![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9618 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-10.16-x86_64-i386-64bit
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 0x00007ff84aeb3680 (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
{"app_name":"ChimeraX","timestamp":"2023-08-22 18:59:16.00 +0200","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.2.1 (22D68)","roots_installed":0,"name":"ChimeraX","incident_id":"5B7F1FC5-9805-4281-B7DB-3F45FA4AD00F"}
{
"uptime" : 420000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 17070,
"osVersion" : {
"train" : "macOS 13.2.1",
"build" : "22D68",
"releaseType" : "User"
},
"captureTime" : "2023-08-22 18:58:40.3265 +0200",
"incident" : "5B7F1FC5-9805-4281-B7DB-3F45FA4AD00F",
"pid" : 99342,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-08-21 21:42:37.0346 +0200",
"procStartAbsTime" : 386309715894321,
"procExitAbsTime" : 422267583703119,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"73F178B2-ADB5-5850-BCEB-46D3D0D2A9DF","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2BC834FB-C761-FDDB-75E1-ECC1D7606BD3",
"throttleTimeout" : 2147483647,
"wakeTime" : 31915,
"bridgeVersion" : {"build":"20P3045","train":"7.2"},
"sleepWakeUUID" : "DAC39327-CE21-451A-911E-578C0795DA35",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486594024\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe52000-7fffffe53000 [ 4K] r-x\/r-x SM=SHM ",
"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: 140737486594024\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe52000-7fffffe53000 [ 4K] r-x\/r-x SM=SHM ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.5.dev202209140201 (2022-09-14)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/linda_cmmc/Desktop/BiP+GRP94/Model Yasser Colorized.pdb"
Chain information for Model Yasser Colorized.pdb #1
---
Chain | Description
A B | No description available
C | No description available
> select #1/A,B:86-285
6254 atoms, 6296 bonds, 396 residues, 1 model selected
> color (#!1 & sel) red
> select #1/A,B:330-338
226 atoms, 228 bonds, 14 residues, 1 model selected
> color (#!1 & sel) light gray
> select #1/A,B:339-595
8532 atoms, 8630 bonds, 514 residues, 1 model selected
> color (#!1 & sel) cyan
> select #1/A,B:596-749
5060 atoms, 5098 bonds, 308 residues, 1 model selected
> color (#!1 & sel) blue
> select #1/C
7774 atoms, 7833 bonds, 500 residues, 1 model selected
> color (#!1 & sel) forest green
> open /Users/linda_cmmc/Downloads/2o1u.pdb
2o1u.pdb title:
Structure of full length GRP94 with amp-PNP bound [more info...]
Chain information for 2o1u.pdb #2
---
Chain | Description | UniProt
A | endoplasmin | ENPL_CANFA
B | endoplasmin | ENPL_CANFA
Non-standard residues in 2o1u.pdb #2
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
> open /Users/linda_cmmc/Downloads/5uls.cif
5uls.cif title:
Structure of GRP94 in the active conformation [more info...]
Chain information for 5uls.cif #3
---
Chain | Description | UniProt
A B | Endoplasmin | ENPL_CANLF
Non-standard residues in 5uls.cif #3
---
ANP — phosphoaminophosphonic acid-adenylate ester
> tile
3 models tiled
> set bgColor white
> set bgColor #ffffff00
> select add #1
28068 atoms, 28311 bonds, 2 pseudobonds, 1746 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #3
9869 atoms, 9858 bonds, 9 pseudobonds, 1484 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.98744,0.15664,0.020867,268.52,-0.12115,-0.8352,0.53643,105.56,0.10146,0.52717,0.84368,4.4119
> view matrix models
> #3,-0.99442,0.10326,-0.021652,278.06,-0.092496,-0.75451,0.64974,80.715,0.050756,0.64811,0.75985,21.106
> view matrix models
> #3,0.36825,-0.87895,-0.30304,213.15,0.9002,0.25558,0.3526,4.5236,-0.23247,-0.40264,0.88535,55.618
> view matrix models
> #3,0.6196,-0.71702,-0.31933,186,0.78225,0.53058,0.32645,14.013,-0.064644,-0.45206,0.88964,38.951
> view matrix models
> #3,0.61459,-0.73692,-0.28149,180.43,0.78182,0.52147,0.34179,11.613,-0.10508,-0.43014,0.89663,41.304
> view matrix models
> #3,0.51897,-0.80725,-0.2811,192,0.84004,0.42083,0.34239,8.1647,-0.1581,-0.41383,0.89652,46.332
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.51897,-0.80725,-0.2811,278.69,0.84004,0.42083,0.34239,-168.42,-0.1581,-0.41383,0.89652,17.179
> select subtract #3
Nothing selected
> select add #1
28068 atoms, 28311 bonds, 2 pseudobonds, 1746 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> view matrix models
> #2,0.17613,-0.56189,0.80824,179.3,0.90544,-0.22966,-0.35698,209.75,0.38621,0.79469,0.46831,-25.597
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.60394,-0.092191,0.79168,167.75,-0.11458,-0.99301,-0.028231,221.71,0.78875,-0.073658,-0.61028,20.839
> view matrix models
> #2,0.92141,-0.28596,0.26313,184.58,-0.11508,-0.84755,-0.51809,228.79,0.37117,0.44709,-0.81384,11.708
> open /Users/linda_cmmc/Desktop/GRP94open_BiPNBD_0956.pdb
Chain information for GRP94open_BiPNBD_0956.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select #4/A,B:86-285
5386 atoms, 5420 bonds, 3 pseudobonds, 336 residues, 2 models selected
> color (#!4 & sel) red
> select #4/A,B:330-338
306 atoms, 312 bonds, 18 residues, 1 model selected
> color (#!4 & sel) light gray
> select #4/A,B:339-595
8130 atoms, 8221 bonds, 2 pseudobonds, 488 residues, 2 models selected
> color (#!4 & sel) cyan
> select #4/A,B:596-749
5040 atoms, 5078 bonds, 308 residues, 1 model selected
> color (#!4 & sel) blue
> select #4/C
5951 atoms, 5996 bonds, 382 residues, 1 model selected
> color (#!4 & sel) forest green
> select add #4
24827 atoms, 25045 bonds, 7 pseudobonds, 1533 residues, 2 models selected
> view matrix models
> #4,0.014632,0.13925,-0.99015,332.37,-0.89272,-0.44422,-0.075667,450.49,-0.45038,0.88503,0.11781,73.79
> view matrix models
> #4,0.79911,-0.59892,-0.052101,159.84,-0.08434,-0.025878,-0.9961,391.37,0.59524,0.80039,-0.071192,-65.669
> view matrix models
> #4,0.93319,0.14471,0.32896,-75.153,0.25845,-0.90627,-0.33449,376.32,0.24972,0.39716,-0.88312,221.28
> select #2,3/A,B:86-285
5681 atoms, 5756 bonds, 5 pseudobonds, 733 residues, 4 models selected
> color (#!2,3 & sel) red
> select #2,3/A,B:330-338
336 atoms, 348 bonds, 36 residues, 2 models selected
> color (#!2,3 & sel) light gray
> select #2,3/A,B:339-595
8018 atoms, 8207 bonds, 2 pseudobonds, 1002 residues, 3 models selected
> color (#!2,3 & sel) cyan
> select #2,3/A,B:596-749
4343 atoms, 4403 bonds, 4 pseudobonds, 605 residues, 3 models selected
> color (#!2,3 & sel) blue
> select add #3
12281 atoms, 12306 bonds, 9 pseudobonds, 1792 residues, 3 models selected
> select subtract #3
2412 atoms, 2448 bonds, 308 residues, 1 model selected
> select add #2
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #1
28068 atoms, 28311 bonds, 2 pseudobonds, 1746 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> view matrix models
> #2,-0.78749,-0.61115,0.079692,196.23,-0.48197,0.53007,-0.69767,197.04,0.38413,-0.58782,-0.71198,36.169
> view matrix models
> #2,-0.78749,-0.61115,0.079692,184.36,-0.48197,0.53007,-0.69767,227.59,0.38413,-0.58782,-0.71198,16.777
> select subtract #2
Nothing selected
> surface
> select add #1
28068 atoms, 28311 bonds, 2 pseudobonds, 1746 residues, 2 models selected
> select subtract #1
3 models selected
> select add #2
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> view matrix models
> #2,0.2811,-0.769,-0.57412,306.59,-0.42272,0.43786,-0.79346,-38.072,0.86156,0.46574,-0.20199,167.47
> select subtract #2
2 models selected
> select add #3
9869 atoms, 9858 bonds, 9 pseudobonds, 1484 residues, 2 models selected
> view matrix models
> #3,0.94519,0.05998,0.32096,-6.6783,-0.32651,0.17062,0.92967,150.84,0.0010005,-0.98351,0.18085,-52.231
> select subtract #3
2 models selected
> select add #3
9869 atoms, 9858 bonds, 9 pseudobonds, 1484 residues, 2 models selected
> select subtract #3
2 models selected
> select add #4
24827 atoms, 25045 bonds, 7 pseudobonds, 1533 residues, 2 models selected
> view matrix models
> #4,0.097834,0.4412,-0.89206,310.62,0.6491,-0.70775,-0.27885,125.43,-0.75438,-0.55176,-0.35562,440.63
> select subtract #4
3 models selected
> select add #3
9869 atoms, 9858 bonds, 9 pseudobonds, 1484 residues, 2 models selected
> select subtract #3
2 models selected
> select add #3
9869 atoms, 9858 bonds, 9 pseudobonds, 1484 residues, 2 models selected
> select subtract #3
2 models selected
> select add #2
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> select subtract #2
2 models selected
> select add #1
28068 atoms, 28311 bonds, 2 pseudobonds, 1746 residues, 2 models selected
> view matrix models
> #1,0.96613,-0.25541,0.036958,8.7221,0.25519,0.92417,-0.28423,36.605,0.03844,0.28404,0.95804,-67.693
> select subtract #1
3 models selected
> select add #2
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> view matrix models
