![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9425 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001f3bf5e00 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 360000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 1719,
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"build" : "22F770820d",
"releaseType" : "User"
},
"captureTime" : "2023-07-21 11:39:33.9438 -0400",
"incident" : "00EB7021-7389-4404-9C34-226CB81ACA45",
"pid" : 64432,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-07-19 00:11:10.5911 -0400",
"procStartAbsTime" : 5083386374047,
"procExitAbsTime" : 8735516580793,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "99DA3F3A-511F-2832-8536-7AEDB6E711CB",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 2208,
"sleepWakeUUID" : "6F3D14E0-146B-4B0D-963A-5EEC94580620",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 68719476712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 68719476712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/TEST/Downloads/cryosparc_P79_J125_007_volume_map.mrc
Opened cryosparc_P79_J125_007_volume_map.mrc as #1, grid size 416,416,416,
pixel 0.855, shown at level 0.0867, step 2, values float32
> volume #1 step 1
> volume #1 level 0.09256
> volume #1 level 0.1069
> set bgColor white
> volume #1 level 0.09509
> volume #1 level 0.1027
> color #1 #797979ff models
> color #1 #919191ff models
> open 6w77
6w77 title:
30S-Inactivated-high-Mg2+ Class A [more info...]
Chain information for 6w77 #2
---
Chain | Description | UniProt
A | RNA (1519-MER) |
C | 30S ribosomal protein S3 | RS3_ECOLI 0-232
D | 30S ribosomal protein S4 | RS4_ECOLI 1-206
E | 30S ribosomal protein S5 | RS5_ECOLI 1-167
F | 30S ribosomal protein S6 | RS6_ECOLI 1-135
H | 30S ribosomal protein S8 | RS8_ECOLI 1-130
I | 30S ribosomal protein S9 | RS9_ECOLI 0-129
J | 30S ribosomal protein S10 | RS10_ECOLI 1-103
K | 30S ribosomal protein S11 | RS11_ECOLI 1-129
L | 30S ribosomal protein S12 | RS12_ECOLI 1-124
M | 30S ribosomal protein S13 | RS13_ECOLI 0-117
N | 30S ribosomal protein S14 | RS14_ECOLI 0-100
O | 30S ribosomal protein S15 | RS15_ECOLI 1-89
P | 30S ribosomal protein S16 | RS16_ECOLI 1-82
Q | 30S ribosomal protein S17 | RS17_ECOLI 1-84
R | 30S ribosomal protein S18 | RS18_ECOLI 1-75
S | 30S ribosomal protein S19 | RS19_ECOLI 0-91
T | 30S ribosomal protein S20 | RS20_ECOLI 1-87
> select add #2
47940 atoms, 52058 bonds, 1470 pseudobonds, 3468 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.55753,-0.7907,-0.25287,236.02,-0.72573,-0.61214,0.31399,317.99,-0.40307,0.0084532,-0.91513,374.82
> view matrix models
> #2,0.30082,-0.43277,-0.84983,321.06,-0.9185,-0.37127,-0.13607,386.39,-0.25663,0.8215,-0.50919,161.07
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.30082,-0.43277,-0.84983,331.35,-0.9185,-0.37127,-0.13607,389.65,-0.25663,0.8215,-0.50919,184.5
> fitmap #2 inMap #1
Fit molecule 6w77 (#2) to map cryosparc_P79_J125_007_volume_map.mrc (#1) using
47940 atoms
average map value = 0.09668, steps = 276
shifted from previous position = 12.9
rotated from previous position = 20.2 degrees
atoms outside contour = 28077, contour level = 0.10268
Position of 6w77 (#2) relative to cryosparc_P79_J125_007_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.21877371 -0.56054250 -0.79870531 368.21832500
-0.97283055 -0.06174983 -0.22313154 358.14923798
0.07575479 0.82582024 -0.55882211 143.26143892
Axis 0.73532173 -0.61300198 -0.28901649
Axis point 0.00000000 290.89925984 247.83235711
Rotation angle (degrees) 134.49918464
Shift along axis 9.80782540
> select subtract #2
Nothing selected
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 47940 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> volume #1 level 0.1035
> undo
> color #2 #73fcd6ff
> undo
> lighting flat
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #1 level 0.09509
> show #!2 models
> open /Users/TEST/Downloads/cryosparc_P50_J423_class_00_final_volume.mrc
Opened cryosparc_P50_J423_class_00_final_volume.mrc as #3, grid size
192,192,192, pixel 1.85, shown at level 0.192, step 1, values float32
> volume flip #3
Opened cryosparc_P50_J423_class_00_final_volume.mrc z flip as #4, grid size
192,192,192, pixel 1.85, shown at step 1, values float32
> hide #!1 models
> hide #!2 models
> select add #4
2 models selected
> view matrix models #4,1,0,0,6.5391,0,1,0,-7.9999,0,0,1,27.644
> ui mousemode right "rotate selected models"
> select subtract #4
Nothing selected
> volume #4 level 0.2139
> volume #4 level 0.1195
> volume #4 level 0.1891
> show #!2 models
> select add #4
2 models selected
> view matrix models
> #4,-0.97988,-0.17419,0.097456,370.42,-0.1434,0.95399,0.26334,-23.635,-0.13884,0.24407,-0.95977,375.37
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.97988,-0.17419,0.097456,363.74,-0.1434,0.95399,0.26334,-18.504,-0.13884,0.24407,-0.95977,327.1
> fitmap #2 inMap #4
Fit molecule 6w77 (#2) to map cryosparc_P50_J423_class_00_final_volume.mrc z
flip (#4) using 47940 atoms
average map value = 0.2166, steps = 132
shifted from previous position = 9.64
rotated from previous position = 8.12 degrees
atoms outside contour = 24362, contour level = 0.18907
Position of 6w77 (#2) relative to cryosparc_P50_J423_class_00_final_volume.mrc
z flip (#4) coordinates:
Matrix rotation and translation
-0.19521377 0.49394263 0.84729704 -15.02456625
-0.94662006 0.13106531 -0.29450358 347.70157749
-0.25651912 -0.85955952 0.44199025 269.46478478
Axis -0.29727769 0.58072112 -0.75788452
Axis point 105.32072348 283.96607224 0.00000000
Rotation angle (degrees) 108.12427432
Shift along axis 2.16092816
> select subtract #4
Nothing selected
> open /Users/TEST/Downloads/cryosparc_P79_J127_008_volume_map.mrc
Opened cryosparc_P79_J127_008_volume_map.mrc as #5, grid size 416,416,416,
pixel 0.855, shown at level 0.0589, step 2, values float32
> volume #5 step 1
> volume #5 level 0.06216
> select add #5
2 models selected
> view matrix models #5,1,0,0,-0.093502,0,1,0,3.1372,0,0,1,-14.095
> hide #!4 models
> fitmap #2 inMap #5
Fit molecule 6w77 (#2) to map cryosparc_P79_J127_008_volume_map.mrc (#5) using
47940 atoms
average map value = 0.07461, steps = 140
shifted from previous position = 4.5
rotated from previous position = 7.53 degrees
atoms outside contour = 24717, contour level = 0.062158
Position of 6w77 (#2) relative to cryosparc_P79_J127_008_volume_map.mrc (#5)
coordinates:
Matrix rotation and translation
0.24290603 -0.55517505 -0.79547302 364.12324903
-0.96577054 -0.06146516 -0.25201052 363.73182507
0.09101608 0.82945928 -0.55110197 140.38635933
Axis 0.74205181 -0.60826556 -0.28173059
Axis point 0.00000000 289.41894277 246.98332142
Rotation angle (degrees) 133.22228220
Shift along axis 9.40164051
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select subtract #5
Nothing selected
> volume #5 level 0.09217
> volume #5 level 0.1125
> fitmap #2 inMap #5
Fit molecule 6w77 (#2) to map cryosparc_P79_J127_008_volume_map.mrc (#5) using
47940 atoms
average map value = 0.07461, steps = 40
shifted from previous position = 0.0142
rotated from previous position = 0.00666 degrees
atoms outside contour = 33656, contour level = 0.11253
Position of 6w77 (#2) relative to cryosparc_P79_J127_008_volume_map.mrc (#5)
coordinates:
Matrix rotation and translation
0.24291875 -0.55517841 -0.79546679 364.11914446
-0.96575673 -0.06137711 -0.25208490 363.73838296
0.09112864 0.82946355 -0.55107694 140.35444861
Axis 0.74204559 -0.60828919 -0.28169596
Axis point 0.00000000 289.43202725 246.97358470
Rotation angle (degrees) 133.21733690
Shift along axis 9.39759880
> volume #5 level 0.04286
> open /Users/TEST/Downloads/cryosparc_P50_J434_class_01_00248_volume.mrc
Opened cryosparc_P50_J434_class_01_00248_volume.mrc as #6, grid size
128,128,128, pixel 2.78, shown at level 0.299, step 1, values float32
> hide #!5 models
> select add #6
2 models selected
> view matrix models #6,1,0,0,1.1666,0,1,0,3.9056,0,0,1,-4.7934
> select subtract #6
Nothing selected
> volume flip #6
Opened cryosparc_P50_J434_class_01_00248_volume.mrc z flip as #7, grid size
128,128,128, pixel 2.78, shown at step 1, values float32
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.97002,-0.13584,0.20151,337.85,-0.107,0.98322,0.14772,-0.93019,-0.21819,0.12173,-0.96828,369.02
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.97002,-0.13584,0.20151,340.31,-0.107,0.98322,0.14772,-12.236,-0.21819,0.12173,-0.96828,353.9
> fitmap #2 inMap #7
Fit molecule 6w77 (#2) to map cryosparc_P50_J434_class_01_00248_volume.mrc z
flip (#7) using 47940 atoms
average map value = 0.3369, steps = 128
shifted from previous position = 3.84
rotated from previous position = 9.4 degrees
atoms outside contour = 24741, contour level = 0.29876
Position of 6w77 (#2) relative to cryosparc_P50_J434_class_01_00248_volume.mrc
z flip (#7) coordinates:
Matrix rotation and translation
-0.20042099 0.49315277 0.84654106 -14.21111600
-0.94586456 0.12775552 -0.29836013 348.30852109
-0.25528742 -0.86051082 0.44085084 268.18724098
Axis -0.29624609 0.58064926 -0.75834339
Axis point 105.24349246 283.14967932 0.00000000
Rotation angle (degrees) 108.41559635
Shift along axis 3.07705095
> select subtract #7
Nothing selected
> volume #7 level 0.3816
> volume #7 level 0.3559
> volume #7 level 0.3958
> volume #7 level 0.3073
> volume #7 level 0.2816
> open /Users/TEST/Downloads/cryosparc_P79_J131_006_volume_map.mrc
Opened cryosparc_P79_J131_006_volume_map.mrc as #8, grid size 416,416,416,
pixel 0.855, shown at level 0.0595, step 2, values float32
> open /Users/TEST/Downloads/cryosparc_P79_J132_006_volume_map.mrc
Opened cryosparc_P79_J132_006_volume_map.mrc as #9, grid size 416,416,416,
pixel 0.855, shown at level 0.0622, step 2, values float32
> hide #!7 models
> hide #!2 models
> show #!2 models
> select add #8
2 models selected
> select add #9
4 models selected
> select subtract #8
2 models selected
> select subtract #9
Nothing selected
> volume #9 step 1
> volume #8 step 1
> volume #8 level 0.07936
> volume #9 level 0.07921
> hide #!9 models
> fitmap #2 inMap #8
Fit molecule 6w77 (#2) to map cryosparc_P79_J131_006_volume_map.mrc (#8) using
47940 atoms
average map value = 0.0742, steps = 156
shifted from previous position = 17.4
rotated from previous position = 9.59 degrees
atoms outside contour = 27387, contour level = 0.079361
Position of 6w77 (#2) relative to cryosparc_P79_J131_006_volume_map.mrc (#8)
coordinates:
Matrix rotation and translation
0.24500821 -0.55258225 -0.79663281 363.74173354
-0.96560833 -0.06533433 -0.25165845 363.90868252
0.08701452 0.83089367 -0.54958547 140.60899868
Axis 0.74291446 -0.60641365 -0.28344414
Axis point 0.00000000 288.68907969 247.30931439
Rotation angle (degrees) 133.23213052
Shift along axis 9.69500422
> volume #8 level 0.09627
> show #!9 models
> hide #!2 models
> fitmap #8 inMap #9
Fit map cryosparc_P79_J131_006_volume_map.mrc in map
cryosparc_P79_J132_006_volume_map.mrc using 401218 points
correlation = 0.9863, correlation about mean = 0.8446, overlap = 8474
steps = 44, shift = 0.186, angle = 0.0708 degrees
Position of cryosparc_P79_J131_006_volume_map.mrc (#8) relative to
cryosparc_P79_J132_006_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999949 -0.00023461 -0.00098620 0.13365912
0.00023531 0.99999972 0.00070796 -0.14308619
0.00098603 -0.00070819 0.99999926 0.12109384
Axis -0.57263374 -0.79748656 0.19001524
Axis point -111.00713067 0.00000000 170.76375953
Rotation angle (degrees) 0.07084795
Shift along axis 0.06058126
> fitmap #8 inMap #9
Fit map cryosparc_P79_J131_006_volume_map.mrc in map
cryosparc_P79_J132_006_volume_map.mrc using 401218 points
correlation = 0.9863, correlation about mean = 0.8446, overlap = 8474
steps = 28, shift = 0.0131, angle = 0.00976 degrees
Position of cryosparc_P79_J131_006_volume_map.mrc (#8) relative to
cryosparc_P79_J132_006_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999941 -0.00023826 -0.00106002 0.14072122
0.00023885 0.99999982 0.00055458 -0.12867685
0.00105988 -0.00055483 0.99999928 0.08293705
Axis -0.45472228 -0.86889948 0.19555395
Axis point -66.32777785 0.00000000 160.26114959
Rotation angle (degrees) 0.06989376
Shift along axis 0.06403684
> fitmap #8 inMap #9
Fit map cryosparc_P79_J131_006_volume_map.mrc in map
cryosparc_P79_J132_006_volume_map.mrc using 401218 points
correlation = 0.9863, correlation about mean = 0.8445, overlap = 8471
steps = 40, shift = 0.00693, angle = 0.0055 degrees
Position of cryosparc_P79_J131_006_volume_map.mrc (#8) relative to
cryosparc_P79_J132_006_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999945 -0.00023551 -0.00102305 0.12876356
0.00023616 0.99999977 0.00064314 -0.13907468
0.00102290 -0.00064338 0.99999927 0.10367319
Axis -0.52245814 -0.83087136 0.19154706
Axis point -88.47787489 0.00000000 160.70654232
Rotation angle (degrees) 0.07054324
Shift along axis 0.06813789
> show #!2 models
> volume #9 level 0.1007
> volume #9 level 0.07832
> volume #9 level 0.08458
> volume #9 level 0.08995
> open /Users/TEST/Downloads/cryosparc_P50_J476_006_volume_map.mrc
Opened cryosparc_P50_J476_006_volume_map.mrc as #10, grid size 416,416,416,
pixel 0.855, shown at level 0.064, step 2, values float32
> volume #10 step 1
> volume flip #10
Opened cryosparc_P50_J476_006_volume_map.mrc z flip as #11, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> select add #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.93413,-0.17427,0.31151,307.82,-0.17353,0.98436,0.030327,27.205,-0.31192,-0.025725,-0.94976,396.16
> hide #!2 models
> fitmap #11 inMap #9
Fit map cryosparc_P50_J476_006_volume_map.mrc z flip in map
cryosparc_P79_J132_006_volume_map.mrc using 720349 points
correlation = 0.9123, correlation about mean = 0.5603, overlap = 7825
steps = 212, shift = 20.1, angle = 17.2 degrees
Position of cryosparc_P50_J476_006_volume_map.mrc z flip (#11) relative to
cryosparc_P79_J132_006_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
-0.99501099 -0.05327031 0.08435287 348.19506360
-0.04061339 0.98856437 0.14522762 -21.26669832
-0.09112456 0.14107722 -0.98579589 350.74274165
Axis -0.02358418 0.99713142 0.07192160
Axis point 181.60548878 0.00000000 168.44404353
Rotation angle (degrees) 174.95195174
Shift along axis -4.19161080
> select subtract #11
Nothing selected
> hide #!9 models
> volume #10 level 0.09411
> volume #11 level 0.0781
> volume #11 level 0.09604
> show #!9 models
> volume #9 level 0.09174
> volume #9 level 0.1016
> show #!10 models
> hide #!10 models
> volume #9 level 0.09532
> volume #9 level 0.05595
> volume #9 level 0.07832
> volume #9 level 0.07295
> volume #9 level 0.09174
> volume #9 level 0.08995
> volume #9 level 0.098
> volume #9 level 0.08547
> volume #9 level 0.09532
> show #!2 models
> fitmap #2 inMap #9
Fit molecule 6w77 (#2) to map cryosparc_P79_J132_006_volume_map.mrc (#9) using
47940 atoms
average map value = 0.07328, steps = 108
shifted from previous position = 0.321
rotated from previous position = 0.122 degrees
atoms outside contour = 30325, contour level = 0.095318
Position of 6w77 (#2) relative to cryosparc_P79_J132_006_volume_map.mrc (#9)
coordinates:
Matrix rotation and translation
0.24562540 -0.55409602 -0.79539032 363.60744515
-0.96545788 -0.06624090 -0.25199848 364.22850474
0.08694399 0.82981308 -0.55122682 141.34560649
Axis 0.74333341 -0.60626877 -0.28265459
Axis point 0.00000000 288.57808983 247.22322739
