#5) relative to cryosparc_J217_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99981049 -0.01931432 0.00243882 3.09612209
0.01931064 0.99981238 0.00152101 -8.34197391
-0.00246774 -0.00147363 0.99999587 -253.78591952
Axis -0.07668656 0.12564696 0.98910667
Axis point -1217.73577238 -829.52197687 0.00000000
Rotation angle (degrees) 1.11878122
Shift along axis -252.30692144
> move y 84.66 models #5
> hide #!2 models
> move y 84.66 models #5
> move y -84.66 models #5
> hide #!4 models
> show #!4 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> fitmap #5 inMap #2
Fit map map 4 resampled copy in map cryosparc_J217_map.mrc using 5117114
points
correlation = 0.4586, correlation about mean = 0.06142, overlap = 4.071e+04
steps = 372, shift = 0.936, angle = 0.385 degrees
Position of map 4 resampled copy (#5) relative to cryosparc_J217_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99966584 -0.02531523 0.00522948 3.51663235
0.02530147 0.99967627 0.00268173 -10.77755150
-0.00529567 -0.00254852 0.99998273 -336.56457284
Axis -0.10065274 0.20254970 0.97408554
Axis point -2233.52574287 -1145.18520155 0.00000000
Rotation angle (degrees) 1.48880632
Shift along axis -330.37963341
> show #!2 models
> hide #!2 models
> show #!6 models
> select ~sel & ##selected
Nothing selected
> move y -84.66 models #6
> fitmap #6 inMap #2
Fit map map 4 resampled copy in map cryosparc_J217_map.mrc using 5117114
points
correlation = 0.8408, correlation about mean = 0.2615, overlap = 1.584e+05
steps = 64, shift = 2.61, angle = 0.367 degrees
Position of map 4 resampled copy (#6) relative to cryosparc_J217_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99997970 0.00594764 0.00228564 -3.81282483
-0.00594925 0.99998206 0.00069571 0.08738145
-0.00228146 -0.00070930 0.99999715 83.91872030
Axis -0.10958981 0.35623131 -0.92794899
Axis point 4644.38980642 2083.49999836 0.00000000
Rotation angle (degrees) 0.36728639
Shift along axis -77.42331694
> move y -84.66 models #6
[Repeated 2 time(s)]
> fitmap #6 inMap #2
Fit map map 4 resampled copy in map cryosparc_J217_map.mrc using 5117114
points
correlation = 0.4565, correlation about mean = 0.06337, overlap = 4.062e+04
steps = 768, shift = 1.69, angle = 1.08 degrees
Position of map 4 resampled copy (#6) relative to cryosparc_J217_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99968170 0.02446326 0.00616838 -9.42162387
-0.02446738 0.99970045 0.00059366 6.16752942
-0.00615201 -0.00074439 0.99998080 338.09741814
Axis -0.02650885 0.24408596 -0.96939121
Axis point 3494.57819164 783.85575624 0.00000000
Rotation angle (degrees) 1.44617389
Shift along axis -325.99350237
> vop add #4,5,6 onGrid #4
Opened volume sum as #7, grid size 600,600,600, pixel 1.04, shown at step 1,
values float32
> volume #7 level 0.4468
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/14pf_1_r1.mrc.pdb
> save
> C:/Users/2803976/Downloads/chimeraxsessionmtwithtubulin/tryingotfixref.cxs
Traceback (most recent call last):
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Users\2803976\AppData\Local\Programs\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.2111
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Python: 3.11.4
Locale: nl_NL.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: HP
Model: HP EliteDesk 800 G4 TWR
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 8,353,464,320
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (1)
comment:1 by , 6 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving session |
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