> #2,-0.10536,-0.96451,0.24213,283.16,-0.6199,-0.12669,-0.77439,-10.183,0.77757,-0.23168,-0.58455,223.48
> select subtract #2
2 models selected
> select add #3
9869 atoms, 9858 bonds, 9 pseudobonds, 1484 residues, 2 models selected
> view matrix models
> #3,0.72716,0.51631,-0.45239,128.75,0.079092,0.59161,0.80234,134.5,0.68189,-0.61921,0.38936,-143.9
> select subtract #3
2 models selected
> select add #4
24827 atoms, 25045 bonds, 7 pseudobonds, 1533 residues, 2 models selected
> view matrix models
> #4,0.13038,0.98111,-0.14288,66.316,0.89832,-0.17788,-0.40171,1.43,-0.41954,-0.075979,-0.90455,386.39
> select subtract #4
3 models selected
> select add #2
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> select subtract #2
2 models selected
> select add #3
9869 atoms, 9858 bonds, 9 pseudobonds, 1484 residues, 2 models selected
> select subtract #3
2 models selected
> select add #1
28068 atoms, 28311 bonds, 2 pseudobonds, 1746 residues, 2 models selected
> view matrix models
> #1,0.3856,-0.84032,-0.38101,217.91,0.54803,0.5408,-0.63812,47.912,0.74228,0.037254,0.66906,-155.11
> surface hidePatches (#!1 & sel)
> select subtract #1
3 models selected
> surface hidePatches
> tile
4 models tiled
> select add #4
24827 atoms, 25045 bonds, 7 pseudobonds, 1533 residues, 2 models selected
> select subtract #4
3 models selected
> hide #!4 models
> select add #2
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> select subtract #2
2 models selected
> rename #2 2o1u_open.pdb
> rename #3 5uls_closed.cif
> tile
3 models tiled
> tile
3 models tiled
> select add #1
28068 atoms, 28311 bonds, 2 pseudobonds, 1746 residues, 2 models selected
> turn x -1 90 models #2 center #2
> show #!2 models
> hide #!1 models
> volume #2 style surface
> save /Users/linda_cmmc/Desktop/image2.png supersample 3
> volume #2 level 1.506
> save /Users/linda_cmmc/Desktop/image3.png supersample 3
> hide #!1 target m
> close #1
> close #2
> open /Users/linda_cmmc/Downloads/cryosparc_P83_J37_002_volume_map_sharp.mrc
Opened cryosparc_P83_J37_002_volume_map_sharp.mrc as #1, grid size
200,200,200, pixel 1.89, shown at level 0.977, step 1, values float32
> volume #1 level 1.505
> open "/Users/linda_cmmc/Desktop/BiP+GRP94/Model Yasser Colorized.pdb"
Chain information for Model Yasser Colorized.pdb #2
---
Chain | Description
A B | No description available
C | No description available
> rename #2 id #1
> rename #1 id #2
> rename #2.2 id #1
ID must be one or more integers separated by '.' characters
> select #1/A,B:86-285
6254 atoms, 6296 bonds, 396 residues, 1 model selected
> color (#!1 & sel) red
> select #1/A,B:330-338
226 atoms, 228 bonds, 14 residues, 1 model selected
> color (#!1 & sel) light gray
> select #1/A,B:339-595
8532 atoms, 8630 bonds, 514 residues, 1 model selected
> color (#!1 & sel) cyan
> select #1/A,B:596-749
5060 atoms, 5098 bonds, 308 residues, 1 model selected
> color (#!1 & sel) blue
> select #1/C
7774 atoms, 7833 bonds, 500 residues, 1 model selected
> color (#!1 & sel) forest green
> select add #1
28068 atoms, 28311 bonds, 2 pseudobonds, 1746 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,0.62358,-0.71473,0.31671,152.23,0.67926,0.69591,0.23304,-116.34,-0.38697,0.069812,0.91945,76.553
> view matrix models
> #2,0.64819,-0.75917,-0.059315,223.37,0.68994,0.55255,0.46762,-133.28,-0.32223,-0.34403,0.88194,149.29
> view matrix models
> #2,0.64819,-0.75917,-0.059315,160.89,0.68994,0.55255,0.46762,-103.05,-0.32223,-0.34403,0.88194,122.15
> select subtract #2
Nothing selected
> select add #1
28068 atoms, 28311 bonds, 2 pseudobonds, 1746 residues, 2 models selected
> view matrix models
> #1,-0.082573,0.87239,0.48178,106.29,-0.85802,0.18368,-0.47965,306.55,-0.50694,-0.45299,0.73336,176.79
> view matrix models
> #1,-0.62745,0.77855,0.012829,267.52,-0.2703,-0.20234,-0.94127,253.84,-0.73023,-0.59407,0.3374,268.39
> view matrix models
> #1,-0.49824,0.86694,0.013204,230.18,-0.37735,-0.20311,-0.90352,274.33,-0.78062,-0.45516,0.42834,257.96
> view matrix models
> #1,-0.49824,0.86694,0.013204,236.3,-0.37735,-0.20311,-0.90352,305.07,-0.78062,-0.45516,0.42834,341.26
> view matrix models
> #1,-0.4933,0.86313,-0.10798,244.32,-0.36601,-0.31857,-0.87439,312.83,-0.78911,-0.39181,0.47306,333.14
> view matrix models
> #1,-0.4933,0.86313,-0.10798,289.62,-0.36601,-0.31857,-0.87439,289.84,-0.78911,-0.39181,0.47306,350.26
> tile
2 models tiled
> open "/Users/linda_cmmc/Desktop/BiP+GRP94/Model Yasser Colorized.pdb"
Chain information for Model Yasser Colorized.pdb #3
---
Chain | Description
A B | No description available
C | No description available
> select subtract #1
Nothing selected
> select add #3
28068 atoms, 28311 bonds, 2 pseudobonds, 1746 residues, 2 models selected
> view matrix models
> #3,0.005132,0.71162,-0.70254,189.31,0.99666,-0.060869,-0.054376,-98.283,-0.081458,-0.69992,-0.70956,214.58
> view matrix models
> #3,0.14999,0.48917,-0.85919,192.95,0.97039,0.093595,0.22268,-128.91,0.18935,-0.86715,-0.46065,156.1
> view matrix models
> #3,0.10942,0.54379,-0.83206,193.95,0.98543,0.05034,0.16249,-123.23,0.13025,-0.83771,-0.53035,170.72
> view matrix models
> #3,0.10942,0.54379,-0.83206,33.714,0.98543,0.05034,0.16249,26.289,0.13025,-0.83771,-0.53035,133.64
> view matrix models
> #3,0.2306,-0.87579,0.42403,68.796,-0.3442,0.33418,0.87741,231.91,-0.91014,-0.34829,-0.22439,284.21
> view matrix models
> #3,0.3538,-0.84227,0.4067,39.867,-0.43465,0.23697,0.86886,262.41,-0.82819,-0.48418,-0.28225,285.13
> view matrix models
> #3,0.37664,-0.82716,0.41707,32.584,-0.38919,0.26727,0.88153,248.46,-0.84064,-0.49434,-0.22126,284.54
> select #3/C
7774 atoms, 7833 bonds, 500 residues, 1 model selected
> color (#!3 & sel) forest green
> select #3/A
10147 atoms, 10239 bonds, 1 pseudobond, 623 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #3/B
10147 atoms, 10239 bonds, 1 pseudobond, 623 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> color #3 #00f900ff
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C:382
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/C:382-529
2224 atoms, 2240 bonds, 148 residues, 1 model selected
> select #1/C:419
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/C:419-529
1711 atoms, 1724 bonds, 111 residues, 1 model selected
> select #1/C:418
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/C:418-529
1723 atoms, 1736 bonds, 112 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui mousemode right "translate selected models"
> select add #1
26345 atoms, 26574 bonds, 2 pseudobonds, 1634 residues, 2 models selected
> view matrix models
> #1,-0.57833,0.80259,-0.14625,32.003,-0.41913,-0.44611,-0.79077,550.53,-0.6999,-0.39603,0.59439,258.75
> view matrix models
> #1,-0.57833,0.80259,-0.14625,186.34,-0.41913,-0.44611,-0.79077,407.55,-0.6999,-0.39603,0.59439,296.73
> view matrix models
> #1,-0.57833,0.80259,-0.14625,189.44,-0.41913,-0.44611,-0.79077,405.77,-0.6999,-0.39603,0.59439,299.87
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.51646,0.84045,-0.16408,173.33,-0.48584,-0.44538,-0.75206,417.32,-0.70514,-0.30869,0.63834,288.55
> view matrix models
> #1,-0.51631,0.84068,-0.16335,167.95,-0.48619,-0.44475,-0.75221,420.81,-0.70502,-0.30895,0.63836,284.18
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 116
shifted from previous position = 11.4
rotated from previous position = 21.3 degrees
atoms outside contour = 10099, contour level = 1.5046
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26791720 0.22265880 -0.93735982 289.54955065
0.41575832 -0.85095548 -0.32096696 203.61651913
-0.86911760 -0.47570771 0.13541336 400.33807719
Axis -0.60283413 -0.26585590 0.75227099
Axis point 295.63464241 186.82147967 0.00000000
Rotation angle (degrees) 172.62606898
Shift along axis 72.47971700
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 120
shifted from previous position = 25.4
rotated from previous position = 0.0214 degrees
atoms outside contour = 10112, contour level = 1.5046
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26759292 0.22281526 -0.93741527 289.43686096
0.41569067 -0.85099969 -0.32093737 203.63616900
-0.86924985 -0.47555535 0.13509927 400.36954292
Axis -0.60297367 -0.26582908 0.75216864
Axis point 295.65755931 186.82242993 0.00000000
Rotation angle (degrees) 172.63366633
Shift along axis 72.49019111
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 96
shifted from previous position = 22.1
rotated from previous position = 0.00652 degrees
atoms outside contour = 10113, contour level = 1.5046
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26752951 0.22285408 -0.93742414 289.41554602
0.41561512 -0.85103959 -0.32092939 203.65004724
-0.86930549 -0.47546573 0.13505669 400.37748679
Axis -0.60300259 -0.26579977 0.75215581
Axis point 295.66530887 186.81551679 0.00000000
Rotation angle (degrees) 172.63793234