Rotation angle (degrees) 133.30809428
Shift along axis 9.50920682
> open /Users/TEST/Downloads/cryosparc_P50_J458_006_volume_map.mrc
Opened cryosparc_P50_J458_006_volume_map.mrc as #12, grid size 416,416,416,
pixel 0.855, shown at level 0.0852, step 2, values float32
> hide #!2 models
> volume #12 step 1
> volume #12 level 0.09266
> volume #12 level 0.1002
> volume #12 level 0.1039
> hide #!12 models
> open /Users/TEST/Downloads/cryosparc_P79_J104_006_volume_map.mrc
Opened cryosparc_P79_J104_006_volume_map.mrc as #13, grid size 416,416,416,
pixel 0.855, shown at level 0.089, step 2, values float32
> volume flip #13
Opened cryosparc_P79_J104_006_volume_map.mrc z flip as #14, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> volume #14 level 0.1033
> show #!2 models
> select add #14
2 models selected
> view matrix models
> #14,0.99959,0.019702,-0.020867,0.57935,0.028683,-0.70972,0.7039,153.12,-0.00094133,-0.70421,-0.70999,430.57
> fitmap #2 inMap #14
Fit molecule 6w77 (#2) to map cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) using 47940 atoms
average map value = 0.08563, steps = 192
shifted from previous position = 23.9
rotated from previous position = 5.61 degrees
atoms outside contour = 30907, contour level = 0.10333
Position of 6w77 (#2) relative to cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) coordinates:
Matrix rotation and translation
0.13753133 -0.59911625 -0.78876160 384.36011301
0.65785723 -0.54007107 0.52492581 75.35257186
-0.74047890 -0.59108627 0.31985626 342.84035407
Axis -0.66365874 -0.02871227 0.74748423
Axis point 316.89136793 184.27313237 0.00000000
Rotation angle (degrees) 122.77502361
Shift along axis -0.97973217
> select subtract #14
Nothing selected
> volume #14 level 0.1114
> fitmap #2 inMap #14
Fit molecule 6w77 (#2) to map cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) using 47940 atoms
average map value = 0.08563, steps = 76
shifted from previous position = 0.0127
rotated from previous position = 0.00428 degrees
atoms outside contour = 33389, contour level = 0.11137
Position of 6w77 (#2) relative to cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) coordinates:
Matrix rotation and translation
0.13751885 -0.59909882 -0.78877701 384.36275068
0.65791248 -0.54004519 0.52488320 75.35172563
-0.74043213 -0.59112757 0.31988820 342.82277881
Axis -0.66364644 -0.02874874 0.74749375
Axis point 316.88001793 184.28199502 0.00000000
Rotation angle (degrees) 122.77347914
Shift along axis -0.98935373
> hide #!2 models
> volume #14 color darkgrey
> volume #14 color #929292
> volume #14 color darkgrey
> show #!2 models
> fitmap #2 inMap #14
Fit molecule 6w77 (#2) to map cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) using 47940 atoms
average map value = 0.08563, steps = 48
shifted from previous position = 0.00304
rotated from previous position = 0.00214 degrees
atoms outside contour = 33384, contour level = 0.11137
Position of 6w77 (#2) relative to cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) coordinates:
Matrix rotation and translation
0.13752241 -0.59908607 -0.78878607 384.36113735
0.65793879 -0.54003077 0.52486505 75.34928754
-0.74040809 -0.59115366 0.31989563 342.81916095
Axis -0.66364471 -0.02876815 0.74749455
Axis point 316.87750007 184.28642437 0.00000000
Rotation angle (degrees) 122.77261314
Shift along axis -0.99144164
> hide #!2 models
> volume #14 level 0.1158
> show #!2 models
> sequence chain #2/A
Alignment identifier is 2/A
> hide #!12 models
> select /A:721
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:721-810
1943 atoms, 2177 bonds, 45 pseudobonds, 90 residues, 2 models selected
> select /A:765
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:721-765
973 atoms, 1089 bonds, 9 pseudobonds, 45 residues, 2 models selected
> select /A:770-771
43 atoms, 47 bonds, 2 residues, 1 model selected
> select /A:721-771
1105 atoms, 1238 bonds, 9 pseudobonds, 51 residues, 2 models selected
> select /A:782-783
42 atoms, 46 bonds, 2 residues, 1 model selected
> select /A:676-783
2339 atoms, 2623 bonds, 45 pseudobonds, 108 residues, 2 models selected
> select /A:788
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:721-788
1478 atoms, 1658 bonds, 9 pseudobonds, 68 residues, 2 models selected
> select /A:765
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:676-765
1944 atoms, 2178 bonds, 44 pseudobonds, 90 residues, 2 models selected
> select /A:721-769
1062 atoms, 1190 bonds, 9 pseudobonds, 49 residues, 2 models selected
> select /A:721-853
2865 atoms, 3208 bonds, 66 pseudobonds, 133 residues, 2 models selected
> select /A:855
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:766-855
1932 atoms, 2162 bonds, 60 pseudobonds, 90 residues, 2 models selected
> select /A:811
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:811-855
962 atoms, 1074 bonds, 22 pseudobonds, 45 residues, 2 models selected
> select /A:781
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /A:781-855
1601 atoms, 1789 bonds, 34 pseudobonds, 75 residues, 2 models selected
> select /A:810
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:780-810
661 atoms, 739 bonds, 13 pseudobonds, 31 residues, 2 models selected
> volume #12 level 0.08892
> volume #14 level 0.07475
> volume #14 level 0.07743
> volume #14 level 0.08815
> volume #14 level 0.08011
> ui tool show "Color Zone"
> color zone #14 near sel distance 5.13
> color zone #14 near sel distance 5.23
> color zone #14 near sel distance 5.33
> color zone #14 near sel distance 5.43
> color zone #14 near sel distance 5.53
> color zone #14 near sel distance 5.63
> color zone #14 near sel distance 5.73
> color zone #14 near sel distance 5.83
> color zone #14 near sel distance 5.93
> color zone #14 near sel distance 6.03
> color zone #14 near sel distance 6.13
> color zone #14 near sel distance 6.23
> color zone #14 near sel distance 6.13
> color zone #14 near sel distance 5
> color single #14
> hide #* target a
> show (#!2 & sel) target ab
> undo
> select ~sel
47279 atoms, 51317 bonds, 1434 pseudobonds, 3437 residues, 29 models selected
> cartoon hide (#!2 & sel)
> undo
> color (#!2 & sel) magenta
> undo
> color (#!2 & sel) magenta
> view matrix models
> #2,-0.90031,-0.37969,0.21276,365.64,-0.43137,0.84347,-0.32011,146.45,-0.057915,-0.37998,-0.92318,386.74
> undo
> select add #2
47940 atoms, 52058 bonds, 1470 pseudobonds, 3468 residues, 3 models selected
> select subtract #2
Nothing selected
> fitmap #2 inMap #14
Fit molecule 6w77 (#2) to map cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) using 47940 atoms
average map value = 0.08563, steps = 80
shifted from previous position = 0.00334
rotated from previous position = 0.00534 degrees
atoms outside contour = 23078, contour level = 0.080113
Position of 6w77 (#2) relative to cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) coordinates:
Matrix rotation and translation
0.13751872 -0.59911920 -0.78876156 384.36250589
0.65787307 -0.54006316 0.52491411 75.35535585
-0.74046717 -0.59109050 0.31987559 342.82445022
Axis -0.66365058 -0.02871905 0.74749122
Axis point 316.88125817 184.27466370 0.00000000
Rotation angle (degrees) 122.77452494
Shift along axis -0.98826664
> volume #14 level 0.07609
> hide #!2 models
> show #!2 models
> hide #!14 models
> select /A:811
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:811-822
257 atoms, 287 bonds, 12 residues, 1 model selected
> select /A:803-804
43 atoms, 47 bonds, 2 residues, 1 model selected
> select /A:803-810
168 atoms, 186 bonds, 8 residues, 1 model selected
> select /A:751
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:751-772
474 atoms, 530 bonds, 1 pseudobond, 22 residues, 2 models selected
> select /A:768-769
45 atoms, 50 bonds, 2 residues, 1 model selected
> select /A:768-774
154 atoms, 172 bonds, 7 residues, 1 model selected
> select /A:768
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /A:768-800
716 atoms, 803 bonds, 10 pseudobonds, 33 residues, 2 models selected
> color (#!2 & sel) magenta
> select add #2
47940 atoms, 52058 bonds, 1470 pseudobonds, 3468 residues, 3 models selected
> select subtract #2
Nothing selected
> open /Users/TEST/Downloads/cryosparc_P79_J105_007_volume_map.mrc
Opened cryosparc_P79_J105_007_volume_map.mrc as #15, grid size 416,416,416,
pixel 0.855, shown at level 0.0903, step 2, values float32
> volume #15 step 1
> volume #15 level 0.12
> volume flip #15
Opened cryosparc_P79_J105_007_volume_map.mrc z flip as #16, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> close #15
> close #16
> open /Users/TEST/Downloads/cryosparc_P79_J124_006_volume_map.mrc
Opened cryosparc_P79_J124_006_volume_map.mrc as #15, grid size 416,416,416,
pixel 0.855, shown at level 0.0839, step 2, values float32
> fitmap #2 inMap #15
Fit molecule 6w77 (#2) to map cryosparc_P79_J124_006_volume_map.mrc (#15)
using 47940 atoms
average map value = 0.08971, steps = 148
shifted from previous position = 22
rotated from previous position = 3.96 degrees
atoms outside contour = 23314, contour level = 0.083944
Position of 6w77 (#2) relative to cryosparc_P79_J124_006_volume_map.mrc (#15)
coordinates:
Matrix rotation and translation
0.21762660 -0.56228857 -0.79779084 368.60451178
-0.97269071 -0.05736753 -0.22490389 357.52905247
0.08069359 0.82494880 -0.55941757 142.53037444
Axis 0.73461992 -0.61470735 -0.28717322
Axis point 0.00000000 291.36904867 247.39296199
Rotation angle (degrees) 134.39325714
Shift along axis 10.07757354
> volume #15 step 1
> volume #15 level 0.0903
> volume #15 level 0.09312
> volume #15 level 0.08959
> volume #15 color silver
> fitmap #2 inMap #15
Fit molecule 6w77 (#2) to map cryosparc_P79_J124_006_volume_map.mrc (#15)
using 47940 atoms
average map value = 0.08971, steps = 40
shifted from previous position = 0.00245
rotated from previous position = 0.0046 degrees
atoms outside contour = 25030, contour level = 0.089593
Position of 6w77 (#2) relative to cryosparc_P79_J124_006_volume_map.mrc (#15)
coordinates:
Matrix rotation and translation
0.21759163 -0.56235066 -0.79775661 368.61296865
-0.97269611 -0.05733953 -0.22488765 357.52173874
0.08072273 0.82490842 -0.55947291 142.54280617
Axis 0.73461166 -0.61473002 -0.28714581
Axis point 0.00000000 291.37495458 247.38753835
Rotation angle (degrees) 134.39575505
Shift along axis 10.07746730
> volume #15 color darkgrey
> hide #!15 models
> show #!15 models
> hide #!15 models
> open /Users/TEST/Downloads/cryosparc_P79_J125_007_volume_map.mrc
Opened cryosparc_P79_J125_007_volume_map.mrc as #16, grid size 416,416,416,
pixel 0.855, shown at level 0.0867, step 2, values float32
> volume #16 step 1
> volume #16 color darkgrey
> fitmap #2 inMap #16
Fit molecule 6w77 (#2) to map cryosparc_P79_J125_007_volume_map.mrc (#16)
using 47940 atoms
average map value = 0.09668, steps = 64
shifted from previous position = 0.248
rotated from previous position = 0.301 degrees
atoms outside contour = 22337, contour level = 0.086659
Position of 6w77 (#2) relative to cryosparc_P79_J125_007_volume_map.mrc (#16)
coordinates:
Matrix rotation and translation
0.21887548 -0.56045413 -0.79873944 368.20733292
-0.97280906 -0.06180082 -0.22321112 358.16341763
0.07573683 0.82587640 -0.55874154 143.24666517
Axis 0.73535036 -0.61295786 -0.28903722
Axis point 0.00000000 290.88425113 247.84036512
Rotation angle (degrees) 134.49390926
Shift along axis 9.81869256
> fitmap #2 inMap #16
Fit molecule 6w77 (#2) to map cryosparc_P79_J125_007_volume_map.mrc (#16)
using 47940 atoms
average map value = 0.09668, steps = 44
shifted from previous position = 0.016
rotated from previous position = 0.00708 degrees
atoms outside contour = 22343, contour level = 0.086659
Position of 6w77 (#2) relative to cryosparc_P79_J125_007_volume_map.mrc (#16)
coordinates:
Matrix rotation and translation
0.21877653 -0.56052407 -0.79871747 368.21574252
-0.97283084 -0.06175639 -0.22312847 358.14605754
0.07574297 0.82583226 -0.55880595 143.25930980
Axis 0.73532172 -0.61299697 -0.28902714
Axis point 0.00000000 290.89533403 247.83396316
Rotation angle (degrees) 134.49868579
Shift along axis 9.80875409
> select /A:1408-1493
1848 atoms, 2069 bonds, 87 pseudobonds, 86 residues, 2 models selected
> color zone #16 near sel distance 5.13
> select add #2
47940 atoms, 52058 bonds, 1470 pseudobonds, 3468 residues, 3 models selected
> select subtract #2
Nothing selected
> open /Users/TEST/Downloads/cryosparc_P79_J106_007_volume_map.mrc
Opened cryosparc_P79_J106_007_volume_map.mrc as #17, grid size 416,416,416,
pixel 0.855, shown at level 0.093, step 2, values float32
> volume #17 step 1
> volume #17 level 0.1319
> volume #17 level 0.1262
> volume flip #17
Opened cryosparc_P79_J106_007_volume_map.mrc z flip as #18, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> hide #!16 models
> select add #18
2 models selected
> view matrix models
> #18,0.98043,0.1904,0.050023,-37.636,0.1112,-0.74533,0.65736,154.17,0.16244,-0.63893,-0.75192,397.19
> view matrix models
> #18,0.92916,0.12004,-0.34964,55.683,0.34365,-0.62906,0.69727,86.978,-0.13625,-0.76803,-0.62575,447.89
> fitmap #2 inMap #18
Fit molecule 6w77 (#2) to map cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) using 47940 atoms
average map value = 0.1162, steps = 240
shifted from previous position = 25.3
rotated from previous position = 17.6 degrees
atoms outside contour = 28432, contour level = 0.12619
Position of 6w77 (#2) relative to cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) coordinates:
Matrix rotation and translation
0.14333150 -0.60719554 -0.78151755 383.47487046
0.65416495 -0.53443886 0.53520402 73.10170075
-0.74264683 -0.58795297 0.32060412 341.79232333
Axis -0.66483173 -0.02300879 0.74663871
Axis point 316.98683422 182.75762983 0.00000000
Rotation angle (degrees) 122.36097724
Shift along axis -1.43286649
> select subtract #18
Nothing selected
> volume #18 level 0.1101
> volume #18 color darkgrey
> fitmap #2 inMap #18
Fit molecule 6w77 (#2) to map cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) using 47940 atoms
average map value = 0.1162, steps = 40
shifted from previous position = 0.0107
rotated from previous position = 0.00632 degrees
atoms outside contour = 24248, contour level = 0.11015
Position of 6w77 (#2) relative to cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) coordinates:
Matrix rotation and translation
0.14327624 -0.60727486 -0.78146605 383.48084718
0.65415004 -0.53442631 0.53523478 73.09716427
-0.74267063 -0.58788246 0.32067828 341.76487353
Axis -0.66480036 -0.02296395 0.74666802
Axis point 316.96655197 182.74449758 0.00000000
Rotation angle (degrees) 122.35991057
Shift along axis -1.43190554
> open /Users/TEST/Downloads/cryosparc_P79_J101_005_volume_map.mrc
Opened cryosparc_P79_J101_005_volume_map.mrc as #19, grid size 416,416,416,
pixel 0.855, shown at level 0.0952, step 2, values float32
> volume #19 step 1
> volume #19 level 0.1361
> hide #!18 models
> select add #19
2 models selected
> view matrix models
> #19,-0.40797,0.39971,-0.82085,334.73,0.85828,0.47447,-0.19553,-31.323,0.31131,-0.78429,-0.53664,352.43
> view matrix models
> #19,0.86859,0.34601,-0.35473,27.867,0.49224,-0.51998,0.69808,46.727,0.057092,-0.78096,-0.62197,413.47
> select subtract #19
Nothing selected
> hide #!2 models
> open 7NAR
7nar title:
Complete Bacterial 30S ribosomal subunit assembly complex state F
(+RsgA)(Consensus Refinement) [more info...]
Chain information for 7nar #20
---
Chain | Description | UniProt
A | 16S rRNA |
B | 30S ribosomal protein S2 | RS2_ECOLI 1-241
C | 30S ribosomal protein S3 | RS3_ECOLI 1-233
D | 30S ribosomal protein S4 | RS4_ECOLI 1-206
E | 30S ribosomal protein S5 | RS5_ECOLI 1-167
F | 30S ribosomal protein S6 | RS6_ECOLI 1-135
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179
H | 30S ribosomal protein S8 | RS8_ECOLI 1-130
I | 30S ribosomal protein S9 | RS9_ECOLI 1-130
J | 30S ribosomal protein S10 | RS10_ECOLI 1-103
K | 30S ribosomal protein S11 | RS11_ECOLI 1-129
L | 30S ribosomal protein S12 | RS12_ECOLI 1-124
M | 30S ribosomal protein S13 | RS13_ECOLI 1-118
N | 30S ribosomal protein S14 | RS14_ECOLI 1-101
O | 30S ribosomal protein S15 | RS15_ECOLI 1-89
P | 30S ribosomal protein S16 | RS16_ECOLI 1-82
Q | 30S ribosomal protein S17 | RS17_ECOLI 1-84
R | 30S ribosomal protein S18 | RS18_ECOLI 1-75
S | 30S ribosomal protein S19 | RS19_ECOLI 1-92
T | 30S ribosomal protein S20 | RS20_ECOLI 1-87
U | 30S ribosomal protein S21 | RS21_ECOLI 1-71
W | Small ribosomal subunit biogenesis GTPase RsgA | RSGA_ECOLI 1-350
Non-standard residues in 7nar #20
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
ZN — zinc ion
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 54321 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select add #20
54452 atoms, 58616 bonds, 1682 pseudobonds, 4352 residues, 3 models selected
> view matrix models
> #20,0.87934,-0.04085,0.47443,-68.174,0.44743,-0.27012,-0.85255,334.36,0.16298,0.96196,-0.21925,40.103
> select subtract #20
Nothing selected
> select add #19
2 models selected
> select subtract #19
Nothing selected
> fitmap #20 inMap #19
Fit molecule 7nar (#20) to map cryosparc_P79_J101_005_volume_map.mrc (#19)
using 54452 atoms
average map value = 0.09083, steps = 384
shifted from previous position = 62.9
rotated from previous position = 13.3 degrees
atoms outside contour = 41842, contour level = 0.13612
Position of 7nar (#20) relative to cryosparc_P79_J101_005_volume_map.mrc (#19)
coordinates:
Matrix rotation and translation
0.96480978 -0.22097515 0.14252030 -1.37576825
-0.23637655 -0.49143276 0.83822428 156.15422996
-0.11518759 -0.84241546 -0.52637248 481.73856722
Axis -0.98840634 0.15156140 -0.00905776
Axis point 0.00000000 213.74905241 197.76314372
Rotation angle (degrees) 121.76912497
Shift along axis 20.66329902
> volume #19 color darkgrey
> volume #19 level 0.0974
> sequence chain #20/A
Alignment identifier is 20/A
> select #20/A:1401
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #20/A:1401-1500
2148 atoms, 2403 bonds, 101 pseudobonds, 100 residues, 2 models selected
> volume #16 level 0.09291
> hide #!19 models
> hide #!16 models
> color (#!20 & sel) orange red
> show #!19 models
> color zone #19 near sel distance 5.13
> select add #20
54452 atoms, 58616 bonds, 1682 pseudobonds, 4352 residues, 3 models selected
> select subtract #20
Nothing selected
> volume #19 level 0.104
> fitmap #20 inMap #19
Fit molecule 7nar (#20) to map cryosparc_P79_J101_005_volume_map.mrc (#19)
using 54452 atoms
average map value = 0.09083, steps = 28
shifted from previous position = 0.0173
rotated from previous position = 0.028 degrees
atoms outside contour = 33652, contour level = 0.10404
Position of 7nar (#20) relative to cryosparc_P79_J101_005_volume_map.mrc (#19)
coordinates:
Matrix rotation and translation
0.96468409 -0.22132936 0.14282114 -1.35399347
-0.23680681 -0.49126170 0.83820311 156.21690007
-0.11535640 -0.84242224 -0.52632465 481.76470931
Axis -0.98836433 0.15183246 -0.00910218
Axis point 0.00000000 213.80403948 197.75582205
Rotation angle (degrees) 121.76598428
Shift along axis 20.67192477
> sequence chain #20/W
Alignment identifier is 20/W
> sequence chain #20/W
Destroying pre-existing alignment with identifier 20/W
Alignment identifier is 20/W
> select #20/W:296-297
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #20/W:34-297
2045 atoms, 2083 bonds, 264 residues, 1 model selected
> color zone #19 near sel distance 5.13
> undo
> color sel orange
> select add #20
54452 atoms, 58616 bonds, 1682 pseudobonds, 4352 residues, 3 models selected
> select subtract #20
Nothing selected
> volume #19 level 0.1162
> volume #19 level 0.1107
> hide #!20 models
> show #!20 models
> volume #19 level 0.1074
> volume #19 level 0.09408
> volume #19 level 0.09851
> select #2/A:1408-1493
1848 atoms, 2069 bonds, 87 pseudobonds, 86 residues, 2 models selected
> color zone #19 near sel distance 5.1
> color zone #19 near sel distance 5
> hide #!19 models
> show #!19 models
> undo
> select #20/A:1450-1500
1092 atoms, 1220 bonds, 1 pseudobond, 51 residues, 2 models selected
> select #20/A:1401-1500
2148 atoms, 2403 bonds, 101 pseudobonds, 100 residues, 2 models selected
> select #20/A:1405-1406
43 atoms, 47 bonds, 2 residues, 1 model selected
> select #20/A:1405-1500
2063 atoms, 2309 bonds, 96 pseudobonds, 96 residues, 2 models selected
> color zone #19 near sel distance 5
> color zone #19 near sel distance 4.9
> color zone #19 near sel distance 4.8
> color zone #19 near sel distance 4.7
> color zone #19 near sel distance 4.6
> color zone #19 near sel distance 4.5
> color zone #19 near sel distance 4.4
> color zone #19 near sel distance 4
> color zone #19 near sel distance 1
> color zone #19 near sel distance 10
> color zone #19 near sel distance 1
> color zone #19 near sel distance 3
> color zone #19 near sel distance 5
> volume splitbyzone #19
Opened cryosparc_P79_J101_005_volume_map.mrc 0 as #21.1, grid size
416,416,416, pixel 0.855, shown at level 0.0985, step 1, values float32
Opened cryosparc_P79_J101_005_volume_map.mrc 1 as #21.2, grid size
416,416,416, pixel 0.855, shown at level 0.0985, step 1, values float32
> select #20/W:300-347
390 atoms, 395 bonds, 48 residues, 1 model selected
> select #20/W:34-347
2456 atoms, 2501 bonds, 314 residues, 1 model selected
> color zone #21.1 near sel distance 5.13
> color zone #21.1 near sel distance 6
> select add #20
54452 atoms, 58616 bonds, 1682 pseudobonds, 4352 residues, 3 models selected
> select subtract #20
Nothing selected
No atoms selected for color zoning
> select #20/W:186
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #20/W:131-186
453 atoms, 458 bonds, 56 residues, 1 model selected
> select #20/W:296-347
425 atoms, 431 bonds, 52 residues, 1 model selected
> select #20/W:34-347
2456 atoms, 2501 bonds, 314 residues, 1 model selected
> color zone #21.1 near sel distance 6.12
> color zone #21.1 near sel distance 6.22
> color zone #21.1 near sel distance 6.32
> color zone #21.1 near sel distance 6.42
> color zone #21.1 near sel distance 6.52
> color zone #21.1 near sel distance 6.62
> color zone #21.1 near sel distance 1
> color zone #21.1 near sel distance 10
> color zone #21.1 near sel distance 9.9
> color zone #21.1 near sel distance 5
> select #20/W:34-347
2456 atoms, 2501 bonds, 314 residues, 1 model selected
> select add #20
54452 atoms, 58616 bonds, 1682 pseudobonds, 4352 residues, 3 models selected
> select subtract #20
Nothing selected
> volume #19 level 0.1251
> volume #21.1 level 0.1162
> volume #21.1 level 0.09298
> open /Users/TEST/Downloads/cryosparc_P79_J110_006_volume_map.mrc
Opened cryosparc_P79_J110_006_volume_map.mrc as #22, grid size 416,416,416,
pixel 0.855, shown at level 0.0715, step 2, values float32
> volume #22 step 1
> volume #22 level 0.08996
> hide #!19 models
> hide #!21.1 models
> hide #!21.2 models
> hide #!22 models
> show #!22 models
> hide #!21 models
> hide #!20 models
> show #!2 models
> fitmap #2 inMap #22
Fit molecule 6w77 (#2) to map cryosparc_P79_J110_006_volume_map.mrc (#22)
using 47940 atoms
average map value = 0.07276, steps = 256
shifted from previous position = 25.1
rotated from previous position = 17.4 degrees
atoms outside contour = 31954, contour level = 0.08996
Position of 6w77 (#2) relative to cryosparc_P79_J110_006_volume_map.mrc (#22)
coordinates:
Matrix rotation and translation
0.23046062 -0.55889787 -0.79656831 366.65949052
-0.96857520 -0.05306244 -0.24299479 360.46416458
0.09354141 0.82753704 -0.55356342 139.27037395
Axis 0.73765443 -0.61333382 -0.28228987
Axis point 0.00000000 291.25745439 246.61944340
Rotation angle (degrees) 133.47852259
Shift along axis 10.06851678
> volume #22 level 0.1091
> volume #22 color darkgrey
> fitmap #2 inMap #22
Fit molecule 6w77 (#2) to map cryosparc_P79_J110_006_volume_map.mrc (#22)
using 47940 atoms
average map value = 0.07276, steps = 64
shifted from previous position = 0.017
rotated from previous position = 0.0114 degrees
atoms outside contour = 36777, contour level = 0.1091
Position of 6w77 (#2) relative to cryosparc_P79_J110_006_volume_map.mrc (#22)
coordinates:
Matrix rotation and translation
0.23042960 -0.55884372 -0.79661527 366.66792275
-0.96860112 -0.05319178 -0.24286313 360.45329203
0.09334915 0.82756530 -0.55355362 139.30287512
Axis 0.73765575 -0.61329404 -0.28237283
Axis point 0.00000000 291.24107128 246.64029812
Rotation angle (degrees) 133.48446683
Shift along axis 10.07549894
> volume #22 level 0.09143
> hide #!22 models
> fitmap #2 inMap #18
Fit molecule 6w77 (#2) to map cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) using 47940 atoms
average map value = 0.1162, steps = 248
shifted from previous position = 25.1
rotated from previous position = 17.4 degrees
atoms outside contour = 24236, contour level = 0.11015
Position of 6w77 (#2) relative to cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) coordinates:
Matrix rotation and translation
0.14335813 -0.60720353 -0.78150646 383.47104128
0.65418759 -0.53440103 0.53521413 73.09250336
-0.74262175 -0.58797911 0.32061428 341.77975729
Axis -0.66483458 -0.02301643 0.74663594
Axis point 316.98250539 182.75882761 0.00000000
Rotation angle (degrees) 122.35844623
Shift along axis -1.44208974
> volume #18 level 0.1147
> open /Users/TEST/Downloads/cryosparc_P50_J463_007_volume_map.mrc
Opened cryosparc_P50_J463_007_volume_map.mrc as #23, grid size 416,416,416,
pixel 0.855, shown at level 0.061, step 2, values float32
> volume #23 step 1
> volume #23 level 0.1013
> open /Users/TEST/Downloads/cryosparc_P50_J456_006_volume_map.mrc
Opened cryosparc_P50_J456_006_volume_map.mrc as #24, grid size 416,416,416,
pixel 0.855, shown at level 0.0844, step 2, values float32
> volume #24 step 1
> flip volume #23
Unknown command: flip volume #23
> volume flip #24
Opened cryosparc_P50_J456_006_volume_map.mrc z flip as #25, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> select add #25
2 models selected
> view matrix models
> #25,-0.94463,-0.32808,0.0063999,392.54,-0.29267,0.85116,0.43574,1.0039,-0.14841,0.40974,-0.90005,283.82
> hide #!18 models
> fitmap #2 inMap #25
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) using 47940 atoms
average map value = 0.1036, steps = 236
shifted from previous position = 10.3
rotated from previous position = 11.4 degrees
atoms outside contour = 21895, contour level = 0.084412
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) coordinates:
Matrix rotation and translation
-0.20194603 0.49699803 0.84392582 -13.67562315
-0.94685570 0.12119851 -0.29795174 349.10507307
-0.25036398 -0.85924612 0.44610986 268.13729461
Axis -0.29594178 0.57696296 -0.76127012
Axis point 105.74042880 282.44069285 -0.00000000
Rotation angle (degrees) 108.50085597
Shift along axis 1.34297476
> volume #25 level 0.09098
> select subtract #25
Nothing selected
> volume #25 level 0.09756
> volume #25 level 0.0877
> fitmap #2 inMap #25
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) using 47940 atoms
average map value = 0.1036, steps = 176
shifted from previous position = 0.011
rotated from previous position = 0.00473 degrees
atoms outside contour = 22682, contour level = 0.087698
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) coordinates:
Matrix rotation and translation
-0.20191598 0.49704967 0.84390259 -13.68305238
-0.94684578 0.12125071 -0.29796201 349.09833612
-0.25042571 -0.85920889 0.44614692 268.14579263
Axis -0.29591050 0.57697112 -0.76127610
Axis point 105.74942374 282.44611116 -0.00000000
Rotation angle (degrees) 108.49725185
Shift along axis 1.33563584
> volume #25 level 0.09427
> volume #25 level 0.09975
> fitmap #2 inMap #25
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) using 47940 atoms
average map value = 0.1036, steps = 124
shifted from previous position = 0.0136
rotated from previous position = 0.00208 degrees
atoms outside contour = 25551, contour level = 0.099747
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) coordinates:
Matrix rotation and translation
-0.20192204 0.49706338 0.84389307 -13.68120424
-0.94685164 0.12121844 -0.29795654 349.10132697
-0.25039868 -0.85920551 0.44616860 268.12399508
Axis -0.29591248 0.57695354 -0.76128865
Axis point 105.75001574 282.43237732 0.00000000
Rotation angle (degrees) 108.49775520
Shift along axis 1.34393236
> volume #25 level 0.1096
> open /Users/TEST/Downloads/cryosparc_P79_J131_006_volume_map.mrc
Opened cryosparc_P79_J131_006_volume_map.mrc as #26, grid size 416,416,416,
pixel 0.855, shown at level 0.0595, step 2, values float32
> volume #26 step 1
> volume #26 color darkgrey
> volume #26 level 0.06663
> fitmap #2 inMap #26
Fit molecule 6w77 (#2) to map cryosparc_P79_J131_006_volume_map.mrc (#26)
using 47940 atoms
average map value = 0.0742, steps = 324
shifted from previous position = 20.7
rotated from previous position = 21.6 degrees
atoms outside contour = 25198, contour level = 0.066631
Position of 6w77 (#2) relative to cryosparc_P79_J131_006_volume_map.mrc (#26)
coordinates:
Matrix rotation and translation
0.24497997 -0.55262997 -0.79660839 363.74767916
-0.96560699 -0.06525145 -0.25168511 363.90360489
0.08710888 0.83086844 -0.54960866 140.60207436
Axis 0.74290037 -0.60644934 -0.28340472
Axis point 0.00000000 288.70087711 247.30195436
Rotation angle (degrees) 133.23089401
Shift along axis 9.69189203
> volume #26 level 0.08722
> volume #26 level 0.0917
> open /Users/TEST/Downloads/cryosparc_P79_J132_006_volume_map.mrc
Opened cryosparc_P79_J132_006_volume_map.mrc as #27, grid size 416,416,416,
pixel 0.855, shown at level 0.0622, step 2, values float32
> volume #27 step 1
> volume #27 color darkgrey
> volume #27 level 0.06785
> volume #27 level 0.07832
> select #2/A:1408-1493
1848 atoms, 2069 bonds, 87 pseudobonds, 86 residues, 2 models selected
> color zone #27 near sel distance 5.13
> select add #2
47940 atoms, 52058 bonds, 1470 pseudobonds, 3468 residues, 3 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> hide #!27 models
> show #!17 models
> hide #!17 models
> show #!18 models
> show #!2 models
> fitmap #2 inMap #18
Fit molecule 6w77 (#2) to map cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) using 47940 atoms
average map value = 0.1162, steps = 236
shifted from previous position = 26.5
rotated from previous position = 16.5 degrees
atoms outside contour = 25490, contour level = 0.11473
Position of 6w77 (#2) relative to cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) coordinates:
Matrix rotation and translation
0.14332511 -0.60719840 -0.78151650 383.47637249
0.65423555 -0.53438447 0.53517204 73.09049814
-0.74258587 -0.58799945 0.32066007 341.76501243
Axis -0.66481440 -0.02304335 0.74665308
Axis point 316.97133504 182.76457002 0.00000000
Rotation angle (degrees) 122.35745172
Shift along axis -1.44496474
> volume #18 level 0.1331
> volume #18 level 0.1594
> fitmap #2 inMap #18
Fit molecule 6w77 (#2) to map cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) using 47940 atoms
average map value = 0.1162, steps = 40
shifted from previous position = 0.011
rotated from previous position = 0.00654 degrees
atoms outside contour = 35697, contour level = 0.15942
Position of 6w77 (#2) relative to cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) coordinates:
Matrix rotation and translation