Shift along axis 72.49779106
> volume #2 level 1.3
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 52
shifted from previous position = 2.6
rotated from previous position = 0.0163 degrees
atoms outside contour = 6392, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26744504 0.22311885 -0.93738526 289.35983811
0.41551830 -0.85101769 -0.32111279 203.69329154
-0.86937776 -0.47538076 0.13489050 400.38775738
Axis -0.60304568 -0.26584670 0.75210467
Axis point 295.67883674 186.82867826 0.00000000
Rotation angle (degrees) 172.65131629
Shift along axis 72.48511488
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 56
shifted from previous position = 4.78
rotated from previous position = 0.0461 degrees
atoms outside contour = 6400, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26800060 0.22259177 -0.93735190 289.57816642
0.41578582 -0.85094775 -0.32095183 203.60858415
-0.86907873 -0.47575291 0.13550401 400.32866994
Axis -0.60279742 -0.26585663 0.75230016
Axis point 295.62556375 186.82034636 0.00000000
Rotation angle (degrees) 172.62272627
Shift along axis 72.47965731
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 56
shifted from previous position = 5.6
rotated from previous position = 0.026 degrees
atoms outside contour = 6388, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26759655 0.22276524 -0.93742612 289.44670182
0.41572099 -0.85099954 -0.32089848 203.62591700
-0.86923423 -0.47557904 0.13511636 400.36829563
Axis -0.60297035 -0.26582325 0.75217335
Axis point 295.65666365 186.82130409 0.00000000
Rotation angle (degrees) 172.63062745
Shift along axis 72.49007946
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 112
shifted from previous position = 21.9
rotated from previous position = 0.029 degrees
atoms outside contour = 6399, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26805696 0.22259228 -0.93733566 289.58596174
0.41576468 -0.85094858 -0.32097701 203.61624574
-0.86907146 -0.47575118 0.13555669 400.32262642
Axis -0.60277454 -0.26585783 0.75231806
Axis point 295.61831418 186.81976872 0.00000000
Rotation angle (degrees) 172.62373429
Shift along axis 72.48192472
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 84
shifted from previous position = 22.4
rotated from previous position = 0.0239 degrees
atoms outside contour = 6389, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26769050 0.22277049 -0.93739805 289.46529896
0.41571269 -0.85098469 -0.32094862 203.63214725
-0.86920927 -0.47560316 0.13519200 400.35848960
Axis -0.60293169 -0.26583880 0.75219885
Axis point 295.64733789 186.82306864 0.00000000
Rotation angle (degrees) 172.63139899
Shift along axis 72.48806626
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 84
shifted from previous position = 19.8
rotated from previous position = 0.00703 degrees
atoms outside contour = 6391, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26761377 0.22285240 -0.93740049 289.43367547
0.41565981 -0.85099994 -0.32097665 203.64689265
-0.86925818 -0.47553749 0.13510852 400.36531350
Axis -0.60296656 -0.26583405 0.75217258
Axis point 295.65457144 186.82257944 0.00000000
Rotation angle (degrees) 172.63631678
Shift along axis 72.48870684
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 72
shifted from previous position = 4.81
rotated from previous position = 0.0283 degrees
atoms outside contour = 6400, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26791835 0.22254588 -0.93738631 289.56661817
0.41590341 -0.85091450 -0.32088763 203.57883714
-0.86904782 -0.47583384 0.13541802 400.33594946
Axis -0.60282776 -0.26587508 0.75226932
Axis point 295.62968774 186.82740879 0.00000000
Rotation angle (degrees) 172.61614481
Shift along axis 72.47511975
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 112
shifted from previous position = 26.7
rotated from previous position = 0.027 degrees
atoms outside contour = 6388, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26756828 0.22279372 -0.93742742 289.43612953
0.41572417 -0.85099335 -0.32091079 203.62618485
-0.86924141 -0.47557679 0.13507810 400.37202172
Axis -0.60298262 -0.26583077 0.75216086
Axis point 295.65972227 186.82342230 0.00000000
Rotation angle (degrees) 172.63147625
Shift along axis 72.48910127
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.61678,0.77383,-0.14412,188.6,-0.40433,-0.46856,-0.78547,423.9,-0.67535,-0.42619,0.60188,292.68
> view matrix models
> #1,-0.61678,0.77383,-0.14412,203.39,-0.40433,-0.46856,-0.78547,407.83,-0.67535,-0.42619,0.60188,291.15
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.48421,0.82693,-0.28589,179.27,-0.35817,-0.48545,-0.79753,400.53,-0.79828,-0.28378,0.53124,307.58
> volume #2 style mesh
> view matrix models
> #1,-0.8685,0.48776,0.088279,261.12,0.43123,0.83132,-0.35063,68.401,-0.24441,-0.26646,-0.93234,290.36
> view matrix models
> #1,-0.86111,0.49812,0.10183,257.45,0.44052,0.83098,-0.33973,65.653,-0.25385,-0.24769,-0.93499,290.59
> view matrix models
> #1,-0.85975,0.51061,0.010628,262.36,0.49084,0.83184,-0.25908,48.921,-0.14113,-0.21752,-0.9658,265.25
> view matrix models
> #1,-0.85746,-0.10815,-0.50306,362.16,0.47532,0.20795,-0.85488,163.42,0.19707,-0.97214,-0.12691,211.51
> view matrix models
> #1,-0.89712,0.0040655,-0.44177,354.38,0.44065,0.080013,-0.8941,187.35,0.031713,-0.99679,-0.073573,246.02
> view matrix models
> #1,-0.84938,-0.12453,-0.51289,362.87,0.47859,0.22795,-0.84793,160.09,0.2225,-0.96568,-0.13402,205.84
> view matrix models
> #1,-0.80887,-0.073794,-0.58333,353.76,0.55583,0.22761,-0.79953,139.98,0.19178,-0.97095,-0.14309,213.69
> view matrix models
> #1,-0.80887,-0.073794,-0.58333,354.75,0.55583,0.22761,-0.79953,138.93,0.19178,-0.97095,-0.14309,213.63
> view matrix models
> #1,-0.65214,-0.53838,0.53372,297.65,-0.37891,-0.37829,-0.84458,403.38,0.65661,-0.75302,0.0427,82.026
> view matrix models
> #1,-0.59955,-0.58293,0.54839,289.99,-0.34539,-0.42966,-0.83433,400.88,0.72198,-0.68963,0.056257,60.189
> view matrix models
> #1,-0.57758,-0.60689,0.54597,288.08,-0.31843,-0.44833,-0.83523,397.22,0.75167,-0.65626,0.065696,50.025
> view matrix models
> #1,-0.57758,-0.60689,0.54597,287.01,-0.31843,-0.44833,-0.83523,398.14,0.75167,-0.65626,0.065696,49.59
> view matrix models
> #1,-0.96992,0.18318,-0.16033,341.23,0.13133,-0.16079,-0.97821,276.02,-0.20496,-0.96984,0.1319,281.68
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 88
shifted from previous position = 11.1
rotated from previous position = 10.1 degrees
atoms outside contour = 6387, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26766955 0.22272208 -0.93741554 289.46929240
0.41570880 -0.85100731 -0.32089366 203.62888241
-0.86921758 -0.47558535 0.13520121 400.35992865
Axis -0.60293942 -0.26581412 0.75220138
Axis point 295.64945076 186.81838748 0.00000000
Rotation angle (degrees) 172.62971443
Shift along axis 72.49141073
> view matrix models
> #1,-0.012508,-0.83561,0.54919,173.79,-0.42337,0.502,0.75416,202.21,-0.90587,-0.22307,-0.36005,388.67
> view matrix models
> #1,-0.4141,0.87207,-0.26079,147.86,-0.25807,-0.38724,-0.88512,367.34,-0.87288,-0.29922,0.38541,337.1
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 100
shifted from previous position = 15.9
rotated from previous position = 0.0184 degrees
atoms outside contour = 6401, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26795380 0.22262384 -0.93735766 289.56790397
0.41578011 -0.85094867 -0.32095680 203.61115578
-0.86909589 -0.47573626 0.13545237 400.33438138
Axis -0.60281767 -0.26585829 0.75228334
Axis point 295.63306952 186.82203123 0.00000000
Rotation angle (degrees) 172.62401132
Shift along axis 72.47652253
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.00898
rotated from previous position = 0.00996 degrees
atoms outside contour = 6405, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26794377 0.22249981 -0.93738998 289.58177462
0.41591406 -0.85091967 -0.32086010 203.58138362
-0.86903488 -0.47584614 0.13545783 400.32850804
Axis -0.60281595 -0.26586615 0.75228194
Axis point 295.62592349 186.82803339 0.00000000
Rotation angle (degrees) 172.61409099
Shift along axis 72.46999589
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 124
shifted from previous position = 27.7
rotated from previous position = 0.0117 degrees
atoms outside contour = 6400, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26795269 0.22264610 -0.93735269 289.55867313
0.41575775 -0.85095349 -0.32097298 203.61871944
-0.86910693 -0.47571722 0.13544844 400.33349857
Axis -0.60281914 -0.26585709 0.75228258
Axis point 295.63051136 186.82178360 0.00000000
Rotation angle (degrees) 172.62571734
Shift along axis 72.47892626
> view matrix models
> #1,-0.61417,0.56307,-0.55295,237.13,-0.20023,-0.78892,-0.58096,397.29,-0.76335,-0.24609,0.59727,292.87
> view matrix models
> #1,-0.61417,0.56307,-0.55295,107.87,-0.20023,-0.78892,-0.58096,529.93,-0.76335,-0.24609,0.59727,289.16