0.14329126 -0.60724682 -0.78148508 383.47723636
0.65416395 -0.53442635 0.53521774 73.09885832
-0.74265548 -0.58791138 0.32066035 341.76962431
Axis -0.66480813 -0.02298421 0.74666049
Axis point 316.96935325 182.74962838 0.00000000
Rotation angle (degrees) 122.36001047
Shift along axis -1.43302911
> volume #18 level 0.1159
> volume #18 level 0.1228
> fitmap #2 inMap #18
Fit molecule 6w77 (#2) to map cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) using 47940 atoms
average map value = 0.1162, steps = 28
shifted from previous position = 0.0152
rotated from previous position = 0.00995 degrees
atoms outside contour = 27562, contour level = 0.12275
Position of 6w77 (#2) relative to cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) coordinates:
Matrix rotation and translation
0.14336602 -0.60715190 -0.78154512 383.47218167
0.65424991 -0.53438276 0.53515619 73.09184276
-0.74256533 -0.58804903 0.32061674 341.77735671
Axis -0.66483454 -0.02307247 0.74663425
Axis point 316.98207353 182.77310227 0.00000000
Rotation angle (degrees) 122.35747561
Shift along axis -1.44927971
> hide #!18 models
> show #!14 models
> fitmap #2 inMap #14
Fit molecule 6w77 (#2) to map cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) using 47940 atoms
average map value = 0.08563, steps = 296
shifted from previous position = 4.6
rotated from previous position = 20.8 degrees
atoms outside contour = 21680, contour level = 0.076093
Position of 6w77 (#2) relative to cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) coordinates:
Matrix rotation and translation
0.13750705 -0.59910039 -0.78877788 384.36456926
0.65792597 -0.54003965 0.52487199 75.35112772
-0.74042234 -0.59113105 0.31990444 342.81782318
Axis -0.66363931 -0.02875498 0.74749984
Axis point 316.87610750 184.28336212 0.00000000
Rotation angle (degrees) 122.77313849
Shift along axis -0.98988795
> volume #14 level 0.1171
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #14
Fit molecule 6w77 (#2) to map cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) using 47940 atoms
average map value = 0.08563, steps = 44
shifted from previous position = 0.0181
rotated from previous position = 0.0104 degrees
atoms outside contour = 34942, contour level = 0.11709
Position of 6w77 (#2) relative to cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) coordinates:
Matrix rotation and translation
0.13749817 -0.59916732 -0.78872859 384.36573515
0.65779888 -0.54010127 0.52496787 75.35760429
-0.74053690 -0.59100690 0.31986865 342.83775160
Axis -0.66364950 -0.02865870 0.74749449
Axis point 316.88827470 184.25959080 0.00000000
Rotation angle (degrees) 122.77676005
Shift along axis -0.97445064
> fitmap #2 inMap #14
Fit molecule 6w77 (#2) to map cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) using 47940 atoms
average map value = 0.08563, steps = 40
shifted from previous position = 0.00518
rotated from previous position = 0.00395 degrees
atoms outside contour = 34935, contour level = 0.11709
Position of 6w77 (#2) relative to cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) coordinates:
Matrix rotation and translation
0.13751807 -0.59913195 -0.78875198 384.36015614
0.65783882 -0.54008235 0.52493727 75.35660831
-0.74049771 -0.59106004 0.31986117 342.83755702
Axis -0.66365495 -0.02869558 0.74748824
Axis point 316.88749205 184.26900588 0.00000000
Rotation angle (degrees) 122.77569223
Shift along axis -0.97787676
> fitmap #2 inMap #14
Fit molecule 6w77 (#2) to map cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) using 47940 atoms
average map value = 0.08563, steps = 76
shifted from previous position = 0.0112
rotated from previous position = 0.00336 degrees
atoms outside contour = 34926, contour level = 0.11709
Position of 6w77 (#2) relative to cryosparc_P79_J104_006_volume_map.mrc z flip
(#14) coordinates:
Matrix rotation and translation
0.13748912 -0.59913562 -0.78875424 384.36684766
0.65787894 -0.54006327 0.52490664 75.35564360
-0.74046745 -0.59107375 0.31990588 342.81701120
Axis -0.66363603 -0.02871453 0.74750431
Axis point 316.87446939 184.27318357 0.00000000
Rotation angle (degrees) 122.77450544
Shift along axis -0.98629804
> volume #14 level 0.1042
> fitmap #2 inMap #15
Fit molecule 6w77 (#2) to map cryosparc_P79_J124_006_volume_map.mrc (#15)
using 47940 atoms
average map value = 0.08971, steps = 152
shifted from previous position = 22
rotated from previous position = 3.96 degrees
atoms outside contour = 25027, contour level = 0.089593
Position of 6w77 (#2) relative to cryosparc_P79_J124_006_volume_map.mrc (#15)
coordinates:
Matrix rotation and translation
0.21759727 -0.56234335 -0.79776023 368.61307115
-0.97269441 -0.05733633 -0.22489583 357.52362749
0.08072803 0.82491364 -0.55946446 142.53955971
Axis 0.73461232 -0.61472898 -0.28714634
Axis point 0.00000000 291.37576893 247.38827685
Rotation angle (degrees) 134.39506156
Shift along axis 10.07785636
> volume #15 level 0.09595
> volume #15 level 0.1002
> open /Users/TEST/Downloads/cryosparc_P79_J110_006_volume_map.mrc
Opened cryosparc_P79_J110_006_volume_map.mrc as #28, grid size 416,416,416,
pixel 0.855, shown at level 0.0715, step 2, values float32
> volume #28 step 1
> volume #28 level 0.1245
> fitmap #2 inMap #28
Fit molecule 6w77 (#2) to map cryosparc_P79_J110_006_volume_map.mrc (#28)
using 47940 atoms
average map value = 0.07276, steps = 116
shifted from previous position = 1.61
rotated from previous position = 1.1 degrees
atoms outside contour = 39794, contour level = 0.12447
Position of 6w77 (#2) relative to cryosparc_P79_J110_006_volume_map.mrc (#28)
coordinates:
Matrix rotation and translation
0.23042654 -0.55890370 -0.79657408 366.66717620
-0.96858735 -0.05307979 -0.24294255 360.45903099
0.09349951 0.82753199 -0.55357805 139.28029531
Axis 0.73764679 -0.61333539 -0.28230641
Axis point 0.00000000 291.25925261 246.62368883
Rotation angle (degrees) 133.48113046
Shift along axis 10.06886304
> hide #!2 models
> volume #28 level 0.1031
> show #!2 models
> fitmap #2 inMap #28
Fit molecule 6w77 (#2) to map cryosparc_P79_J110_006_volume_map.mrc (#28)
using 47940 atoms
average map value = 0.07276, steps = 64
shifted from previous position = 0.00917
rotated from previous position = 0.00485 degrees
atoms outside contour = 35454, contour level = 0.10312
Position of 6w77 (#2) relative to cryosparc_P79_J110_006_volume_map.mrc (#28)
coordinates:
Matrix rotation and translation
0.23038944 -0.55890926 -0.79658091 366.67094499
-0.96860314 -0.05312110 -0.24287057 360.44880944
0.09342736 0.82752558 -0.55359980 139.29917871
Axis 0.73764106 -0.61333053 -0.28233194
Axis point 0.00000000 291.25374020 246.62838446
Rotation angle (degrees) 133.48508525
Shift along axis 10.06867799
> volume #28 level 0.134
> hide #!2 models
> show #!2 models
> volume #28 level 0.1201
> volume #28 color silver
> volume #28 color darkgrey
> fitmap #2 inMap #28
Fit molecule 6w77 (#2) to map cryosparc_P79_J110_006_volume_map.mrc (#28)
using 47940 atoms
average map value = 0.07276, steps = 140
shifted from previous position = 0.0112
rotated from previous position = 0.00558 degrees
atoms outside contour = 38989, contour level = 0.12005
Position of 6w77 (#2) relative to cryosparc_P79_J110_006_volume_map.mrc (#28)
coordinates:
Matrix rotation and translation
0.23044313 -0.55884313 -0.79661178 366.66539219
-0.96859542 -0.05317763 -0.24288896 360.45514096
0.09337490 0.82756661 -0.55354732 139.29734910
Axis 0.73765807 -0.61329576 -0.28236304
Axis point 0.00000000 291.24130988 246.63807857
Rotation angle (degrees) 133.48312533
Shift along axis 10.07565601
> hide #!2 models
> volume #28 level 0.09944
> show #!2 models
> fitmap #2 inMap #28
Fit molecule 6w77 (#2) to map cryosparc_P79_J110_006_volume_map.mrc (#28)
using 47940 atoms
average map value = 0.07276, steps = 44
shifted from previous position = 0.0104
rotated from previous position = 0.00804 degrees
atoms outside contour = 34541, contour level = 0.099442
Position of 6w77 (#2) relative to cryosparc_P79_J110_006_volume_map.mrc (#28)
coordinates:
Matrix rotation and translation
0.23054568 -0.55876512 -0.79663683 366.64010850
-0.96856833 -0.05319091 -0.24299407 360.47795500
0.09340277 0.82761843 -0.55346513 139.26394116
Axis 0.73768356 -0.61326351 -0.28236649
Axis point 0.00000000 291.23356209 246.63473746
Rotation angle (degrees) 133.47635598
Shift along axis 10.07293533
> volume #28 color #919191
> volume #28 level 0.1156
> volume #28 level 0.09723
> volume #28 level 0.1017
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!28 models
> fitmap #2 inMap #25
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) using 47940 atoms
average map value = 0.1036, steps = 328
shifted from previous position = 19.4
rotated from previous position = 22.3 degrees
atoms outside contour = 27809, contour level = 0.1096
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) coordinates:
Matrix rotation and translation
-0.20193315 0.49702891 0.84391071 -13.67866802
-0.94684928 0.12122522 -0.29796125 349.10177004
-0.25039862 -0.85922450 0.44613207 268.13410024
Axis -0.29592214 0.57696697 -0.76127472
Axis point 105.74603895 282.43936787 0.00000000
Rotation angle (degrees) 108.49898941
Shift along axis 1.34430037
> volume #25 level 0.1206
> volume #25 level 0.09756
> volume #25 level 0.1151
> fitmap #2 inMap #25
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) using 47940 atoms
average map value = 0.1036, steps = 76
shifted from previous position = 0.0123
rotated from previous position = 0.00146 degrees
atoms outside contour = 29011, contour level = 0.11508
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) coordinates:
Matrix rotation and translation
-0.20193227 0.49702648 0.84391235 -13.67796443
-0.94684329 0.12124772 -0.29797115 349.10037916
-0.25042200 -0.85922273 0.44612235 268.15137099
Axis -0.29591527 0.57697878 -0.76126844
Axis point 105.74806360 282.44908691 0.00000000
Rotation angle (degrees) 108.49857634
Shift along axis 1.33585099
> hide #!2 models
> show #!2 models
> volume #19 level 0.1228
> fitmap #2 inMap #25
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) using 47940 atoms
average map value = 0.1036, steps = 64
shifted from previous position = 0.0038
rotated from previous position = 0.00467 degrees
atoms outside contour = 29008, contour level = 0.11508
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) coordinates:
Matrix rotation and translation
-0.20190538 0.49708151 0.84388637 -13.68447638
-0.94683376 0.12129355 -0.29798278 349.09551348
-0.25047971 -0.85918442 0.44616373 268.14931369
Axis -0.29588299 0.57698389 -0.76127711
Axis point 105.75783461 282.44908598 0.00000000
Rotation angle (degrees) 108.49512979
Shift along axis 1.33555622
> volume #25 level 0.1238
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #25
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) using 47940 atoms
average map value = 0.1036, steps = 84
shifted from previous position = 0.00526
rotated from previous position = 0.00487 degrees
atoms outside contour = 30835, contour level = 0.12384
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#25) coordinates:
Matrix rotation and translation
-0.20190589 0.49704387 0.84390842 -13.68368393
-0.94685419 0.12123613 -0.29794123 349.09662521
-0.25040205 -0.85921430 0.44614977 268.14257307
Axis -0.29592440 0.57696189 -0.76127769
Axis point 105.74659076 282.44272093 0.00000000
Rotation angle (degrees) 108.49730131
Shift along axis 1.33382583
> volume #25 level 0.114
> volume #25 level 0.07565
> volume #25 level 0.1096
> hide #!2 models
> fitmap #15 inMap #25
Fit map cryosparc_P79_J124_006_volume_map.mrc in map
cryosparc_P50_J456_006_volume_map.mrc z flip using 494383 points
correlation = 0.8874, correlation about mean = 0.4811, overlap = 8315
steps = 308, shift = 19.3, angle = 21.7 degrees
Position of cryosparc_P79_J124_006_volume_map.mrc (#15) relative to
cryosparc_P50_J456_006_volume_map.mrc z flip (#25) coordinates:
Matrix rotation and translation
-0.99502822 -0.03807587 -0.09202768 377.40554352
-0.05487723 0.98071459 0.18758304 -11.97676673
0.08311050 0.19170065 -0.97792818 310.44227861
Axis 0.02339674 -0.99515755 -0.09546751
Axis point 181.70484957 0.00000000 164.15930572
Rotation angle (degrees) 174.95171678
Shift along axis -8.88832249
> volume #15 level 0.1072
> show #!2 models
> hide #!2 models
> open /Users/TEST/Downloads/cryosparc_P79_J60_class_04_00143_volume.mrc
Opened cryosparc_P79_J60_class_04_00143_volume.mrc as #29, grid size
128,128,128, pixel 2.78, shown at level 0.314, step 1, values float32
> hide #!25 models
> open /Users/TEST/Downloads/cryosparc_P79_J60_class_05_00143_volume.mrc
Opened cryosparc_P79_J60_class_05_00143_volume.mrc as #30, grid size
128,128,128, pixel 2.78, shown at level 0.305, step 1, values float32
> volume #30 level 0.3509
> show #!2 models
> select add #30
2 models selected
> view matrix models
> #30,-0.46427,-0.84971,-0.2499,459,-0.76448,0.24197,0.59751,170.45,-0.44724,0.46845,-0.76192,300.39
> fitmap #2 inMap #30
Fit molecule 6w77 (#2) to map cryosparc_P79_J60_class_05_00143_volume.mrc
(#30) using 47940 atoms
average map value = 0.322, steps = 180
shifted from previous position = 20.8
rotated from previous position = 46.4 degrees
atoms outside contour = 28119, contour level = 0.35095
Position of 6w77 (#2) relative to cryosparc_P79_J60_class_05_00143_volume.mrc
(#30) coordinates:
Matrix rotation and translation
-0.17419701 0.63105817 0.75592393 -22.25346723
-0.74243746 0.42011856 -0.52181128 310.85525313
-0.64687094 -0.65212421 0.39533783 313.01605405
Axis -0.06623062 0.71296049 -0.69806937
Axis point 188.30118548 0.00000000 321.52952448
Rotation angle (degrees) 100.33308414
Shift along axis 4.59445717
> select subtract #30
Nothing selected
No atoms selected for color zoning
> open /Users/TEST/Downloads/cryosparc_P79_J59_011_volume_map.mrc
Opened cryosparc_P79_J59_011_volume_map.mrc as #31, grid size 416,416,416,
pixel 0.855, shown at level 0.0677, step 2, values float32
> hide #!30 models
> show #!30 models
> hide #!2 models
> hide #!30 models
> volume #31 step 1
> volume #31 level 0.08503
> volume #31 level 0.09476
> volume #31 level 0.1056
> open /Users/TEST/Downloads/cryosparc_P50_J425_010_volume_map.mrc
Opened cryosparc_P50_J425_010_volume_map.mrc as #32, grid size 416,416,416,
pixel 0.855, shown at level 0.0632, step 2, values float32
> volume #32 step 1
> select add #32
2 models selected
> view matrix models
> #32,-0.96805,-0.025733,0.24942,303.83,0.062806,0.93813,0.34055,-62.789,-0.24275,0.34534,-0.90654,332.61
> select subtract #32
Nothing selected
> volume flip #32
Opened cryosparc_P50_J425_010_volume_map.mrc z flip as #33, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> select add #33
2 models selected
> view matrix models
> #33,0.9668,-0.03728,-0.25279,53.469,0.096187,0.96963,0.22487,-53.786,0.23673,-0.24172,0.94103,25.071
> view matrix models
> #33,0.99866,0.015443,-0.049476,4.0727,-0.033549,0.92023,-0.38993,83.417,0.039508,0.39107,0.91951,-40.292
> fitmap #33 inMap #31
Fit map cryosparc_P50_J425_010_volume_map.mrc z flip in map
cryosparc_P79_J59_011_volume_map.mrc using 718267 points
correlation = 0.8744, correlation about mean = 0.5228, overlap = 9790
steps = 156, shift = 14.2, angle = 8.03 degrees
Position of cryosparc_P50_J425_010_volume_map.mrc z flip (#33) relative to
cryosparc_P79_J59_011_volume_map.mrc (#31) coordinates:
Matrix rotation and translation
0.98226173 0.03402963 -0.18440133 31.27559674
-0.10785359 0.90697750 -0.40713558 107.38100696
0.15339319 0.41980204 0.89455953 -73.94285358
Axis 0.91428099 -0.37347329 -0.15686931
Axis point 0.00000000 229.21529944 211.45900350
Rotation angle (degrees) 26.88709655
Shift along axis 0.09010996
> select subtract #33
Nothing selected
> volume #32 level 0.09087
> volume #33 level 0.113
> volume #33 level 0.08533
> volume #33 level 0.1172
> fitmap #31 inMap #33
Fit map cryosparc_P79_J59_011_volume_map.mrc in map