> select subtract #1
Nothing selected
> select add #1
26345 atoms, 26574 bonds, 2 pseudobonds, 1634 residues, 2 models selected
> view matrix models
> #1,-0.64421,0.51172,-0.56845,263.11,-0.23462,-0.8396,-0.48993,389.12,-0.72797,-0.18225,0.66094,271.6
> view matrix models
> #1,-0.70666,0.65326,0.27181,209.25,-0.64485,-0.75272,0.13256,422.51,0.29119,-0.081602,0.95318,34.903
> view matrix models
> #1,-0.24579,0.96927,0.010209,91.751,-0.35924,-0.081307,-0.9297,363,-0.90029,-0.23218,0.36819,337.87
> view matrix models
> #1,-0.32926,0.47239,-0.81758,216.9,-0.35597,-0.86408,-0.3559,408.1,-0.87457,0.17385,0.45266,279.17
> view matrix models
> #1,-0.83597,0.45145,-0.31202,291.27,-0.54641,-0.73749,0.39691,386.47,-0.050926,0.50229,0.8632,44.727
> view matrix models
> #1,-0.16099,0.44845,0.87919,62.711,0.83516,-0.41278,0.36348,54.415,0.52591,0.79278,-0.30807,-25.407
> view matrix models
> #1,-0.39487,0.76227,-0.51286,181.45,-0.43878,-0.64691,-0.62368,423.17,-0.80719,-0.021247,0.58991,285.05
> view matrix models
> #1,0.59798,-0.63399,0.49039,31.412,-0.7389,-0.19899,0.64376,352.63,-0.31055,-0.7473,-0.58745,317.94
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 60
shifted from previous position = 5.81
rotated from previous position = 2.22 degrees
atoms outside contour = 6403, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26813581 0.22243149 -0.93735128 289.62907425
0.41584640 -0.85094411 -0.32088298 203.58940319
-0.86900804 -0.47583437 0.13567126 400.31109508
Axis -0.60273638 -0.26584441 0.75235338
Axis point 295.60757158 186.81588766 0.00000000
Rotation angle (degrees) 172.61477111
Shift along axis 72.48232164
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 263
> open /Users/linda_cmmc/Downloads/cryosparc_P83_J37_002_volume_map_sharp.mrc
Opened cryosparc_P83_J37_002_volume_map_sharp.mrc as #5, grid size
200,200,200, pixel 1.89, shown at level 0.977, step 1, values float32
> select add #5
2 models selected
> view matrix models
> #5,-0.85535,-0.37709,-0.35521,495.29,0.0062456,0.67812,-0.73493,192.08,0.51801,-0.63084,-0.57767,303.06
> volume #5 level 1.562
> volume #5 style mesh
> view matrix models
> #5,-0.90629,-0.31944,-0.27677,480.17,0.048786,0.57139,-0.81923,219.21,0.41984,-0.75596,-0.50226,332.45
> view matrix models
> #5,-0.90603,-0.31981,-0.27719,480.27,0.048591,0.57203,-0.81879,219.05,0.42042,-0.75532,-0.50273,332.3
> view matrix models
> #5,-0.22779,-0.51423,-0.82685,483.74,0.43941,0.7035,-0.55857,71.285,0.86892,-0.49057,0.065709,92.688
> view matrix models
> #5,-0.21693,-0.48126,-0.84931,479.39,0.4471,0.72443,-0.52469,59.732,0.86778,-0.49355,0.05802,94.856
> view matrix models
> #5,-0.087714,-0.50794,-0.85691,460.66,0.29795,0.80747,-0.50913,70.19,0.95054,-0.29998,0.080517,37.89
> view matrix models
> #5,-0.33042,-0.43182,-0.83926,490.28,0.56787,0.61929,-0.54221,59.354,0.75389,-0.65575,0.040594,151.01
> view matrix models
> #5,0.57535,-0.037692,-0.81704,234.96,-0.70599,0.4815,-0.51936,329.5,0.41298,0.87563,0.25042,-111.51
> view matrix models
> #5,0.57535,-0.037692,-0.81704,294.69,-0.70599,0.4815,-0.51936,249.12,0.41298,0.87563,0.25042,-119.45
> view matrix models
> #5,0.49156,-0.23144,-0.83953,351.88,-0.52634,0.68907,-0.49815,170.86,0.69378,0.68675,0.2169,-132.19
> view matrix models
> #5,0.49127,-0.087014,-0.86665,329.33,-0.55041,0.74014,-0.38632,145.78,0.67506,0.6668,0.31571,-142.46
> view matrix models
> #5,0.49127,-0.087014,-0.86665,334.8,-0.55041,0.74014,-0.38632,136.38,0.67506,0.6668,0.31571,-151.4
> view matrix models
> #5,0.49565,-0.097435,-0.86304,335.28,-0.54777,0.73607,-0.39769,138.68,0.674,0.66986,0.31146,-151.01
> view matrix models
> #5,0.49565,-0.097435,-0.86304,216.06,-0.54777,0.73607,-0.39769,259.4,0.674,0.66986,0.31146,-295.54
> view matrix models
> #5,-0.42755,-0.25096,-0.86846,425.99,0.65248,0.57925,-0.48861,71.819,0.62568,-0.77556,-0.083912,59.684
> view matrix models
> #5,-0.42755,-0.25096,-0.86846,441.7,0.65248,0.57925,-0.48861,58.754,0.62568,-0.77556,-0.083912,90.183
> view matrix models
> #5,-0.42755,-0.25096,-0.86846,324.15,0.65248,0.57925,-0.48861,208.44,0.62568,-0.77556,-0.083912,71.333
> view matrix models
> #5,0.3786,-0.23322,-0.8957,168.69,-0.34859,0.86055,-0.37141,328.84,0.85741,0.45285,0.2445,-266.32
> view matrix models
> #5,0.3786,-0.23322,-0.8957,186.89,-0.34859,0.86055,-0.37141,273.98,0.85741,0.45285,0.2445,-391.13
> view matrix models
> #5,0.27271,-0.30707,-0.91178,224.44,-0.18821,0.91236,-0.36356,231.49,0.94351,0.27075,0.19102,-363.67
> view matrix models
> #5,0.27271,-0.30707,-0.91178,232.19,-0.18821,0.91236,-0.36356,222.28,0.94351,0.27075,0.19102,-359.82
> select subtract #5
Nothing selected
> select add #5
2 models selected
> view matrix models
> #5,-0.93562,0.3245,-0.13896,194.05,0.32001,0.61354,-0.72191,267.32,-0.149,-0.71991,-0.67789,211.56
Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26793917 0.22250939 -0.93738902 289.57883827
0.41591610 -0.85091614 -0.32086683 203.58054826
-0.86903533 -0.47584798 0.13544853 400.32965883
Axis -0.60281802 -0.26587000 0.75227892
Axis point 295.62643139 186.82856746 0.00000000
Rotation angle (degrees) 172.61435075
Shift along axis 72.47026116
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 28
shifted from previous position = 0.0395
rotated from previous position = 0.0302 degrees
atoms outside contour = 6389, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26756093 0.22278293 -0.93743209 289.43657239
0.41569075 -0.85101671 -0.32089214 203.63435879
-0.86925966 -0.47554005 0.13509002 400.37155689
Axis -0.60298623 -0.26581050 0.75216513
Axis point 295.66073245 186.81986313 0.00000000
Rotation angle (degrees) 172.63238723
Shift along axis 72.49110700
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 60
shifted from previous position = 0.00624
rotated from previous position = 0.0067 degrees
atoms outside contour = 6391, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26763969 0.22282211 -0.93740029 289.44644857
0.41560923 -0.85103314 -0.32095416 203.65134753
-0.86927440 -0.47549228 0.13516332 400.36577862
Axis -0.60295634 -0.26580459 0.75219118
Axis point 295.65575361 186.81379694 0.00000000
Rotation angle (degrees) 172.63727929
Shift along axis 72.49657483
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 28
shifted from previous position = 0.0349
rotated from previous position = 0.0313 degrees
atoms outside contour = 6400, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26807010 0.22256821 -0.93733763 289.59159086
0.41579799 -0.85093613 -0.32096688 203.60719804
-0.86905147 -0.47578472 0.13556712 400.32071760
Axis -0.60276778 -0.26586530 0.75232084
Axis point 295.61555874 186.82100462 0.00000000
Rotation angle (degrees) 172.62155838
Shift along axis 72.48104734
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 60
shifted from previous position = 0.0356
rotated from previous position = 0.0369 degrees
atoms outside contour = 6390, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26752450 0.22288037 -0.93741932 289.41734971
0.41569700 -0.85098675 -0.32096349 203.63584621
-0.86926788 -0.47554800 0.13500910 400.37813198
Axis -0.60300332 -0.26584517 0.75213918
Axis point 295.66762944 186.82669791 0.00000000
Rotation angle (degrees) 172.63563384
Shift along axis 72.48485103
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.0438
rotated from previous position = 0.0445 degrees
atoms outside contour = 6404, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26816621 0.22245697 -0.93733654 289.63035555
0.41577772 -0.85096730 -0.32091051 203.60840877
-0.86903152 -0.47578100 0.13570803 400.30922064
Axis -0.60272594 -0.26582990 0.75236687
Axis point 295.60603041 186.81252739 0.00000000
Rotation angle (degrees) 172.61851971
Shift along axis 72.48646288
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.0504
rotated from previous position = 0.0463 degrees
atoms outside contour = 6391, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26748287 0.22286854 -0.93743402 289.40426460
0.41569485 -0.85099977 -0.32093174 203.63507570
-0.86928172 -0.47553024 0.13498256 400.38110611
Axis -0.60302038 -0.26583196 0.75213017
Axis point 295.66805302 186.82484403 0.00000000
Rotation angle (degrees) 172.63517338
Shift along axis 72.48932791
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.00563
rotated from previous position = 0.00616 degrees
atoms outside contour = 6391, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26755292 0.22280578 -0.93742894 289.42616333
0.41565572 -0.85102955 -0.32090347 203.63968094
-0.86927888 -0.47550636 0.13508494 400.37377148
Axis -0.60299088 -0.26580272 0.75216416
Axis point 295.66044615 186.81639377 0.00000000
Rotation angle (degrees) 172.63460076
Shift along axis 72.49748277
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 72
shifted from previous position = 3.13
rotated from previous position = 0.0273 degrees
atoms outside contour = 6401, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26796333 0.22262410 -0.93735488 289.56870893
0.41576649 -0.85095425 -0.32095965 203.61400383
-0.86909947 -0.47572616 0.13546490 400.33328407
Axis -0.60281404 -0.26585415 0.75228771
Axis point 295.63181200 186.82061260 0.00000000
Rotation angle (degrees) 172.62458737
Shift along axis 72.47809617
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 44
shifted from previous position = 0.0417
rotated from previous position = 0.0238 degrees
atoms outside contour = 6391, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26762613 0.22280791 -0.93740754 289.44244277
0.41563542 -0.85102621 -0.32093861 203.64389434
-0.86926605 -0.47551133 0.13514999 400.36548361
Axis -0.60296103 -0.26580799 0.75218622
Axis point 295.65410761 186.81443653 0.00000000
Rotation angle (degrees) 172.63567928
Shift along axis 72.49670928
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 28
shifted from previous position = 0.0467
rotated from previous position = 0.0276 degrees
atoms outside contour = 6403, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26800235 0.22257232 -0.93735602 289.58702959
0.41579739 -0.85094775 -0.32093685 203.60353176
-0.86907265 -0.47576202 0.13551101 400.32973845
Axis -0.60279599 -0.26585433 0.75230211
Axis point 295.62837198 186.81978543 0.00000000
Rotation angle (degrees) 172.62155452
Shift along axis 72.47812647
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.0522
rotated from previous position = 0.0372 degrees
atoms outside contour = 6390, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26745976 0.22290089 -0.93743292 289.39543958
0.41568880 -0.85099633 -0.32094869 203.63764622
-0.86929172 -0.47552123 0.13494988 400.38369155
Axis -0.60303081 -0.26583790 0.75211971
Axis point 295.67122644 186.82629565 0.00000000
Rotation angle (degrees) 172.63654502
Shift along axis 72.48749413
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 60
shifted from previous position = 0.0398
rotated from previous position = 0.0322 degrees
atoms outside contour = 6399, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26795825 0.22265534 -0.93734891 289.55705671
0.41570711 -0.85097700 -0.32097623 203.63202191
-0.86912944 -0.47567084 0.13546691 400.33264497
Axis -0.60281824 -0.26583954 0.75228951
Axis point 295.63024895 186.81825253 0.00000000
Rotation angle (degrees) 172.62808465
Shift along axis 72.48233304
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.00584
rotated from previous position = 0.0106 degrees
atoms outside contour = 6403, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26798669 0.22258698 -0.93735702 289.57482862
0.41586717 -0.85090746 -0.32095326 203.59347550
-0.86904409 -0.47582721 0.13546526 400.32901472
Axis -0.60280116 -0.26588790 0.75228611
Axis point 295.62400049 186.82914169 0.00000000
Rotation angle (degrees) 172.61928018
Shift along axis 72.47287177
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 28
shifted from previous position = 0.0433
rotated from previous position = 0.0355 degrees
atoms outside contour = 6391, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26750164 0.22288257 -0.93742533 289.40593474
0.41565361 -0.85101401 -0.32094739 203.64651440
-0.86929567 -0.47549817 0.13500570 400.37926255
Axis -0.60301387 -0.26582285 0.75213861
Axis point 295.66710615 186.82267099 0.00000000
Rotation angle (degrees) 172.63737908
Shift along axis 72.49101408
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.00916
rotated from previous position = 0.0104 degrees
atoms outside contour = 6390, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26766023 0.22288916 -0.93737849 289.43954287
0.41556534 -0.85103034 -0.32101840 203.66490973
-0.86928905 -0.47546587 0.13516197 400.36720177
Axis -0.60295032 -0.26581561 0.75219211
Axis point 295.65599391 186.81509800 0.00000000
Rotation angle (degrees) 172.64154850
Shift along axis 72.49807543
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 28
shifted from previous position = 0.0364
rotated from previous position = 0.0274 degrees
atoms outside contour = 6400, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26800222 0.22264134 -0.93733967 289.56910652
0.41577200 -0.85093804 -0.32099548 203.61455253
-0.86908484 -0.47574709 0.13548526 400.32960336
Axis -0.60279816 -0.26587048 0.75229467
Axis point 295.62550238 186.82277730 0.00000000
Rotation angle (degrees) 172.62510640
Shift along axis 72.47900486
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 60
shifted from previous position = 0.00162
rotated from previous position = 0.00263 degrees
atoms outside contour = 6400, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26797484 0.22261550 -0.93735363 289.56858550
0.41576292 -0.85095699 -0.32095701 203.61604191
-0.86909762 -0.47572529 0.13547980 400.33078351
Axis -0.60280916 -0.26585128 0.75229263
Axis point 295.62817760 186.82017219 0.00000000
Rotation angle (degrees) 172.62444252
Shift along axis 72.47971661
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.012
rotated from previous position = 0.0107 degrees
atoms outside contour = 6405, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26792333 0.22248395 -0.93739959 289.58178093
0.41590154 -0.85093579 -0.32083360 203.58514386
-0.86904718 -0.47582474 0.13545414 400.32880134
Axis -0.60282438 -0.26585066 0.75228066
Axis point 295.62825414 186.82627179 0.00000000
Rotation angle (degrees) 172.61395015
Shift along axis 72.46941465
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 28
shifted from previous position = 0.0447
rotated from previous position = 0.0235 degrees
atoms outside contour = 6390, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26765555 0.22273445 -0.93741660 289.45780016
0.41571580 -0.85100188 -0.32089902 203.62893820
-0.86921855 -0.47558930 0.13518115 400.36095745
Axis -0.60294533 -0.26581953 0.75219472
Axis point 295.64716326 186.82010041 0.00000000
Rotation angle (degrees) 172.62985481
Shift along axis 72.49362167
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.0108
rotated from previous position = 0.0142 degrees
atoms outside contour = 6391, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26761759 0.22293288 -0.93738027 289.42196590
0.41554966 -0.85103193 -0.32103449 203.66732993
-0.86930968 -0.47544253 0.13511143 400.37326120
Axis -0.60296933 -0.26581827 0.75217594
Axis point 295.66056077 186.81515675 0.00000000
Rotation angle (degrees) 172.64367032
Shift along axis 72.50006664
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 72
shifted from previous position = 5.9
rotated from previous position = 0.0261 degrees
atoms outside contour = 6399, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26792122 0.22267954 -0.93735375 289.54453286
0.41576576 -0.85094356 -0.32098894 203.61739981
-0.86911280 -0.47571934 0.13540331 400.33805964
Axis -0.60283275 -0.26586810 0.75226779
Axis point 295.63295148 186.82436175 0.00000000
Rotation angle (degrees) 172.62654760
Shift along axis 72.47913082
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.00643
rotated from previous position = 0.0102 degrees
atoms outside contour = 6401, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26790242 0.22256702 -0.93738584 289.55943630
0.41591126 -0.85090595 -0.32090012 203.58069435
-0.86904898 -0.47583925 0.13539164 400.33641930
Axis -0.60283464 -0.26588399 0.75226066
Axis point 295.63033380 186.83057980 0.00000000
Rotation angle (degrees) 172.61656938
Shift along axis 72.47203244
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 28
shifted from previous position = 0.0354
rotated from previous position = 0.0299 degrees
atoms outside contour = 6389, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26752751 0.22282030 -0.93743275 289.42414026
0.41567660 -0.85101791 -0.32090728 203.63786029
-0.86927671 -0.47552038 0.13504952 400.37582151
Axis -0.60300124 -0.26581300 0.75215222
Axis point 295.66506182 186.82040619 0.00000000
Rotation angle (degrees) 172.63423884
Shift along axis 72.49085724
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 48
shifted from previous position = 0.00848
rotated from previous position = 0.0111 degrees
atoms outside contour = 6391, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26765298 0.22291064 -0.93737545 289.43264679
0.41554788 -0.85103389 -0.32103159 203.66834436
-0.86929963 -0.47544945 0.13515172 400.36868934
Axis -0.60295420 -0.26581514 0.75218917
Axis point 295.65650169 186.81421170 0.00000000
Rotation angle (degrees) 172.64301491
Shift along axis 72.50023217
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 28
shifted from previous position = 0.0408
rotated from previous position = 0.024 degrees