cryosparc_P50_J425_010_volume_map.mrc z flip using 335508 points
correlation = 0.8778, correlation about mean = 0.444, overlap = 7382
steps = 52, shift = 0.0937, angle = 0.156 degrees
Position of cryosparc_P79_J59_011_volume_map.mrc (#31) relative to
cryosparc_P50_J425_010_volume_map.mrc z flip (#33) coordinates:
Matrix rotation and translation
0.98232127 -0.10759543 0.15319326 -7.81000948
0.03338291 0.90589136 0.42219244 -67.66332757
-0.18420243 -0.40961457 0.89346818 116.30275355
Axis -0.91544898 0.37132236 0.15515435
Axis point 0.00000000 228.93600134 211.35870162
Rotation angle (degrees) 27.02095974
Shift along axis 0.06963740
> volume #31 level 0.1218
> volume #33 level 0.1297
> fitmap #31 inMap #33
Fit map cryosparc_P79_J59_011_volume_map.mrc in map
cryosparc_P50_J425_010_volume_map.mrc z flip using 248134 points
correlation = 0.8855, correlation about mean = 0.4179, overlap = 6420
steps = 48, shift = 0.0324, angle = 0.0421 degrees
Position of cryosparc_P79_J59_011_volume_map.mrc (#31) relative to
cryosparc_P50_J425_010_volume_map.mrc z flip (#33) coordinates:
Matrix rotation and translation
0.98221884 -0.10810884 0.15348827 -7.75721421
0.03364261 0.90568087 0.42262320 -67.73629084
-0.18470069 -0.40994472 0.89321386 116.47807710
Axis -0.91516701 0.37174071 0.15581461
Axis point 0.00000000 229.02542117 211.44834713
Rotation angle (degrees) 27.05670591
Shift along axis 0.06779603
> volume #33 level 0.1047
> volume #31 level 0.138
> volume #33 level 0.1158
> volume #33 color #ff7e79
> volume #31 color #fffb00
> volume #33 color silver
> ui mousemode right zoom
> volume #31 level 0.1542
> fitmap #31 inMap #33
Fit map cryosparc_P79_J59_011_volume_map.mrc in map
cryosparc_P50_J425_010_volume_map.mrc z flip using 132805 points
correlation = 0.9004, correlation about mean = 0.3727, overlap = 4587
steps = 48, shift = 0.0997, angle = 0.149 degrees
Position of cryosparc_P79_J59_011_volume_map.mrc (#31) relative to
cryosparc_P50_J425_010_volume_map.mrc z flip (#33) coordinates:
Matrix rotation and translation
0.98182200 -0.10982022 0.15480671 -7.66886781
0.03437369 0.90500634 0.42400710 -68.00409155
-0.18666561 -0.41097821 0.89233003 117.09916029
Axis -0.91398857 0.37378118 0.15783702
Axis point 0.00000000 229.40013999 211.84318474
Rotation angle (degrees) 27.17958797
Shift along axis 0.07318992
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/TEST/Desktop/movie1.mp4
Movie saved to /Users/TEST/Desktop/movie1.mp4
> fitmap #31 inMap #33
Fit map cryosparc_P79_J59_011_volume_map.mrc in map
cryosparc_P50_J425_010_volume_map.mrc z flip using 132805 points
correlation = 0.9004, correlation about mean = 0.3727, overlap = 4587
steps = 40, shift = 0.00214, angle = 0.00403 degrees
Position of cryosparc_P79_J59_011_volume_map.mrc (#31) relative to
cryosparc_P50_J425_010_volume_map.mrc z flip (#33) coordinates:
Matrix rotation and translation
0.98182563 -0.10979936 0.15479847 -7.67272001
0.03437090 0.90503541 0.42394528 -67.99770752
-0.18664701 -0.41091976 0.89236084 117.07798843
Axis -0.91398067 0.37380242 0.15783248
Axis point 0.00000000 229.39695876 211.84304888
Rotation angle (degrees) 27.17560465
Shift along axis 0.07372008
> volume #31 level 0.1402
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> volume #31 level 0.1477
> fitmap #31 inMap #33
Fit map cryosparc_P79_J59_011_volume_map.mrc in map
cryosparc_P50_J425_010_volume_map.mrc z flip using 151143 points
correlation = 0.8973, correlation about mean = 0.381, overlap = 4941
steps = 48, shift = 0.0298, angle = 0.0363 degrees
Position of cryosparc_P79_J59_011_volume_map.mrc (#31) relative to
cryosparc_P50_J425_010_volume_map.mrc z flip (#33) coordinates:
Matrix rotation and translation
0.98192922 -0.10936728 0.15444686 -7.68868686
0.03418280 0.90517929 0.42365319 -67.95231899
-0.18613590 -0.41071801 0.89256046 116.92875944
Axis -0.91431226 0.37321397 0.15730361
Axis point 0.00000000 229.27373731 211.76642152
Rotation angle (degrees) 27.14754671
Shift along axis 0.06242105
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/TEST/Desktop/movie1.mp4
Movie saved to /Users/TEST/Desktop/movie1.mp4
> open /Users/TEST/Downloads/cryosparc_P50_J447_class_01_00100_volume.mrc
Opened cryosparc_P50_J447_class_01_00100_volume.mrc as #34, grid size
128,128,128, pixel 2.78, shown at level 0.244, step 1, values float32
> open /Users/TEST/Downloads/cryosparc_P50_J447_class_00_00100_volume.mrc
Opened cryosparc_P50_J447_class_00_00100_volume.mrc as #35, grid size
128,128,128, pixel 2.78, shown at level 0.236, step 1, values float32
> volume #35 level 0.2424
> volume #34 level 0.3064
> volume #34 level 0.3662
> volume #35 level 0.2786
> volume #35 level 0.3269
> volume #35 level 0.3419
> volume #35 level 0.4203
> open /Users/TEST/Downloads/cryosparc_P50_J449_006_volume_map.mrc
Opened cryosparc_P50_J449_006_volume_map.mrc as #36, grid size 416,416,416,
pixel 0.855, shown at level 0.0609, step 2, values float32
> volume #36 step 1
> volume #36 level 0.07953
> volume #36 level 0.09316
> open /Users/TEST/Downloads/cryosparc_P79_J106_007_volume_map.mrc
Opened cryosparc_P79_J106_007_volume_map.mrc as #37, grid size 416,416,416,
pixel 0.855, shown at level 0.093, step 2, values float32
> volume #37 step 1
> volume #37 level 0.1376
> show #!2 models
> fitmap #2 inMap #18
Fit molecule 6w77 (#2) to map cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) using 47940 atoms
average map value = 0.1162, steps = 568
shifted from previous position = 18.5
rotated from previous position = 53.6 degrees
atoms outside contour = 27567, contour level = 0.12275
Position of 6w77 (#2) relative to cryosparc_P79_J106_007_volume_map.mrc z flip
(#18) coordinates:
Matrix rotation and translation
0.14337212 -0.60717494 -0.78152610 383.46988459
0.65418994 -0.53441116 0.53520114 73.09860027
-0.74261698 -0.58799943 0.32058807 341.78452266
Axis -0.66484449 -0.02303108 0.74662666
Axis point 316.98608713 182.76353586 0.00000000
Rotation angle (degrees) 122.35920408
Shift along axis -1.44594186
> volume #18 level 0.1079
> volume #18 level 0.1159
> open /Users/TEST/Downloads/cryosparc_P50_J498_006_volume_map.mrc
Opened cryosparc_P50_J498_006_volume_map.mrc as #38, grid size 416,416,416,
pixel 0.855, shown at level 0.0597, step 2, values float32
> open /Users/TEST/Downloads/cryosparc_P50_J497_007_volume_map.mrc
Opened cryosparc_P50_J497_007_volume_map.mrc as #39, grid size 416,416,416,
pixel 0.855, shown at level 0.0592, step 2, values float32
> hide #!2 models
> hide #!18 models
> volume #39 step 1
> volume #39 level 0.09368
> volume #38 step 1
> volume #38 level 0.07816
> volume #38 level 0.07976
> fitmap #38 inMap #39
Fit map cryosparc_P50_J498_006_volume_map.mrc in map
cryosparc_P50_J497_007_volume_map.mrc using 525715 points
correlation = 0.9683, correlation about mean = 0.8031, overlap = 1.107e+04
steps = 60, shift = 0.542, angle = 0.865 degrees
Position of cryosparc_P50_J498_006_volume_map.mrc (#38) relative to
cryosparc_P50_J497_007_volume_map.mrc (#39) coordinates:
Matrix rotation and translation
0.99989503 0.00403146 -0.01391676 2.42233167
-0.00397214 0.99998292 0.00428792 -0.35647707
0.01393381 -0.00423219 0.99989396 -1.45325608
Axis -0.28208236 -0.92207068 -0.26498151
Axis point 105.04065287 0.00000000 173.88427917
Rotation angle (degrees) 0.86532427
Shift along axis 0.03048601
> volume #38 level 0.08699
> show #!2 models
> select add #2
47940 atoms, 52058 bonds, 1470 pseudobonds, 3468 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.30928,0.69084,0.65352,33.253,-0.88293,0.046655,-0.46717,375.3,-0.35323,-0.7215,0.59553,238.14
> select subtract #2
Nothing selected
> hide #!39 models
> fitmap #2 inMap #38
Fit molecule 6w77 (#2) to map cryosparc_P50_J498_006_volume_map.mrc (#38)
using 47940 atoms
average map value = 0.07566, steps = 448
shifted from previous position = 29.7
rotated from previous position = 16.4 degrees
atoms outside contour = 29810, contour level = 0.086993
Position of 6w77 (#2) relative to cryosparc_P50_J498_006_volume_map.mrc (#38)
coordinates:
Matrix rotation and translation
-0.20358118 0.49470540 0.84487945 -13.67596762
-0.94675851 0.12035499 -0.29860174 349.65628459
-0.24940535 -0.86068650 0.44386453 268.93878374
Axis -0.29660673 0.57744358 -0.76064667
Axis point 105.37180188 283.16951983 0.00000000
Rotation angle (degrees) 108.64362358
Shift along axis 1.39577288
> show #!39 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!38 models
> fitmap #2 inMap #39
Fit molecule 6w77 (#2) to map cryosparc_P50_J497_007_volume_map.mrc (#39)
using 47940 atoms
average map value = 0.07962, steps = 112
shifted from previous position = 0.159
rotated from previous position = 0.141 degrees
atoms outside contour = 30760, contour level = 0.093684
Position of 6w77 (#2) relative to cryosparc_P50_J497_007_volume_map.mrc (#39)
coordinates:
Matrix rotation and translation
-0.20393384 0.50501983 0.83866917 -13.55115912
-0.94720446 0.11471803 -0.29940521 350.42005620
-0.24741604 -0.85545003 0.45496214 266.05265388
Axis -0.29315410 0.57259833 -0.76563165
Axis point 106.81740219 280.94206979 0.00000000
Rotation angle (degrees) 108.48925649
Shift along axis 0.92418671
> show #!38 models
> volume #39 level 0.1101
> ui mousemode right zoom
> volume #38 level 0.09984
> volume #39 level 0.1159
> open /Users/TEST/Downloads/cryosparc_P79_J83_009_volume_map.mrc
Opened cryosparc_P79_J83_009_volume_map.mrc as #40, grid size 416,416,416,
pixel 0.855, shown at level 0.0758, step 2, values float32
> volume flip #40
Opened cryosparc_P79_J83_009_volume_map.mrc z flip as #41, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> volume #41 level 0.1005
> volume #41 level 0.2588
> open /Users/TEST/Downloads/cryosparc_P79_J63_010_volume_map.mrc
Opened cryosparc_P79_J63_010_volume_map.mrc as #42, grid size 416,416,416,
pixel 0.855, shown at level 0.0602, step 2, values float32
> volume #42 step 1
> volume #42 level 0.1067
> open /Users/TEST/Downloads/cryosparc_P79_J62_009_volume_map.mrc
Opened cryosparc_P79_J62_009_volume_map.mrc as #43, grid size 416,416,416,
pixel 0.855, shown at level 0.09, step 2, values float32
> volume flip #43
Opened cryosparc_P79_J62_009_volume_map.mrc z flip as #44, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> volume #44 level 0.1284
> hide #!2 models
> volume #44 level 0.1375
> volume #44 level 0.1239
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2
47940 atoms, 52058 bonds, 1470 pseudobonds, 3468 residues, 3 models selected
> ui mousemode right "rotate selected models"
> select subtract #2
Nothing selected
> select add #44
2 models selected
> view matrix models
> #44,0.56552,0.3624,0.74085,-120.38,0.82237,-0.17974,-0.53982,154.14,-0.062469,0.91453,-0.39967,111.43
> view matrix models
> #44,0.57346,0.81923,0.0023673,-64.374,0.70142,-0.4895,-0.51807,223.43,-0.42326,0.29875,-0.85533,360.9
> fitmap #2 inMap #44
Fit molecule 6w77 (#2) to map cryosparc_P79_J62_009_volume_map.mrc z flip
(#44) using 47940 atoms
average map value = 0.03992, steps = 140
shifted from previous position = 11.3
rotated from previous position = 1.2 degrees
atoms outside contour = 42877, contour level = 0.12391
Position of 6w77 (#2) relative to cryosparc_P79_J62_009_volume_map.mrc z flip
(#44) coordinates:
Matrix rotation and translation
-0.67025051 0.73578274 0.09689218 153.68472764
0.24050956 0.09184167 0.96629206 -41.42818389
0.70208224 0.67096121 -0.23851970 9.02222878
Axis -0.35329820 -0.72397638 -0.59248509
Axis point 88.24312531 0.00000000 43.12369199
Rotation angle (degrees) 155.29397777
Shift along axis -29.64904753
> show #!44 models
> view matrix models
> #44,-0.88159,0.4661,0.074468,235.03,-0.26952,-0.6266,0.73125,187.99,0.3875,0.6246,0.67803,-114.07
> fitmap #2 inMap #44
Fit molecule 6w77 (#2) to map cryosparc_P79_J62_009_volume_map.mrc z flip
(#44) using 47940 atoms
average map value = 0.1074, steps = 316
shifted from previous position = 21.3
rotated from previous position = 27.1 degrees
atoms outside contour = 31196, contour level = 0.12391
Position of 6w77 (#2) relative to cryosparc_P79_J62_009_volume_map.mrc z flip
(#44) coordinates:
Matrix rotation and translation
0.13920317 -0.60098225 -0.78704694 384.10304242
0.65463305 -0.54049911 0.52850389 75.18144254
-0.74301960 -0.58879633 0.31818363 342.09334581
Axis -0.66453387 -0.02618603 0.74679919
Axis point 316.82296897 183.40717081 0.00000000
Rotation angle (degrees) 122.78963468
Shift along axis -1.74315210
> select subtract #44
Nothing selected
> fitmap #2 inMap #44
Fit molecule 6w77 (#2) to map cryosparc_P79_J62_009_volume_map.mrc z flip
(#44) using 47940 atoms
average map value = 0.1074, steps = 40
shifted from previous position = 0.00451
rotated from previous position = 0.00577 degrees
atoms outside contour = 31185, contour level = 0.12391
Position of 6w77 (#2) relative to cryosparc_P79_J62_009_volume_map.mrc z flip
(#44) coordinates:
Matrix rotation and translation
0.13915802 -0.60105654 -0.78699820 384.11124757
0.65461689 -0.54048607 0.52853725 75.17392206
-0.74304230 -0.58873248 0.31824877 342.07773054
Axis -0.66450733 -0.02614321 0.74682430
Axis point 316.81187870 183.39594010 0.00000000
Rotation angle (degrees) 122.78850918
Shift along axis -1.73806398
> volume #44 level 0.133
> volume #44 level 0.1443
> hide #!2 models
> show #!2 models
> volume #44 level 0.09338
> volume #44 level 0.1103
> volume #44 level 0.1262
> volume #44 step 2
> volume #44 level 0.03907
> volume #44 step 1
> volume #44 level 0.07752
> volume #44 level 0.1035
> volume #43 level 0.1015
> volume #44 level 0.1092
> volume #44 color darkgrey
> ui mousemode right zoom
> select add #42
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #42,-0.39067,-0.60736,-0.69173,476.59,-0.72937,0.66268,-0.16993,218.25,0.5616,0.43814,-0.70188,133.3
> volume #42 color darkgrey
> ui mousemode right "translate selected models"
> view matrix models
> #42,-0.39067,-0.60736,-0.69173,479.15,-0.72937,0.66268,-0.16993,236.53,0.5616,0.43814,-0.70188,157.74
> fitmap #2 inMap #42
Fit molecule 6w77 (#2) to map cryosparc_P79_J63_010_volume_map.mrc (#42) using
47940 atoms
average map value = 0.07948, steps = 440
shifted from previous position = 17.3
rotated from previous position = 39.1 degrees
atoms outside contour = 33086, contour level = 0.10672
Position of 6w77 (#2) relative to cryosparc_P79_J63_010_volume_map.mrc (#42)
coordinates:
Matrix rotation and translation
0.22795926 -0.56189747 -0.79517662 366.36640059
-0.96984461 -0.05870789 -0.23654776 361.39135628
0.08623244 0.82512100 -0.55833623 141.89822885
Axis 0.73783179 -0.61255605 -0.28351251
Axis point 0.00000000 291.23935339 246.85081779
Rotation angle (degrees) 133.99076515
Shift along axis 8.71439197
> select subtract #42
Nothing selected
> volume #42 level 0.1108
> hide #!42 models
> open /Users/TEST/Downloads/cryosparc_P50_J449_006_volume_map(1).mrc
Opened cryosparc_P50_J449_006_volume_map(1).mrc as #45, grid size 416,416,416,
pixel 0.855, shown at level 0.0609, step 2, values float32
> select add #45
2 models selected
> view matrix models #45,1,0,0,-25.201,0,1,0,21.425,0,0,1,22.672
> ui mousemode right "rotate selected models"
> view matrix models
> #45,-0.92491,-0.0029299,-0.38016,383.17,-0.13165,0.94057,0.31306,-5.3843,0.35665,0.3396,-0.87033,260.34
> view matrix models
> #45,0.016487,-0.88718,0.46113,214.85,0.99369,0.065709,0.090893,-2.6142,-0.11094,0.45672,0.88267,-16.706
> view matrix models
> #45,0.80387,-0.53746,0.25483,55.455,0.46328,0.83444,0.29847,-87.128,-0.37305,-0.12187,0.91977,124.66
> view matrix models
> #45,0.023464,-0.92435,0.38083,235.71,0.92071,0.16841,0.35204,-58.475,-0.38954,0.34237,0.85501,57.399
> ui mousemode right "translate selected models"
> view matrix models
> #45,0.023464,-0.92435,0.38083,270.11,0.92071,0.16841,0.35204,-68.331,-0.38954,0.34237,0.85501,58.988
> fitmap #2 inMap #45