atoms outside contour = 6401, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26793114 0.22268337 -0.93735000 289.55214860
0.41575227 -0.85094777 -0.32099525 203.61874409
-0.86911620 -0.47571002 0.13541429 400.33773328
Axis -0.60282903 -0.26586551 0.75227168
Axis point 295.63574779 186.82274306 0.00000000
Rotation angle (degrees) 172.62725136
Shift along axis 72.47709713
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 60
shifted from previous position = 0.000699
rotated from previous position = 0.00285 degrees
atoms outside contour = 6399, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26794215 0.22263610 -0.93735809 289.55937054
0.41575629 -0.85095969 -0.32095843 203.61661492
-0.86911088 -0.47571081 0.13544561 400.33493782
Axis -0.60282334 -0.26585057 0.75228153
Axis point 295.63242391 186.82009253 0.00000000
Rotation angle (degrees) 172.62537895
Shift along axis 72.47984071
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 60
shifted from previous position = 0.00147
rotated from previous position = 0.00172 degrees
atoms outside contour = 6400, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26795298 0.22261647 -0.93735965 289.56505667
0.41577707 -0.85095301 -0.32094923 203.61152184
-0.86909760 -0.47573195 0.13545657 400.33381908
Axis -0.60281792 -0.26585389 0.75228469
Axis point 295.63098665 186.82103307 0.00000000
Rotation angle (degrees) 172.62385849
Shift along axis 72.47908309
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 60
shifted from previous position = 0.0372
rotated from previous position = 0.0285 degrees
atoms outside contour = 6390, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26753637 0.22286694 -0.93741913 289.42079816
0.41569814 -0.85098850 -0.32095737 203.63552703
-0.86926368 -0.47555116 0.13502501 400.37617431
Axis -0.60299807 -0.26584252 0.75214432
Axis point 295.66549401 186.82604062 0.00000000
Rotation angle (degrees) 172.63512484
Shift along axis 72.48550181
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 72
shifted from previous position = 10.7
rotated from previous position = 0.0194 degrees
atoms outside contour = 6398, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26784586 0.22274936 -0.93735869 289.51751504
0.41572076 -0.85095840 -0.32100788 203.62841980
-0.86915755 -0.47566010 0.13532416 400.34897972
Axis -0.60286660 -0.26586227 0.75224273
Axis point 295.64276903 186.82402563 0.00000000
Rotation angle (degrees) 172.63071013
Shift along axis 72.48205739
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 60
shifted from previous position = 0.00729
rotated from previous position = 0.00672 degrees
atoms outside contour = 6399, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26792189 0.22266947 -0.93735595 289.54821647
0.41576498 -0.85094731 -0.32098001 203.61698693
-0.86911297 -0.47571735 0.13540925 400.33758631
Axis -0.60283227 -0.26586390 0.75226966
Axis point 295.63370068 186.82353521 0.00000000
Rotation angle (degrees) 172.62620940
Shift along axis 72.47840818
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 60
shifted from previous position = 0.00417
rotated from previous position = 0.00336 degrees
atoms outside contour = 6404, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26796479 0.22263004 -0.93735305 289.56483881
0.41577466 -0.85094747 -0.32096704 203.61525300
-0.86909511 -0.47573551 0.13546003 400.33129932
Axis -0.60281338 -0.26586036 0.75228605
Axis point 295.62904573 186.82272223 0.00000000
Rotation angle (degrees) 172.62448558
Shift along axis 72.47687051
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 44
shifted from previous position = 0.0341
rotated from previous position = 0.0245 degrees
atoms outside contour = 6388, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26757971 0.22277989 -0.93742745 289.44108020
0.41571928 -0.85099862 -0.32090315 203.62646538
-0.86924023 -0.47557384 0.13509607 400.37034360
Axis -0.60297770 -0.26582523 0.75216676
Axis point 295.65865644 186.82189062 0.00000000
Rotation angle (degrees) 172.63119072
Shift along axis 72.48969744
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 40
shifted from previous position = 0.00376
rotated from previous position = 0.00411 degrees
atoms outside contour = 6388, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26758277 0.22283879 -0.93741258 289.43754291
0.41567118 -0.85100420 -0.32095067 203.63864963
-0.86926230 -0.47553626 0.13508640 400.37335906
Axis -0.60297885 -0.26582800 0.75216486
Axis point 295.66357281 186.82136744 0.00000000
Rotation angle (degrees) 172.63528155
Shift along axis 72.48920042
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 26345 atoms
average map value = 1.661, steps = 96
shifted from previous position = 22.1
rotated from previous position = 0.0133 degrees
atoms outside contour = 6388, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.26772480 0.22266395 -0.93741357 289.48952552
0.41574287 -0.85099822 -0.32087364 203.61966946
-0.86918427 -0.47562884 0.13526238 400.35273165
Axis -0.60291443 -0.26581612 0.75222070
Axis point 295.64220040 186.81813417 0.00000000
Rotation angle (degrees) 172.62636405
Shift along axis 72.49081061
> open "/Users/linda_cmmc/Desktop/BiP+GRP94/Model Yasser Colorized.pdb"
Chain information for Model Yasser Colorized.pdb #4
---
Chain | Description
A B | No description available
C | No description available
> select subtract #1
Nothing selected
> select #1/C
6051 atoms, 6096 bonds, 388 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 76
shifted from previous position = 14.5
rotated from previous position = 9.89 degrees
atoms outside contour = 3578, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29825197 0.31303768 -0.90169462 285.79883902
0.50453404 -0.75022023 -0.42733478 179.34257341
-0.81024143 -0.58238906 0.06581650 398.26413483
Axis -0.58995517 -0.34796381 0.72861107
Axis point 295.08222986 199.29456263 0.00000000
Rotation angle (degrees) 172.44881044
Shift along axis 59.16642861
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 36
shifted from previous position = 0.00302
rotated from previous position = 0.0082 degrees
atoms outside contour = 3579, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29833141 0.31292927 -0.90170597 285.82540244
0.50450898 -0.75026256 -0.42729005 179.34663718
-0.81022779 -0.58239280 0.06595126 398.25410817
Axis -0.58991955 -0.34792915 0.72865645
Axis point 295.06858404 199.28473982 0.00000000
Rotation angle (degrees) 172.44597784
Shift along axis 59.17651045
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 76
shifted from previous position = 12.7
rotated from previous position = 0.0465 degrees
atoms outside contour = 3574, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29770966 0.31335471 -0.90176371 285.61429609
0.50475435 -0.75009636 -0.42729206 179.25522854
-0.81030366 -0.58237812 0.06514378 398.32210396
Axis -0.59018684 -0.34805526 0.72837973
Axis point 295.13043176 199.31425137 0.00000000
Rotation angle (degrees) 172.45023597
Shift along axis 59.17322471
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 28
shifted from previous position = 0.0509
rotated from previous position = 0.0359 degrees
atoms outside contour = 3575, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29823515 0.31311513 -0.90167329 285.78776056
0.50453525 -0.75018838 -0.42738926 179.34188745
-0.81024687 -0.58238846 0.06575493 398.27034528
Axis -0.58996411 -0.34799089 0.72859089
Axis point 295.08927152 199.30012264 0.00000000
Rotation angle (degrees) 172.45162403
Shift along axis 59.16228044
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 76
shifted from previous position = 9.14
rotated from previous position = 0.00553 degrees
atoms outside contour = 3577, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29814855 0.31310374 -0.90170588 285.76454872
0.50457545 -0.75019439 -0.42733126 179.32576006
-0.81025371 -0.58238684 0.06568491 398.27580405
Axis -0.58999950 -0.34798320 0.72856591
Axis point 295.09267250 199.29863567 0.00000000
Rotation angle (degrees) 172.44931773
Shift along axis 59.16687952
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 100
shifted from previous position = 16.3
rotated from previous position = 0.0183 degrees
atoms outside contour = 3570, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29786316 0.31320524 -0.90176495 285.67052576
0.50466929 -0.75017604 -0.42725264 179.28484223
-0.81030023 -0.58235589 0.06538474 398.30471938
Axis -0.59012045 -0.34799530 0.72846216
Axis point 295.11279837 199.30191313 0.00000000
Rotation angle (degrees) 172.44853964
Shift along axis 59.17961442
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 72
shifted from previous position = 11.4
rotated from previous position = 0.00391 degrees
atoms outside contour = 3570, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29790915 0.31315476 -0.90176729 285.68543506