Fit molecule 6w77 (#2) to map cryosparc_P50_J449_006_volume_map(1).mrc (#45)
using 47940 atoms
average map value = 0.08267, steps = 724
shifted from previous position = 5.72
rotated from previous position = 30.9 degrees
atoms outside contour = 25140, contour level = 0.06093
Position of 6w77 (#2) relative to cryosparc_P50_J449_006_volume_map(1).mrc
(#45) coordinates:
Matrix rotation and translation
-0.20522334 0.50407414 0.83892352 -13.21087530
-0.94631935 0.11651357 -0.30150340 350.76149169
-0.24972603 -0.85576508 0.45310381 266.18195374
Axis -0.29228377 0.57408731 -0.76484898
Axis point 107.07330503 281.26568992 -0.00000000
Rotation angle (degrees) 108.53011031
Shift along axis 1.64004932
> select subtract #45
Nothing selected
> color #45 darkgrey models
> volume #45 step 1
> volume #45 level 0.1118
> fitmap #2 inMap #45
Fit molecule 6w77 (#2) to map cryosparc_P50_J449_006_volume_map(1).mrc (#45)
using 47940 atoms
average map value = 0.08267, steps = 380
shifted from previous position = 0.0117
rotated from previous position = 0.0084 degrees
atoms outside contour = 32796, contour level = 0.11176
Position of 6w77 (#2) relative to cryosparc_P50_J449_006_volume_map(1).mrc
(#45) coordinates:
Matrix rotation and translation
-0.20522168 0.50403538 0.83894722 -13.21079107
-0.94635685 0.11640101 -0.30142917 350.76232586
-0.24958526 -0.85580323 0.45310932 266.16564042
Axis -0.29234848 0.57403627 -0.76486256
Axis point 107.05606241 281.24984651 0.00000000
Rotation angle (degrees) 108.53329432
Shift along axis 1.63231797
> volume #45 level 0.1105
> volume #45 level 0.1155
> fitmap #2 inMap #45
Fit molecule 6w77 (#2) to map cryosparc_P50_J449_006_volume_map(1).mrc (#45)
using 47940 atoms
average map value = 0.08267, steps = 588
shifted from previous position = 0.0129
rotated from previous position = 0.0113 degrees
atoms outside contour = 33279, contour level = 0.11548
Position of 6w77 (#2) relative to cryosparc_P50_J449_006_volume_map(1).mrc
(#45) coordinates:
Matrix rotation and translation
-0.20522003 0.50415135 0.83887793 -13.21219515
-0.94631434 0.11650707 -0.30152163 350.76380778
-0.24974774 -0.85572048 0.45317607 266.16360398
Axis -0.29224707 0.57406771 -0.76487771
Axis point 107.08549151 281.25335053 -0.00000000
Rotation angle (degrees) 108.52802321
Shift along axis 1.64079099
> select add #38
2 models selected
> select add #39
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #38,-0.12373,-0.98131,0.14738,342.67,0.88644,-0.042552,0.46088,-60.603,-0.446,0.18768,0.87514,70.081,#39,-0.12973,-0.98017,0.1498,342.85,0.87976,-0.044096,0.47337,-62.062,-0.45737,0.1932,0.86804,72.519
> ui mousemode right "translate selected models"
> view matrix models
> #38,-0.12373,-0.98131,0.14738,353.77,0.88644,-0.042552,0.46088,-47.803,-0.446,0.18768,0.87514,91.278,#39,-0.12973,-0.98017,0.1498,353.95,0.87976,-0.044096,0.47337,-49.262,-0.45737,0.1932,0.86804,93.716
> select subtract #38
2 models selected
> select subtract #39
Nothing selected
> hide #!45 models
> hide #!39 models
> fitmap #2 inMap #38
Fit molecule 6w77 (#2) to map cryosparc_P50_J498_006_volume_map.mrc (#38)
using 47940 atoms
average map value = 0.07566, steps = 660
shifted from previous position = 11.9
rotated from previous position = 16.7 degrees
atoms outside contour = 31583, contour level = 0.099845
Position of 6w77 (#2) relative to cryosparc_P50_J498_006_volume_map.mrc (#38)
coordinates:
Matrix rotation and translation
-0.20358204 0.49472998 0.84486485 -13.67204776
-0.94674299 0.12039884 -0.29863330 349.65483166
-0.24946359 -0.86066624 0.44387110 268.95453884
Axis -0.29657677 0.57746152 -0.76064474
Axis point 105.38219114 283.17762613 0.00000000
Rotation angle (degrees) 108.64212548
Shift along axis 1.38816733
> show #!39 models
> vop subtract #38 #39 minrms True
Opened volume difference as #46, grid size 416,416,416, pixel 0.855, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P50_J497_007_volume_map.mrc #39" above
level 0.11588 is 0.90118
> show #!38 models
> show #!39 models
> hide #!39 models
> hide #!38 models
> show #!39 models
> hide #!39 models
> show #!37 models
> hide #!37 models
> show #!38 models
> show #!39 models
> hide #!39 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> volume #38 color silver
> volume #38 color darkgrey
> open /Users/TEST/Downloads/cryosparc_P50_J451_003_volume_map.mrc
Opened cryosparc_P50_J451_003_volume_map.mrc as #47, grid size 416,416,416,
pixel 0.855, shown at level 0.089, step 2, values float32
> volume #47 step 1
> volume #47 level 0.124
> volume #46 level 0.05387
> close #46
> fitmap #2 inMap #39
Fit molecule 6w77 (#2) to map cryosparc_P50_J497_007_volume_map.mrc (#39)
using 47940 atoms
average map value = 0.07962, steps = 80
shifted from previous position = 0.176
rotated from previous position = 0.144 degrees
atoms outside contour = 33481, contour level = 0.11588
Position of 6w77 (#2) relative to cryosparc_P50_J497_007_volume_map.mrc (#39)
coordinates:
Matrix rotation and translation
-0.20392622 0.50501384 0.83867463 -13.55412019
-0.94721300 0.11470009 -0.29938511 350.41753898
-0.24738967 -0.85545598 0.45496531 266.04420583
Axis -0.29316820 0.57258803 -0.76563395
Axis point 106.81241166 280.93664845 0.00000000
Rotation angle (degrees) 108.48947269
Shift along axis 0.92604914
> volume #39 color #929292
> open /Users/TEST/Downloads/cryosparc_P50_J473_005_volume_map.mrc
Opened cryosparc_P50_J473_005_volume_map.mrc as #46, grid size 416,416,416,
pixel 0.855, shown at level 0.0906, step 2, values float32
> volume #46 step 1
> select add #46
2 models selected
> view matrix models #46,1,0,0,7.4835,0,1,0,29.679,0,0,1,35.757
> ui mousemode right "rotate selected models"
> view matrix models
> #46,-0.2319,-0.97261,0.016179,383.71,0.77399,-0.17442,0.6087,-25.381,-0.5892,0.15368,0.79324,152.85
> fitmap #2 inMap #46
Fit molecule 6w77 (#2) to map cryosparc_P50_J473_005_volume_map.mrc (#46)
using 47940 atoms
average map value = 0.1305, steps = 256
shifted from previous position = 20.5
rotated from previous position = 13.4 degrees
atoms outside contour = 17533, contour level = 0.090591
Position of 6w77 (#2) relative to cryosparc_P50_J473_005_volume_map.mrc (#46)
coordinates:
Matrix rotation and translation
-0.20105148 0.49385320 0.84598307 -13.75441338
-0.94766413 0.12059702 -0.29561644 348.75078875
-0.24801415 -0.86114191 0.44376075 269.18805601
Axis -0.29828101 0.57701839 -0.76031455
Axis point 105.05132626 282.93105149 0.00000000
Rotation angle (degrees) 108.56297880
Shift along axis 0.67070062
> hide #!46 models
> show #!46 models
> select subtract #46
Nothing selected
> volume #46 level 0.1026
> volume #46 color darkgrey
> volume #46 level 0.1107
> fitmap #2 inMap #46
Fit molecule 6w77 (#2) to map cryosparc_P50_J473_005_volume_map.mrc (#46)
using 47940 atoms
average map value = 0.1305, steps = 116
shifted from previous position = 0.00473
rotated from previous position = 0.00462 degrees
atoms outside contour = 23141, contour level = 0.11068
Position of 6w77 (#2) relative to cryosparc_P50_J473_005_volume_map.mrc (#46)
coordinates:
Matrix rotation and translation
-0.20104783 0.49384026 0.84599149 -13.75336666
-0.94768523 0.12053273 -0.29557504 348.75346662
-0.24793650 -0.86115833 0.44377227 269.17756856
Axis -0.29831410 0.57698689 -0.76032547
Axis point 105.04437720 282.92119830 0.00000000
Rotation angle (degrees) 108.56446348
Shift along axis 0.66644195
> select #2/A:1408-1493
1848 atoms, 2069 bonds, 87 pseudobonds, 86 residues, 2 models selected
> color zone #46 near sel distance 5
> select add #2
47940 atoms, 52058 bonds, 1470 pseudobonds, 3468 residues, 3 models selected
> select subtract #2
Nothing selected
> volume #46 level 0.09863
> open /Users/TEST/Downloads/cryosparc_P50_J475_006_volume_map.mrc
Opened cryosparc_P50_J475_006_volume_map.mrc as #48, grid size 416,416,416,
pixel 0.855, shown at level 0.0914, step 2, values float32
> select add #48
2 models selected
> view matrix models
> #48,-0.4466,-0.3772,0.81134,176.98,-0.79048,-0.25846,-0.55528,440.19,0.41915,-0.88934,-0.18274,274.67
> view matrix models
> #48,-0.39019,-0.842,0.37255,318.24,0.60079,0.073781,0.796,-96.688,-0.69771,0.53441,0.47707,129.42
> view matrix models
> #48,-0.77504,-0.57886,0.25345,365.2,0.51434,-0.34486,0.78519,-12.013,-0.36711,0.73891,0.56501,22.28
> ui mousemode right "translate selected models"
> view matrix models
> #48,-0.77504,-0.57886,0.25345,350.47,0.51434,-0.34486,0.78519,26.532,-0.36711,0.73891,0.56501,70.766
> hide #!46 models
> view matrix models
> #48,-0.77504,-0.57886,0.25345,373,0.51434,-0.34486,0.78519,28.184,-0.36711,0.73891,0.56501,54.124
> fitmap #2 inMap #48
Fit molecule 6w77 (#2) to map cryosparc_P50_J475_006_volume_map.mrc (#48)
using 47940 atoms
average map value = 0.1193, steps = 560
shifted from previous position = 8.82
rotated from previous position = 43.3 degrees
atoms outside contour = 18938, contour level = 0.091353
Position of 6w77 (#2) relative to cryosparc_P50_J475_006_volume_map.mrc (#48)
coordinates:
Matrix rotation and translation
-0.19840262 0.49226895 0.84753038 -14.23755100
-0.94798485 0.12323080 -0.29349435 347.96718822
-0.24891999 -0.86167598 0.44221418 269.80250254
Axis -0.29948444 0.57793107 -0.75914738
Axis point 104.65263747 283.36196069 0.00000000
Rotation angle (degrees) 108.45011139
Shift along axis 0.54511296
> select subtract #48
Nothing selected
> volume #48 step 1
> volume #48 level 0.09956
> volume #48 level 0.1119
> volume #48 color darkgrey
> volume #48 color #929292
> volume #48 color darkgrey
> fitmap #2 inMap #48
Fit molecule 6w77 (#2) to map cryosparc_P50_J475_006_volume_map.mrc (#48)
using 47940 atoms
average map value = 0.1193, steps = 48
shifted from previous position = 0.0162
rotated from previous position = 0.0107 degrees
atoms outside contour = 24133, contour level = 0.11188
Position of 6w77 (#2) relative to cryosparc_P50_J475_006_volume_map.mrc (#48)
coordinates:
Matrix rotation and translation
-0.19851935 0.49214111 0.84757728 -14.22088772
-0.94795636 0.12323376 -0.29358513 347.98072945
-0.24893544 -0.86174858 0.44206400 269.83853059
Axis -0.29948876 0.57799077 -0.75910022
Axis point 104.63976763 283.38967769 0.00000000
Rotation angle (degrees) 108.45808308
Shift along axis 0.55415802
> volume #48 level 0.1057
> open /Users/TEST/Downloads/cryosparc_P50_J455_007_volume_map.mrc
Opened cryosparc_P50_J455_007_volume_map.mrc as #49, grid size 416,416,416,
pixel 0.855, shown at level 0.0631, step 2, values float32
> volume #49 step 1
> select add #49
2 models selected
> view matrix models #49,1,0,0,-6.557,0,1,0,19.7,0,0,1,63.097
> ui mousemode right "rotate selected models"
> view matrix models
> #49,0.86832,-0.43541,0.23757,45.809,-0.3241,-0.86064,-0.39276,460.9,0.37548,0.26404,-0.88843,300.71
> select subtract #49
Nothing selected
> volume flip #49
Opened cryosparc_P50_J455_007_volume_map.mrc z flip as #50, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> select add #50
2 models selected
> view matrix models
> #50,-0.94114,-0.326,0.089339,365.54,0.24812,-0.4868,0.83753,88.581,-0.22954,0.8104,0.53903,69.125
> ui mousemode right "translate selected models"
> view matrix models
> #50,-0.94114,-0.326,0.089339,374.3,0.24812,-0.4868,0.83753,89.862,-0.22954,0.8104,0.53903,19.017
> select subtract #50
Nothing selected
> fitmap #2 inMap #50
Fit molecule 6w77 (#2) to map cryosparc_P50_J455_007_volume_map.mrc z flip
(#50) using 47940 atoms
average map value = 0.09446, steps = 308
shifted from previous position = 12.8
rotated from previous position = 19.7 degrees
atoms outside contour = 23095, contour level = 0.063068
Position of 6w77 (#2) relative to cryosparc_P50_J455_007_volume_map.mrc z flip
(#50) coordinates:
Matrix rotation and translation
-0.19676605 0.49589665 0.84579531 -14.80131493
-0.94898258 0.12047476 -0.29140689 348.25319422
-0.24640468 -0.85998395 0.44689192 267.36583400
Axis -0.29950604 0.57533184 -0.76111064
Axis point 104.81407070 282.01461224 0.00000000
Rotation angle (degrees) 108.34268447
Shift along axis 1.29925409
> volume #50 level 0.1145
> volume #50 level 0.1157
> volume #50 level 0.1238
> volume #50 level 0.1051
> volume #50 level 0.08995
> hide #!50 models
> show #!50 models
> hide #!2 models
> volume #50 level 0.1016
> show #!2 models
> fitmap #2 inMap #50
Fit molecule 6w77 (#2) to map cryosparc_P50_J455_007_volume_map.mrc z flip
(#50) using 47940 atoms
average map value = 0.09446, steps = 64
shifted from previous position = 0.00698
rotated from previous position = 0.00295 degrees
atoms outside contour = 29343, contour level = 0.10163
Position of 6w77 (#2) relative to cryosparc_P50_J455_007_volume_map.mrc z flip
(#50) coordinates:
Matrix rotation and translation
-0.19673467 0.49593461 0.84578035 -14.80334458
-0.94898702 0.12048390 -0.29138864 348.24788375
-0.24641262 -0.85996078 0.44693212 267.35645951
Axis -0.29949922 0.57532004 -0.76112224
Axis point 104.81997473 282.00634183 -0.00000000
Rotation angle (degrees) 108.34024824
Shift along axis 1.29662708
> volume #50 level 0.04904
> volume #50 level 0.1215
> volume #50 level 0.09579
> volume #50 level 0.1157
> volume #50 level 0.1262
> fitmap #2 inMap #50
Fit molecule 6w77 (#2) to map cryosparc_P50_J455_007_volume_map.mrc z flip
(#50) using 47940 atoms
average map value = 0.09446, steps = 64
shifted from previous position = 0.00439
rotated from previous position = 0.000938 degrees
atoms outside contour = 32705, contour level = 0.12617
Position of 6w77 (#2) relative to cryosparc_P50_J455_007_volume_map.mrc z flip
(#50) coordinates:
Matrix rotation and translation
-0.19674198 0.49592278 0.84578559 -14.80397016
-0.94898794 0.12047598 -0.29138892 348.25217769
-0.24640324 -0.85996871 0.44692204 267.35612746
Axis -0.29950458 0.57532040 -0.76111986
Axis point 104.81783586 282.00842892 0.00000000
Rotation angle (degrees) 108.34101196
Shift along axis 1.30037996
> volume #50 level 0.1063
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #50 level 0.1203
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #50
Fit molecule 6w77 (#2) to map cryosparc_P50_J455_007_volume_map.mrc z flip
(#50) using 47940 atoms
average map value = 0.09446, steps = 120
shifted from previous position = 0.00132
rotated from previous position = 0.00278 degrees
atoms outside contour = 31925, contour level = 0.12033
Position of 6w77 (#2) relative to cryosparc_P50_J455_007_volume_map.mrc z flip
(#50) coordinates:
Matrix rotation and translation
-0.19674422 0.49593325 0.84577893 -14.80386294
-0.94897533 0.12051369 -0.29141439 348.24694585
-0.24645002 -0.85995739 0.44691803 267.36213730
Axis -0.29948355 0.57533837 -0.76111455
Axis point 104.82163556 282.01211039 0.00000000
Rotation angle (degrees) 108.34006267
Shift along axis 1.30013053
> open /Users/TEST/Downloads/cryosparc_P50_J456_006_volume_map.mrc
Opened cryosparc_P50_J456_006_volume_map.mrc as #51, grid size 416,416,416,
pixel 0.855, shown at level 0.0844, step 2, values float32
> hide #!50 models
> select add #51
2 models selected
> view matrix models #51,1,0,0,-11.416,0,1,0,15.044,0,0,1,56.6
> view matrix models #51,1,0,0,-7.0929,0,1,0,4.5604,0,0,1,31.689
> ui mousemode right "rotate selected models"
> view matrix models
> #51,-0.96704,-0.039266,0.25158,297.11,-0.058685,0.99581,-0.070154,28.436,-0.24777,-0.082606,-0.96529,450.59
> select subtract #51
Nothing selected
> volume flip #51
Opened cryosparc_P50_J456_006_volume_map.mrc z flip as #52, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> select add #52
2 models selected
> view matrix models
> #52,-0.86334,-0.50409,-0.023218,401.5,0.33986,-0.61485,0.71165,87.159,-0.37301,0.60651,0.70215,75.65
> ui mousemode right "translate selected models"
> view matrix models
> #52,-0.86334,-0.50409,-0.023218,413.33,0.33986,-0.61485,0.71165,109.78,-0.37301,0.60651,0.70215,44.742
> fitmap #2 inMap #52
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#52) using 47940 atoms