0.50467371 -0.75018112 -0.42723850 179.27545107
-0.81028056 -0.58237650 0.06544485 398.30088324
Axis -0.59009963 -0.34798878 0.72848215
Axis point 295.10679753 199.29610675 0.00000000
Rotation angle (degrees) 172.44657032
Shift along axis 59.18636911
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 64
shifted from previous position = 8.9
rotated from previous position = 0.0342 degrees
atoms outside contour = 3578, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29839436 0.31288025 -0.90170215 285.84519820
0.50448857 -0.75027901 -0.42728525 179.35377150
-0.81021731 -0.58239794 0.06603452 398.24616188
Axis -0.58989222 -0.34791605 0.72868483
Axis point 295.06055132 199.28104441 0.00000000
Rotation angle (degrees) 172.44513908
Shift along axis 59.17802225
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 76
shifted from previous position = 7.74
rotated from previous position = 0.0395 degrees
atoms outside contour = 3572, contour level = 1.3
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29785054 0.31325497 -0.90175184 285.65820210
0.50464723 -0.75017263 -0.42728468 179.29361456
-0.81031860 -0.58233354 0.06535607 398.30597267
Axis -0.59012757 -0.34800177 0.72845330
Axis point 295.11386760 199.30380485 0.00000000
Rotation angle (degrees) 172.45129529
Shift along axis 59.17802362
> volume #2 level 1.573
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 60
shifted from previous position = 6.41
rotated from previous position = 0.00679 degrees
atoms outside contour = 7776, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29786515 0.31314258 -0.90178605 285.68305305
0.50467806 -0.75019875 -0.42720241 179.28396329
-0.81029403 -0.58236034 0.06542188 398.30203753
Axis -0.59011788 -0.34797498 0.72847396
Axis point 295.11164183 199.29929085 0.00000000
Rotation angle (degrees) 172.44582880
Shift along axis 59.17965002
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 72
shifted from previous position = 11.7
rotated from previous position = 0.00909 degrees
atoms outside contour = 7783, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29799125 0.31307787 -0.90176686 285.70470280
0.50461551 -0.75023142 -0.42721892 179.29762498
-0.81028662 -0.58235304 0.06557845 398.28940335
Axis -0.59006453 -0.34795210 0.72852810
Axis point 295.09124360 199.28899273 0.00000000
Rotation angle (degrees) 172.44630829
Shift along axis 59.19382776
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 92
shifted from previous position = 19.3
rotated from previous position = 0.0115 degrees
atoms outside contour = 7778, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29792407 0.31291178 -0.90184670 285.72664898
0.50463571 -0.75031844 -0.42704220 179.29753420
-0.81029874 -0.58233020 0.06563147 398.28927533
Axis -0.59008851 -0.34787877 0.72854369
Axis point 295.09698229 199.28151321 0.00000000
Rotation angle (degrees) 172.43908090
Shift along axis 59.19331898
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 72
shifted from previous position = 10.8
rotated from previous position = 0.035 degrees
atoms outside contour = 7783, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29847717 0.31280175 -0.90170197 285.87614720
0.50440765 -0.75034617 -0.42726286 179.38081245
-0.81023719 -0.58235358 0.06618161 398.23855250
Axis -0.58985737 -0.34786849 0.72873575
Axis point 295.05236246 199.27234314 0.00000000
Rotation angle (degrees) 172.44576624
Shift along axis 59.18358391
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 56
shifted from previous position = 3.36
rotated from previous position = 0.00935 degrees
atoms outside contour = 7783, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29839633 0.31291204 -0.90169046 285.84431350
0.50446524 -0.75028004 -0.42731098 179.36419379
-0.81023111 -0.58237953 0.06602757 398.24717895
Axis -0.58989277 -0.34791846 0.72868324
Axis point 295.06318700 199.28307751 0.00000000
Rotation angle (degrees) 172.44730853
Shift along axis 59.17443871
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 84
shifted from previous position = 14.1
rotated from previous position = 0.00383 degrees
atoms outside contour = 7784, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29845965 0.31290967 -0.90167033 285.85890034
0.50445914 -0.75026398 -0.42734639 179.36538016
-0.81021159 -0.58240149 0.06607338 398.24167499
Axis -0.58986601 -0.34793051 0.72869915
Axis point 295.05793251 199.28320834 0.00000000
Rotation angle (degrees) 172.44762227
Shift along axis 59.17323029
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 52
shifted from previous position = 3.49
rotated from previous position = 0.00874 degrees
atoms outside contour = 7781, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29834024 0.31299020 -0.90168190 285.81953646
0.50450005 -0.75023709 -0.42734530 179.35002208
-0.81023010 -0.58239286 0.06592235 398.25506265
Axis -0.58991750 -0.34795142 0.72864748
Axis point 295.07041844 199.28855317 0.00000000
Rotation angle (degrees) 172.44865522
Shift along axis 59.17250940
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 108
shifted from previous position = 13.8
rotated from previous position = 0.0329 degrees
atoms outside contour = 7780, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29786432 0.31323673 -0.90175363 285.66905563
0.50468153 -0.75015193 -0.42728052 179.28196336
-0.81029218 -0.58237002 0.06535871 398.30557556
Axis -0.59012039 -0.34801368 0.72845344
Axis point 295.11517327 199.30553687 0.00000000
Rotation angle (degrees) 172.44921270
Shift along axis 59.17535690
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 92
shifted from previous position = 11.5
rotated from previous position = 0.0348 degrees
atoms outside contour = 7783, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29833107 0.31292560 -0.90170735 285.82511874
0.50448911 -0.75027869 -0.42728518 179.35427912
-0.81024029 -0.58237398 0.06596389 398.25418069
Axis -0.58992014 -0.34791851 0.72866106
Axis point 295.06816372 199.28366380 0.00000000
Rotation angle (degrees) 172.44666868
Shift along axis 59.17764873
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 88
shifted from previous position = 19.5
rotated from previous position = 0.00566 degrees
atoms outside contour = 7786, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29842279 0.31289551 -0.90168744 285.84072014
0.50447359 -0.75027287 -0.42731374 179.35468918
-0.81021617 -0.58239765 0.06605100 398.24447113
Axis -0.58988093 -0.34792233 0.72869098
Axis point 295.05462972 199.27936948 0.00000000
Rotation angle (degrees) 172.44640278
Shift along axis 59.18366453
> select add #1
20294 atoms, 20478 bonds, 2 pseudobonds, 1246 residues, 2 models selected
> view matrix models
> #1,-0.38952,0.79407,-0.46661,167.38,-0.32099,-0.5919,-0.73934,391.03,-0.86327,-0.13821,0.48544,314.77
> view matrix models
> #1,-0.38952,0.79407,-0.46661,168.34,-0.32099,-0.5919,-0.73934,390.6,-0.86327,-0.13821,0.48544,316.03
> view matrix models
> #1,-0.47746,0.78665,-0.39143,183.46,-0.53597,-0.61375,-0.57969,428.63,-0.69625,-0.066982,0.71466,257.7
> view matrix models
> #1,-0.32332,0.68079,-0.65726,176.24,-0.19977,-0.72802,-0.6558,371.33,-0.92496,-0.080729,0.37138,329.3
> view matrix models
> #1,-0.96519,0.11863,-0.23312,336.16,-0.25223,-0.65807,0.70945,288.52,-0.069246,0.74355,0.66509,48.238
> view matrix models
> #1,-0.97761,0.046588,-0.20521,343.73,-0.18345,-0.66638,0.7227,273.35,-0.10308,0.74416,0.66,55.928
> view matrix models
> #1,-0.93854,-0.030176,-0.34386,351.92,-0.27344,-0.54296,0.79399,276.54,-0.21066,0.83921,0.50134,81.415
> view matrix models
> #1,-0.4507,0.60815,-0.65348,209.45,-0.12934,-0.7688,-0.62627,360.63,-0.88326,-0.19774,0.42515,331.04
> view matrix models
> #1,-0.31729,0.66869,-0.67244,175.89,-0.27865,-0.74352,-0.6079,389.65,-0.90647,-0.005507,0.42224,318.26
> view matrix models
> #1,0.089407,-0.68179,-0.72607,213.88,-0.070657,-0.73149,0.67818,257.75,-0.99349,-0.0093329,-0.11357,372.73
> view matrix models
> #1,-0.93621,0.34806,0.048585,289.81,-0.32694,-0.91331,0.24284,361.46,0.1289,0.21147,0.96885,37.333
> view matrix models
> #1,-0.17629,0.34415,0.92222,71.637,-0.58087,0.72,-0.37973,298.5,-0.79467,-0.60263,0.072979,377.55
> view matrix models
> #1,0.065324,-0.65722,0.75087,124.22,-0.55209,0.60301,0.57583,237.81,-0.83122,-0.45216,-0.32345,398.11
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 80
shifted from previous position = 7.76
rotated from previous position = 15 degrees
atoms outside contour = 7781, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29832213 0.31283278 -0.90174252 285.83735772
0.50444396 -0.75035817 -0.42719892 179.37379758
-0.81027168 -0.58232146 0.06604185 398.25324911
Axis -0.58992291 -0.34785879 0.72868733
Axis point 295.06642196 199.27676587 0.00000000
Rotation angle (degrees) 172.44505156
Shift along axis 59.18333632