average map value = 0.1036, steps = 304
shifted from previous position = 9.9
rotated from previous position = 17.3 degrees
atoms outside contour = 21892, contour level = 0.084412
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#52) coordinates:
Matrix rotation and translation
-0.20191408 0.49707416 0.84388868 -13.68313983
-0.94684893 0.12123372 -0.29795905 349.09877827
-0.25041549 -0.85919717 0.44617531 268.12434440
Axis -0.29590518 0.57695703 -0.76128885
Axis point 105.75180251 282.43285882 -0.00000000
Rotation angle (degrees) 108.49684928
Shift along axis 1.34383034
> select subtract #52
Nothing selected
> volume #52 color silver
> volume #52 level 0.09098
> volume #52 level 0.1019
> fitmap #2 inMap #52
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#52) using 47940 atoms
average map value = 0.1036, steps = 100
shifted from previous position = 0.00563
rotated from previous position = 0.00554 degrees
atoms outside contour = 26060, contour level = 0.10194
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#52) coordinates:
Matrix rotation and translation
-0.20195900 0.49699617 0.84392386 -13.67347836
-0.94684517 0.12121970 -0.29797668 349.10593941
-0.25039345 -0.85924426 0.44609699 268.14334044
Axis -0.29592788 0.57697792 -0.76126419
Axis point 105.74311296 282.44560757 0.00000000
Rotation angle (degrees) 108.50099598
Shift along axis 1.34486154
> volume #52 color darkgrey
> fitmap #2 inMap #52
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#52) using 47940 atoms
average map value = 0.1036, steps = 116
shifted from previous position = 0.00355
rotated from previous position = 0.00285 degrees
atoms outside contour = 26059, contour level = 0.10194
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#52) coordinates:
Matrix rotation and translation
-0.20194211 0.49699040 0.84393130 -13.67506866
-0.94686046 0.12118975 -0.29794028 349.10470106
-0.25034926 -0.85925182 0.44610722 268.13381133
Axis -0.29595121 0.57695884 -0.76126959
Axis point 105.73864451 282.43808738 0.00000000
Rotation angle (degrees) 108.50108145
Shift along axis 1.34408004
> volume #52 level 0.1052
> fitmap #2 inMap #52
Fit molecule 6w77 (#2) to map cryosparc_P50_J456_006_volume_map.mrc z flip
(#52) using 47940 atoms
average map value = 0.1036, steps = 172
shifted from previous position = 0.0108
rotated from previous position = 0.00694 degrees
atoms outside contour = 26824, contour level = 0.10522
Position of 6w77 (#2) relative to cryosparc_P50_J456_006_volume_map.mrc z flip
(#52) coordinates:
Matrix rotation and translation
-0.20191597 0.49705804 0.84389772 -13.68263094
-0.94683899 0.12127123 -0.29797538 349.09733732
-0.25045155 -0.85920119 0.44614731 268.14548072
Axis -0.29589830 0.57698003 -0.76127409
Axis point 105.75275827 282.44680569 0.00000000
Rotation angle (degrees) 108.49661921
Shift along axis 1.33865167
> open /Users/TEST/Downloads/cryosparc_P50_J457_007_volume_map.mrc
Opened cryosparc_P50_J457_007_volume_map.mrc as #53, grid size 416,416,416,
pixel 0.855, shown at level 0.0789, step 2, values float32
> volume #53 step 1
> volume flip #53
Opened cryosparc_P50_J457_007_volume_map.mrc z flip as #54, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> select add #54
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #54,-0.93255,-0.28401,-0.22291,425.3,0.011858,-0.64117,0.76731,135.76,-0.36085,0.71291,0.60129,14.904
> ui mousemode right "translate selected models"
> view matrix models
> #54,-0.93255,-0.28401,-0.22291,416.61,0.011858,-0.64117,0.76731,168.23,-0.36085,0.71291,0.60129,49.743
> fitmap #2 inMap #54
Fit molecule 6w77 (#2) to map cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) using 47940 atoms
average map value = 0.09551, steps = 376
shifted from previous position = 11.3
rotated from previous position = 19.3 degrees
atoms outside contour = 22884, contour level = 0.078909
Position of 6w77 (#2) relative to cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) coordinates:
Matrix rotation and translation
-0.20433783 0.49602770 0.84392096 -13.45296857
-0.94645531 0.12000763 -0.29970073 349.53984996
-0.24993681 -0.85997367 0.44494595 268.32855584
Axis -0.29565184 0.57722057 -0.76118750
Axis point 105.60810871 282.64570506 0.00000000
Rotation angle (degrees) 108.64430713
Shift along axis 1.49064459
> volume #53 level 0.08575
> volume #54 level 0.1014
> select subtract #54
Nothing selected
> color #54 darkgrey models
> fitmap #2 inMap #54
Fit molecule 6w77 (#2) to map cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) using 47940 atoms
average map value = 0.09551, steps = 160
shifted from previous position = 0.0161
rotated from previous position = 0.00633 degrees
atoms outside contour = 28510, contour level = 0.10139
Position of 6w77 (#2) relative to cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) coordinates:
Matrix rotation and translation
-0.20431217 0.49607276 0.84390069 -13.45878315
-0.94643407 0.12009602 -0.29973238 349.53049145
-0.25003818 -0.85993533 0.44496308 268.35149619
Axis -0.29560801 0.57724988 -0.76118229
Axis point 105.61956848 282.66025690 -0.00000000
Rotation angle (degrees) 108.64034091
Shift along axis 1.48055107
> hide #!2 models
> volume #54 level 0.06523
> volume #54 level 0.1102
> volume #54 level 0.0965
> show #!2 models
> fitmap #2 inMap #54
Fit molecule 6w77 (#2) to map cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) using 47940 atoms
average map value = 0.09551, steps = 104
shifted from previous position = 0.0127
rotated from previous position = 0.00865 degrees
atoms outside contour = 27373, contour level = 0.0965
Position of 6w77 (#2) relative to cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) coordinates:
Matrix rotation and translation
-0.20434818 0.49598381 0.84394425 -13.44775174
-0.94645898 0.11999793 -0.29969302 349.53688619
-0.24991445 -0.86000033 0.44490697 268.34099354
Axis -0.29567309 0.57722712 -0.76117428
Axis point 105.60149552 282.65021047 0.00000000
Rotation angle (degrees) 108.64609173
Shift along axis 1.48404725
> volume #54 level 0.1121
> hide #!2 models
> volume #54 level 0.1033
> show #!2 models
> fitmap #2 inMap #54
Fit molecule 6w77 (#2) to map cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) using 47940 atoms
average map value = 0.09551, steps = 136
shifted from previous position = 0.00854
rotated from previous position = 0.00575 degrees
atoms outside contour = 28942, contour level = 0.10334
Position of 6w77 (#2) relative to cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) coordinates:
Matrix rotation and translation
-0.20436315 0.49601064 0.84392485 -13.44580407
-0.94643086 0.12006684 -0.29975420 349.53676985
-0.25000866 -0.85997524 0.44490254 268.34654160
Axis -0.29562495 0.57726152 -0.76116689
Axis point 105.61310996 282.65746644 0.00000000
Rotation angle (degrees) 108.64459488
Shift along axis 1.49253917
> fitmap #2 inMap #54
Fit molecule 6w77 (#2) to map cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) using 47940 atoms
average map value = 0.09551, steps = 124
shifted from previous position = 0.0187
rotated from previous position = 0.00461 degrees
atoms outside contour = 28952, contour level = 0.10334
Position of 6w77 (#2) relative to cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) coordinates:
Matrix rotation and translation
-0.20435456 0.49603915 0.84391018 -13.45241970
-0.94644926 0.12000394 -0.29972131 349.54415848
-0.24994605 -0.85996757 0.44495253 268.34534891
Axis -0.29563849 0.57722117 -0.76119222
Axis point 105.61072599 282.65499703 0.00000000
Rotation angle (degrees) 108.64472513
Shift along axis 1.47894998
> volume #54 level 0.0623
> volume #54 level 0.08868
> volume #54 level 0.09552
> fitmap #2 inMap #54
Fit molecule 6w77 (#2) to map cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) using 47940 atoms
average map value = 0.09551, steps = 140
shifted from previous position = 0.00535
rotated from previous position = 0.0029 degrees
atoms outside contour = 27143, contour level = 0.095522
Position of 6w77 (#2) relative to cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) coordinates:
Matrix rotation and translation
-0.20435471 0.49605470 0.84390100 -13.45383790
-0.94643644 0.12004231 -0.29974640 349.54441269
-0.24999444 -0.85995325 0.44495303 268.34788337
Axis -0.29561565 0.57723789 -0.76118842
Axis point 105.61635262 282.65966356 0.00000000
Rotation angle (degrees) 108.64355444
Shift along axis 1.48414249
> volume #54 level 0.09064
> fitmap #2 inMap #54
Fit molecule 6w77 (#2) to map cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) using 47940 atoms
average map value = 0.09551, steps = 104
shifted from previous position = 0.00558
rotated from previous position = 0.00314 degrees
atoms outside contour = 25936, contour level = 0.090636
Position of 6w77 (#2) relative to cryosparc_P50_J457_007_volume_map.mrc z flip
(#54) coordinates:
Matrix rotation and translation
-0.20431051 0.49607257 0.84390120 -13.45920520
-0.94643782 0.12008523 -0.29972487 349.53117939
-0.25002536 -0.85993695 0.44496717 268.34755956
Axis -0.29561309 0.57724390 -0.76118485
Axis point 105.61849586 282.65775664 -0.00000000
Rotation angle (degrees) 108.64049304
Shift along axis 1.48136064
> hide #!2 models
> fitmap #52 inMap #54
Fit map cryosparc_P50_J456_006_volume_map.mrc z flip in map
cryosparc_P50_J457_007_volume_map.mrc z flip using 498959 points
correlation = 0.958, correlation about mean = 0.7545, overlap = 1.107e+04
steps = 296, shift = 11.2, angle = 19.4 degrees
Position of cryosparc_P50_J456_006_volume_map.mrc z flip (#52) relative to
cryosparc_P50_J457_007_volume_map.mrc z flip (#54) coordinates:
Matrix rotation and translation
0.99999445 -0.00258221 -0.00208286 0.82109354
0.00258209 0.99999662 -0.00005745 -0.55742574
0.00208300 0.00005207 0.99999779 -0.50966943
Axis 0.01650493 -0.62776851 0.77822509
Axis point 224.35177668 317.71534559 0.00000000
Rotation angle (degrees) 0.19010751
Shift along axis -0.03315112
> hide #!52 models
> show #!2 models
> hide #!54 models
> open /Users/TEST/Downloads/cryosparc_P50_J458_006_volume_map.mrc
Opened cryosparc_P50_J458_006_volume_map.mrc as #55, grid size 416,416,416,
pixel 0.855, shown at level 0.0852, step 2, values float32
> volume #55 step 1
> select add #55
2 models selected
> view matrix models #55,1,0,0,-11.694,0,1,0,22.903,0,0,1,16.412
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #55,-0.94265,-0.073201,0.32566,290.1,-0.035687,0.99217,0.11972,8.4985,-0.33188,0.10123,-0.93788,417.61
> volume flip #55
Opened cryosparc_P50_J458_006_volume_map.mrc z flip as #56, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> view matrix models
> #55,-0.94265,-0.073201,0.32566,290.1,-0.035687,0.99217,0.11972,8.4985,-0.33188,0.10123,-0.93788,417.61
> select subtract #55
Nothing selected
> select add #56
2 models selected
> view matrix models
> #56,-0.89083,-0.19623,-0.40977,425.76,-0.20154,-0.63764,0.7435,194.31,-0.40718,0.74492,0.52848,78.003
> fitmap #2 inMap #56
Fit molecule 6w77 (#2) to map cryosparc_P50_J458_006_volume_map.mrc z flip
(#56) using 47940 atoms
average map value = 0.1054, steps = 248
shifted from previous position = 19.6
rotated from previous position = 12.6 degrees
atoms outside contour = 22481, contour level = 0.085174
Position of 6w77 (#2) relative to cryosparc_P50_J458_006_volume_map.mrc z flip
(#56) coordinates:
Matrix rotation and translation
-0.19821813 0.50003767 0.84301361 -14.28069023
-0.94756668 0.12218519 -0.29527648 348.48873744
-0.25065314 -0.85734075 0.44959971 267.20707654
Axis -0.29592244 0.57580698 -0.76215236
Axis point 105.98022819 281.78366075 0.00000000
Rotation angle (degrees) 108.25318560
Shift along axis 1.23572115
> volume #56 color darkgrey
> volume #56 level 0.09753
> volume #56 level 0.03686
> volume #56 level 0.05821
> volume #56 level 0.09416
> select subtract #56
Nothing selected
> volume #56 level 0.05147
> volume #56 level 0.08854
> fitmap #2 inMap #56
Fit molecule 6w77 (#2) to map cryosparc_P50_J458_006_volume_map.mrc z flip
(#56) using 47940 atoms
average map value = 0.1054, steps = 144
shifted from previous position = 0.00531
rotated from previous position = 0.00174 degrees
atoms outside contour = 23347, contour level = 0.088545
Position of 6w77 (#2) relative to cryosparc_P50_J458_006_volume_map.mrc z flip
(#56) coordinates:
Matrix rotation and translation
-0.19824046 0.50004322 0.84300507 -14.27463785
-0.94755740 0.12218822 -0.29530500 348.49483709
-0.25067055 -0.85733708 0.44959699 267.20615704
Axis -0.29590662 0.57581386 -0.76215331
Axis point 105.98575569 281.78388214 0.00000000
Rotation angle (degrees) 108.25384978
Shift along axis 1.24005801
> open /Users/TEST/Downloads/cryosparc_P50_J461_006_volume_map.mrc
Opened cryosparc_P50_J461_006_volume_map.mrc as #57, grid size 416,416,416,
pixel 0.855, shown at level 0.0754, step 2, values float32
> hide #!56 models
> select add #57
2 models selected
> view matrix models
> #57,-0.82503,0.082081,0.55909,193.31,0.13085,0.99025,0.047712,-28.984,-0.54973,0.11252,-0.82773,402.08
> select subtract #57
Nothing selected
> volume flip #57
Opened cryosparc_P50_J461_006_volume_map.mrc z flip as #58, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> select add #58
2 models selected
> view matrix models
> #58,-0.39985,-0.47788,0.78214,173.53,0.84952,0.12717,0.512,-91.112,-0.34414,0.86917,0.35512,38.955
> view matrix models
> #58,-0.83778,-0.078607,-0.54032,413.66,-0.10571,-0.94751,0.30174,278.16,-0.53568,0.30991,0.7855,85.702
> ui mousemode right "translate selected models"
> view matrix models
> #58,-0.83778,-0.078607,-0.54032,392.54,-0.10571,-0.94751,0.30174,295.58,-0.53568,0.30991,0.7855,117.86
> volume #58 color darkgrey
> fitmap #2 inMap #58
Fit molecule 6w77 (#2) to map cryosparc_P50_J461_006_volume_map.mrc z flip
(#58) using 47940 atoms
average map value = 0.09453, steps = 452
shifted from previous position = 28.6
rotated from previous position = 32.2 degrees
atoms outside contour = 22887, contour level = 0.075428
Position of 6w77 (#2) relative to cryosparc_P50_J461_006_volume_map.mrc z flip
(#58) coordinates:
Matrix rotation and translation
-0.20240011 0.49772132 0.84339056 -13.84118250
-0.94782520 0.11703503 -0.29653017 349.47791942
-0.24629564 -0.85940459 0.44806492 267.33246110
Axis -0.29691465 0.57480637 -0.76252168
Axis point 105.44591909 281.86335767 0.00000000
Rotation angle (degrees) 108.58130726
Shift along axis 1.14498717
> volume #58 level 0.1002
> select subtract #58
Nothing selected
> volume #58 level 0.06949
> volume #58 level 0.09719
> fitmap #2 inMap #58
Fit molecule 6w77 (#2) to map cryosparc_P50_J461_006_volume_map.mrc z flip
(#58) using 47940 atoms
average map value = 0.09453, steps = 140
shifted from previous position = 0.00393
rotated from previous position = 0.00668 degrees
atoms outside contour = 28222, contour level = 0.097193
Position of 6w77 (#2) relative to cryosparc_P50_J461_006_volume_map.mrc z flip
(#58) coordinates:
Matrix rotation and translation
-0.20239870 0.49769629 0.84340567 -13.84016152
-0.94785476 0.11694240 -0.29647224 349.48441578
-0.24618303 -0.85943169 0.44807482 267.31707971
Axis -0.29696379 0.57476323 -0.76253507
Axis point 105.43524550 281.85096429 0.00000000
Rotation angle (degrees) 108.58376517
Shift along axis 1.14217083
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #58
Fit molecule 6w77 (#2) to map cryosparc_P50_J461_006_volume_map.mrc z flip
(#58) using 47940 atoms
average map value = 0.09453, steps = 120
shifted from previous position = 0.00638
rotated from previous position = 0.00463 degrees
atoms outside contour = 28213, contour level = 0.097193
Position of 6w77 (#2) relative to cryosparc_P50_J461_006_volume_map.mrc z flip
(#58) coordinates:
Matrix rotation and translation
-0.20233351 0.49774074 0.84339509 -13.85345701
-0.94786213 0.11698105 -0.29643343 349.46718037
-0.24620825 -0.85940069 0.44812042 267.30831234
Axis -0.29696005 0.57475572 -0.76254219
Axis point 105.43651060 281.84406286 -0.00000000
Rotation angle (degrees) 108.57924845
Shift along axis 1.13831750
> open /Users/TEST/Downloads/cryosparc_P50_J462_006_volume_map.mrc
Opened cryosparc_P50_J462_006_volume_map.mrc as #59, grid size 416,416,416,
pixel 0.855, shown at level 0.0849, step 2, values float32
> volume flip #59
Opened cryosparc_P50_J462_006_volume_map.mrc z flip as #60, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> select add #60
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #60,-0.95392,-0.21656,-0.20772,415.5,0.13255,-0.92513,0.35577,226.83,-0.26921,0.31184,0.9112,12.328
> ui mousemode right "translate selected models"
> view matrix models
> #60,-0.95392,-0.21656,-0.20772,394.5,0.13255,-0.92513,0.35577,235.1,-0.26921,0.31184,0.9112,56.61
> ui mousemode right "rotate selected models"
> view matrix models
> #60,-0.82077,-0.2969,-0.48804,432.28,0.12592,-0.92734,0.35239,237.21,-0.5572,0.22778,0.79853,140.42
> view matrix models
> #60,-0.81985,-0.29549,-0.49044,432.3,0.12426,-0.92795,0.35138,237.77,-0.55894,0.22714,0.79749,141
> view matrix models
> #60,-0.81969,-0.29118,-0.49328,432.06,0.11821,-0.92861,0.35173,238.89,-0.56048,0.23,0.79559,141.14
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #60,-0.81969,-0.29118,-0.49328,414.13,0.11821,-0.92861,0.35173,260.61,-0.56048,0.23,0.79559,138.72
> view matrix models
> #60,-0.81969,-0.29118,-0.49328,420.57,0.11821,-0.92861,0.35173,253.09,-0.56048,0.23,0.79559,139.32
> fitmap #2 inMap #60
Fit molecule 6w77 (#2) to map cryosparc_P50_J462_006_volume_map.mrc z flip
(#60) using 47940 atoms
average map value = 0.105, steps = 220
shifted from previous position = 9.55
rotated from previous position = 13.4 degrees
atoms outside contour = 21670, contour level = 0.084943
Position of 6w77 (#2) relative to cryosparc_P50_J462_006_volume_map.mrc z flip
(#60) coordinates:
Matrix rotation and translation
-0.20377121 0.49574999 0.84422110 -13.21980785
-0.94650123 0.12063965 -0.29930169 349.35024028
-0.25022534 -0.86004537 0.44464508 268.41349512
Axis -0.29585299 0.57743898 -0.76094365
Axis point 105.72819286 282.56285162 -0.00000000
Rotation angle (degrees) 108.61716539
Shift along axis 1.39202033
> select subtract #60
Nothing selected
> volume #60 level 0.06132
> volume #60 level 0.07098
> volume #60 level 0.09461
> volume #60 level 0.0989
> hide #!2 models
> fitmap #58 inMap #60
Fit map cryosparc_P50_J461_006_volume_map.mrc z flip in map
cryosparc_P50_J462_006_volume_map.mrc z flip using 456567 points
correlation = 0.9679, correlation about mean = 0.7999, overlap = 1.074e+04
steps = 216, shift = 11, angle = 13.5 degrees
Position of cryosparc_P50_J461_006_volume_map.mrc z flip (#58) relative to
cryosparc_P50_J462_006_volume_map.mrc z flip (#60) coordinates:
Matrix rotation and translation
0.99999841 0.00177735 -0.00026117 -0.04048959
-0.00177831 0.99999147 -0.00373508 1.13552987
0.00025452 0.00373554 0.99999302 -0.78339123
Axis 0.90119510 -0.06220808 -0.42892604
Axis point 0.00000000 184.00809828 307.40800695
Rotation angle (degrees) 0.23748263
Shift along axis 0.22888874
> volume #58 color #941751
> fitmap #58 inMap #60
Fit map cryosparc_P50_J461_006_volume_map.mrc z flip in map
cryosparc_P50_J462_006_volume_map.mrc z flip using 456567 points
correlation = 0.9679, correlation about mean = 0.7998, overlap = 1.074e+04
steps = 28, shift = 0.0181, angle = 0.00791 degrees
Position of cryosparc_P50_J461_006_volume_map.mrc z flip (#58) relative to
cryosparc_P50_J462_006_volume_map.mrc z flip (#60) coordinates:
Matrix rotation and translation
0.99999844 0.00177258 -0.00015674 -0.06698095
-0.00177314 0.99999181 -0.00364487 1.11110482
0.00015027 0.00364513 0.99999337 -0.76332727
Axis 0.89862781 -0.03784489 -0.43707644
Axis point 0.00000000 182.22455868 306.83311669
Rotation angle (degrees) 0.23240287
Shift along axis 0.23139179
> show #!2 models
> hide #!58 models
> fitmap #2 inMap #60
Fit molecule 6w77 (#2) to map cryosparc_P50_J462_006_volume_map.mrc z flip
(#60) using 47940 atoms
average map value = 0.105, steps = 164
shifted from previous position = 0.00136
rotated from previous position = 0.00152 degrees
atoms outside contour = 25099, contour level = 0.098904
Position of 6w77 (#2) relative to cryosparc_P50_J462_006_volume_map.mrc z flip
(#60) coordinates:
Matrix rotation and translation
-0.20377805 0.49573848 0.84422620 -13.21858125
-0.94650611 0.12061863 -0.29929474 349.35311813
-0.25020133 -0.86005495 0.44464007 268.41297293
Axis -0.29586344 0.57743237 -0.76094460
Axis point 105.72547530 282.56219846 0.00000000
Rotation angle (degrees) 108.61815887
Shift along axis 1.39129333
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #60
Fit molecule 6w77 (#2) to map cryosparc_P50_J462_006_volume_map.mrc z flip
(#60) using 47940 atoms
average map value = 0.105, steps = 100
shifted from previous position = 0.00212
rotated from previous position = 0.00163 degrees
atoms outside contour = 25099, contour level = 0.098904
Position of 6w77 (#2) relative to cryosparc_P50_J462_006_volume_map.mrc z flip
(#60) coordinates:
Matrix rotation and translation
-0.20377775 0.49574340 0.84422339 -13.21735740
-0.94649890 0.12064203 -0.29930811 349.34999075
-0.25022884 -0.86004883 0.44463642 268.41837274
Axis -0.29585211 0.57744335 -0.76094068
Axis point 105.72838832 282.56488728 0.00000000
Rotation angle (degrees) 108.61755284
Shift along axis 1.38975262
> open /Users/TEST/Downloads/cryosparc_P50_J463_007_volume_map.mrc
Opened cryosparc_P50_J463_007_volume_map.mrc as #61, grid size 416,416,416,
pixel 0.855, shown at level 0.061, step 2, values float32
> volume flip #61
Opened cryosparc_P50_J463_007_volume_map.mrc z flip as #62, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> select add #62
2 models selected
> view matrix models #62,1,0,0,-13.233,0,1,0,-7.7622,0,0,1,34.271
> ui mousemode right "rotate selected models"
> view matrix models
> #62,-0.57856,-0.5129,-0.63419,461.54,0.34995,-0.85844,0.375,198.91,-0.73675,-0.0049709,0.67615,218.78
> ui mousemode right "translate selected models"
> view matrix models
> #62,-0.57856,-0.5129,-0.63419,452.49,0.34995,-0.85844,0.375,197.06,-0.73675,-0.0049709,0.67615,242.09
> fitmap #2 inMap #62
Fit molecule 6w77 (#2) to map cryosparc_P50_J463_007_volume_map.mrc z flip
(#62) using 47940 atoms
average map value = 0.09843, steps = 288
shifted from previous position = 20.5
rotated from previous position = 21.7 degrees
atoms outside contour = 22401, contour level = 0.061035
Position of 6w77 (#2) relative to cryosparc_P50_J463_007_volume_map.mrc z flip
(#62) coordinates:
Matrix rotation and translation
-0.19943688 0.49027253 0.84844432 -14.27084447
-0.94813597 0.12215312 -0.29345661 348.43116055
-0.24751384 -0.86296666 0.44048319 268.95479702
Axis -0.30038833 0.57806362 -0.75868920
Axis point 104.27562724 283.20476342 0.00000000
Rotation angle (degrees) 108.56620868
Shift along axis 1.64907279
> volume #62 level 0.1321
> volume #62 level 0.1096
> volume #62 color darkgrey
> select subtract #62
Nothing selected
> fitmap #2 inMap #62
Fit molecule 6w77 (#2) to map cryosparc_P50_J463_007_volume_map.mrc z flip
(#62) using 47940 atoms
average map value = 0.09843, steps = 80
shifted from previous position = 0.00761
rotated from previous position = 0.00829 degrees
atoms outside contour = 28877, contour level = 0.10962
Position of 6w77 (#2) relative to cryosparc_P50_J463_007_volume_map.mrc z flip
(#62) coordinates:
Matrix rotation and translation
-0.19932754 0.49036095 0.84841892 -14.29146851
-0.94814739 0.12221456 -0.29339412 348.41314688
-0.24755816 -0.86290772 0.44057374 268.93572057
Axis -0.30037630 0.57804684 -0.75870675
Axis point 104.28419660 283.19379648 0.00000000
Rotation angle (degrees) 108.55831134
Shift along axis 1.64859221
> volume #62 level 0.0954
> volume #62 level 0.112
> fitmap #2 inMap #60
Fit molecule 6w77 (#2) to map cryosparc_P50_J462_006_volume_map.mrc z flip
(#60) using 47940 atoms
average map value = 0.105, steps = 416
shifted from previous position = 20.5
rotated from previous position = 21.7 degrees
atoms outside contour = 25110, contour level = 0.098904
Position of 6w77 (#2) relative to cryosparc_P50_J462_006_volume_map.mrc z flip
(#60) coordinates:
Matrix rotation and translation
-0.20375572 0.49582890 0.84417849 -13.22695894
-0.94646641 0.12075019 -0.29936723 349.34266283
-0.25036964 -0.85998437 0.44468185 268.43092728
Axis -0.29577767 0.57747592 -0.76094489
Axis point 105.74671739 282.57654154 0.00000000
Rotation angle (degrees) 108.61224397
Shift along axis 1.38807202
> volume #60 level 0.115
> volume #58 color darkgrey
> volume #58 level 0.04476
> volume #54 level 0.04861
> volume #54 level 0.07598
> volume #53 level 0.08966
> volume #52 level 0.04279
> volume #50 level 0.1379
> select add #50
2 models selected
> view matrix models
> #50,-0.94114,-0.326,0.089339,343.99,0.24812,-0.4868,0.83753,70.364,-0.22954,0.8104,0.53903,56.799
> ui mousemode right "rotate selected models"
> view matrix models
> #50,-0.65098,0.082913,-0.75455,384.84,-0.17991,-0.98255,0.047254,388.95,-0.73746,0.16652,0.65454,238.77
> fitmap #2 inMap #50
Fit molecule 6w77 (#2) to map cryosparc_P50_J455_007_volume_map.mrc z flip
(#50) using 47940 atoms
average map value = 0.09446, steps = 484
shifted from previous position = 46.5
rotated from previous position = 28.6 degrees
atoms outside contour = 34173, contour level = 0.13786
Position of 6w77 (#2) relative to cryosparc_P50_J455_007_volume_map.mrc z flip
(#50) coordinates:
Matrix rotation and translation
-0.19673678 0.49591801 0.84578960 -14.80965001
-0.94899775 0.12044967 -0.29136787 348.25212158
-0.24636965 -0.85997515 0.44692817 267.33737970
Axis -0.29951984 0.57530632 -0.76112450
Axis point 104.81119874 281.99938851 0.00000000
Rotation angle (degrees) 108.34146396
Shift along axis 1.31039864
> select subtract #50
Nothing selected
> volume #50 level 0.08761
> open /Users/TEST/Downloads/cryosparc_P79_J106_007_volume_map.mrc
Opened cryosparc_P79_J106_007_volume_map.mrc as #63, grid size 416,416,416,
pixel 0.855, shown at level 0.093, step 2, values float32
> hide #!50 models
> hide #!2 models
> select add #63
2 models selected
> select subtract #63
Nothing selected
> volume #63 step 1
> volume #63 level 0.1296
> volume flip #63
Opened cryosparc_P79_J106_007_volume_map.mrc z flip as #64, grid size
416,416,416, pixel 0.855, shown at step 1, values float32
> show #!2 models
> select add #2
47940 atoms, 52058 bonds, 1470 pseudobonds, 3468 residues, 3 models selected
> view matrix models
> #2,0.50035,-0.4037,-0.76595,265.96,0.86066,0.13542,0.49084,-34.381,-0.09443,-0.90481,0.41521,340.01
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.50035,-0.4037,-0.76595,264.44,0.86066,0.13542,0.49084,-66.101,-0.09443,-0.90481,0.41521,262.22
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.68749,-0.47961,-0.54528,208.6,0.46868,-0.28051,0.83765,7.7935,-0.5547,-0.83144,0.031937,391.28
> select subtract #2
Nothing selected
> fitmap #2 inMap #64
Fit molecule 6w77 (#2) to map cryosparc_P79_J106_007_volume_map.mrc z flip
(#64) using 47940 atoms
average map value = 0.1162, steps = 432
shifted from previous position = 28.1
rotated from previous position = 35.3 degrees
atoms outside contour = 29290, contour level = 0.12963
Position of 6w77 (#2) relative to cryosparc_P79_J106_007_volume_map.mrc z flip
(#64) coordinates:
Matrix rotation and translation
0.14336168 -0.60717582 -0.78152729 383.47312864
0.65421736 -0.53439446 0.53518424 73.09329536
-0.74259480 -0.58801364 0.32061328 341.77788057
Axis -0.66483508 -0.02304463 0.74663463
Axis point 316.98264460 182.76622533 0.00000000
Rotation angle (degrees) 122.35813779
Shift along axis -1.44759565
> volume #64 color #929292
> volume #64 level 0.1388
> open /Users/TEST/Downloads/cryosparc_P79_J132_006_volume_map.mrc
Opened cryosparc_P79_J132_006_volume_map.mrc as #65, grid size 416,416,416,
pixel 0.855, shown at level 0.0622, step 2, values float32
> hide #!2 models
> show #!2 models
> select add #2
47940 atoms, 52058 bonds, 1470 pseudobonds, 3468 residues, 3 models selected
> view matrix models
> #2,0.19571,-0.72855,-0.65644,373.58,-0.97852,-0.10089,-0.17977,400.02,0.064747,0.67752,-0.73265,182.94
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.19571,-0.72855,-0.65644,365.16,-0.97852,-0.10089,-0.17977,360.77,0.064747,0.67752,-0.73265,205.07
> fitmap #2 inMap #65
Fit molecule 6w77 (#2) to map cryosparc_P79_J132_006_volume_map.mrc (#65)
using 47940 atoms
average map value = 0.07328, steps = 216
shifted from previous position = 13.3
rotated from previous position = 13.8 degrees
atoms outside contour = 23573, contour level = 0.062209
Position of 6w77 (#2) relative to cryosparc_P79_J132_006_volume_map.mrc (#65)
coordinates:
Matrix rotation and translation
0.24562380 -0.55410386 -0.79538534 363.60690906
-0.96545782 -0.06623818 -0.25199934 364.22571018
0.08694893 0.82980804 -0.55123358 141.34638320
Axis 0.74333327 -0.60627098 -0.28265022
Axis point 0.00000000 288.57697305 247.22124339
Rotation angle (degrees) 133.30831716
Shift along axis 9.51005072
> volume #65 step 1
> volume #65 level 0.07374
> volume #65 level 0.09387
> select subtract #2
Nothing selected
> volume #65 level 0.0979
> volume #65 level 0.07696
> open /Users/TEST/Downloads/cryosparc_P79_J110_006_volume_map.mrc
Opened cryosparc_P79_J110_006_volume_map.mrc as #66, grid size 416,416,416,
pixel 0.855, shown at level 0.0715, step 2, values float32
> volume #66 step 1
> volume #66 level 0.09502
> fitmap #2 inMap #66
Fit molecule 6w77 (#2) to map cryosparc_P79_J110_006_volume_map.mrc (#66)
using 47940 atoms
average map value = 0.07276, steps = 84
shifted from previous position = 1.91
rotated from previous position = 0.969 degrees
atoms outside contour = 33352, contour level = 0.095024
Position of 6w77 (#2) relative to cryosparc_P79_J110_006_volume_map.mrc (#66)
coordinates:
Matrix rotation and translation
0.23042604 -0.55887494 -0.79659439 366.66906763
-0.96859605 -0.05314686 -0.24289312 360.45131346
0.09341039 0.82754709 -0.55357049 139.29850007
Axis 0.73765208 -0.61331204 -0.28234331
Axis point 0.00000000 291.24601890 246.63375606
Rotation angle (degrees) 133.48350064
Shift along axis 10.07506909
> hide #!2 models
> volume #66 level 0.07883
> open /Users/TEST/Downloads/cryosparc_P79_J132_006_volume_map.mrc
Opened cryosparc_P79_J132_006_volume_map.mrc as #67, grid size 416,416,416,
pixel 0.855, shown at level 0.0622, step 2, values float32
> hide #!66 models
> volume #67 step 1
> volume #67 level 0.07429
> show #!2 models
> fitmap #2 inMap #67
Fit molecule 6w77 (#2) to map cryosparc_P79_J132_006_volume_map.mrc (#67)
using 47940 atoms
average map value = 0.07328, steps = 56
shifted from previous position = 1.91
rotated from previous position = 0.967 degrees
atoms outside contour = 25970, contour level = 0.074292
Position of 6w77 (#2) relative to cryosparc_P79_J132_006_volume_map.mrc (#67)
coordinates:
Matrix rotation and translation
0.24558885 -0.55413608 -0.79537368 363.61485389
-0.96546960 -0.06625514 -0.25194975 364.22176350
0.08691685 0.82978517 -0.55127307 141.36351477
Axis 0.74332749 -0.60627682 -0.28265290
Axis point 0.00000000 288.57921974 247.22274732
Rotation angle (degrees) 133.31191566
Shift along axis 9.50889631
> volume #67 level 0.09685
> volume #67 level 0.08557
> volume #67 level 0.1057
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/TEST/Downloads/cryosparc_P79_J111_007_volume_map.mrc
Opened cryosparc_P79_J111_007_volume_map.mrc as #1, grid size 416,416,416,
pixel 0.855, shown at level 0.0103, step 2, values float32
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4.1 (c) (22F770820d)
Kernel Version: Darwin 22.5.0
Time since boot: 5 days, 18 hours, 53 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2410:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Songzhe,
--Eric