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 40
shifted from previous position = 0.0455
rotated from previous position = 0.0403 degrees
atoms outside contour = 7782, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29783043 0.31322044 -0.90177048 285.66180440
0.50469396 -0.75016225 -0.42724771 179.27804549
-0.81029689 -0.58236549 0.06534068 398.30723507
Axis -0.59013404 -0.34800447 0.72844678
Axis point 295.11606179 199.30455324 0.00000000
Rotation angle (degrees) 172.44800356
Shift along axis 59.17730570
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 44
shifted from previous position = 0.00447
rotated from previous position = 0.00233 degrees
atoms outside contour = 7781, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29786222 0.31319620 -0.90176840 285.67512419
0.50468872 -0.75016668 -0.42724613 179.27979255
-0.81028847 -0.58237282 0.06537973 398.30408443
Axis -0.59012012 -0.34800038 0.72846001
Axis point 295.11407889 199.30329674 0.00000000
Rotation angle (degrees) 172.44738773
Shift along axis 59.17652081
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 76
shifted from previous position = 7.29
rotated from previous position = 0.00267 degrees
atoms outside contour = 7777, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29789431 0.31317192 -0.90176623 285.68647725
0.50467005 -0.75018067 -0.42724361 179.28720186
-0.81028830 -0.58236785 0.06542607 398.30044330
Axis -0.59010643 -0.34799020 0.72847596
Axis point 295.11082450 199.30153736 0.00000000
Rotation angle (degrees) 172.44733157
Shift along axis 59.17668104
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 28
shifted from previous position = 0.031
rotated from previous position = 0.0352 degrees
atoms outside contour = 7784, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29841395 0.31293039 -0.90167827 285.84147708
0.50447043 -0.75026162 -0.42733721 179.35895345
-0.81022139 -0.58239341 0.06602441 398.24664901
Axis -0.58988559 -0.34793251 0.72868234
Axis point 295.06056223 199.28322843 0.00000000
Rotation angle (degrees) 172.44782095
Shift along axis 59.17672196
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 52
shifted from previous position = 4.21
rotated from previous position = 0.046 degrees
atoms outside contour = 7783, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29777357 0.31333743 -0.90174862 285.64082378
0.50468884 -0.75012986 -0.42731062 179.28090623
-0.81032098 -0.58234427 0.06523094 398.31823939
Axis -0.59016107 -0.34803434 0.72841061
Axis point 295.13027225 199.31251320 0.00000000
Rotation angle (degrees) 172.45247071
Shift along axis 59.16922460
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 64
shifted from previous position = 10.2
rotated from previous position = 0.035 degrees
atoms outside contour = 7783, contour level = 1.5729
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29824588 0.31301104 -0.90170588 285.79149307
0.50451799 -0.75024646 -0.42730767 179.34232738
-0.81025366 -0.58236959 0.06583821 398.26457422
Axis -0.58995754 -0.34794438 0.72861842
Axis point 295.07733250 199.28874453 0.00000000
Rotation angle (degrees) 172.44846708
Shift along axis 59.17690305
> view matrix models
> #1,-0.5571,0.83043,-0.0040786,171.67,-0.51178,-0.34719,-0.78583,411.85,-0.654,-0.4357,0.61842,299.49
> view matrix models
> #1,-0.57604,0.75934,-0.30263,86.859,-0.29518,-0.53848,-0.78925,489.3,-0.76227,-0.3653,0.53432,291.65
> volume #2 level 1.426
> view matrix models
> #1,-0.6465,0.72207,-0.24628,212.62,-0.30664,-0.54153,-0.78276,385.27,-0.69858,-0.43054,0.57151,300.25
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 80
shifted from previous position = 14.5
rotated from previous position = 4.54 degrees
atoms outside contour = 5383, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29836912 0.31296825 -0.90167996 285.81805969
0.50446386 -0.75026367 -0.42734136 179.35566510
-0.81024199 -0.58237042 0.06597434 398.25345597
Axis -0.58990569 -0.34793334 0.72866568
Axis point 295.06251889 199.28206934 0.00000000
Rotation angle (degrees) 172.44940937
Shift along axis 59.18411229
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 72
shifted from previous position = 9.64
rotated from previous position = 0.00564 degrees
atoms outside contour = 5382, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29844838 0.31291095 -0.90167362 285.85057657
0.50445618 -0.75026935 -0.42734046 179.36338353
-0.81021759 -0.58239389 0.06606681 398.24291472
Axis -0.58987090 -0.34792685 0.72869694
Axis point 295.05626851 199.28132376 0.00000000
Rotation angle (degrees) 172.44776766
Shift along axis 59.17811682
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 68
shifted from previous position = 13.8
rotated from previous position = 0.00647 degrees
atoms outside contour = 5381, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29834653 0.31289694 -0.90171218 285.83097706
0.50450114 -0.75027836 -0.42727156 179.34856968
-0.81022710 -0.58238981 0.06598609 398.25101336
Axis -0.58991257 -0.34791650 0.72866814
Axis point 295.06465304 199.28169846 0.00000000
Rotation angle (degrees) 172.44512843
Shift along axis 59.17921172
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 96
shifted from previous position = 14.3
rotated from previous position = 0.00621 degrees
atoms outside contour = 5380, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29831499 0.31299539 -0.90168845 285.81361551
0.50449895 -0.75024402 -0.42733443 179.35150754
-0.81024008 -0.58238114 0.06590320 398.25754587
Axis -0.58992836 -0.34794668 0.72864095
Axis point 295.07296067 199.28898597 0.00000000
Rotation angle (degrees) 172.44883668
Shift along axis 59.17243820
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 84
shifted from previous position = 15.2
rotated from previous position = 0.0133 degrees
atoms outside contour = 5381, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29845176 0.31285475 -0.90169200 285.85659621
0.50441061 -0.75032759 -0.42729201 179.37547867
-0.81024471 -0.58234906 0.06612934 398.24172034
Axis -0.58986934 -0.34788453 0.72871841
Axis point 295.05308658 199.27315632 0.00000000
Rotation angle (degrees) 172.44756998
Shift along axis 59.18607703
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 88
shifted from previous position = 20.6
rotated from previous position = 0.0235 degrees
atoms outside contour = 5379, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29817711 0.31309656 -0.90169893 285.76495525
0.50455008 -0.75020629 -0.42734030 179.33040503
-0.81025899 -0.58237536 0.06572145 398.27369406
Axis -0.58998789 -0.34797585 0.72857882
Axis point 295.08688919 199.29501134 0.00000000
Rotation angle (degrees) 172.45017332
Shift along axis 59.17326222
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 64
shifted from previous position = 9.24
rotated from previous position = 0.0187 degrees
atoms outside contour = 5380, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29827510 0.31282530 -0.90176067 285.82819429
0.50449212 -0.75034311 -0.42716849 179.35505013
-0.81025902 -0.58234487 0.06599077 398.25520429
Axis -0.58994140 -0.34786616 0.72866884
Axis point 295.06950050 199.27689969 0.00000000
Rotation angle (degrees) 172.44265244
Shift along axis 59.18271675
> view matrix models
> #1,-0.21746,0.50918,0.83274,68.652,-0.79602,0.40121,-0.45319,379.93,-0.56485,-0.76143,0.31807,330.07
> view matrix models
> #1,0.38188,-0.89245,0.24023,108.32,-0.23946,0.15551,0.95837,184.94,-0.89265,-0.42351,-0.15432,399.91
> view matrix models
> #1,-0.11716,-0.49399,-0.86154,254.11,-0.92853,-0.25323,0.27147,422.23,-0.35227,0.83177,-0.42902,181.51
> open /Users/linda_cmmc/Downloads/2o1u.pdb
> /Users/linda_cmmc/Downloads/5uls.pdb
2o1u.pdb title:
Structure of full length GRP94 with amp-PNP bound [more info...]
Chain information for 2o1u.pdb #5
---
Chain | Description | UniProt
A B | endoplasmin | ENPL_CANFA 73-286 328-754
Non-standard residues in 2o1u.pdb #5
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
5uls.pdb title:
Structure of GRP94 In the active conformation [more info...]
Chain information for 5uls.pdb #6
---
Chain | Description | UniProt
A B | endoplasmin | ENPL_CANLF 48-286 328-754
Non-standard residues in 5uls.pdb #6
---
ANP — phosphoaminophosphonic acid-adenylate ester
> tile
6 models tiled
> select subtract #1
Nothing selected
> select add #5
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> view matrix models
> #5,0.87185,0.48196,-0.08713,119.54,-0.43499,0.84375,0.31444,187.28,0.22506,-0.23624,0.94527,122.79
> fitmap #5 inMap #2
Fit molecule 2o1u.pdb (#5) to map cryosparc_P83_J37_002_volume_map_sharp.mrc
(#2) using 9544 atoms
average map value = 1.633, steps = 208
shifted from previous position = 15.7
rotated from previous position = 64.6 degrees
atoms outside contour = 3211, contour level = 1.4259
Position of 2o1u.pdb (#5) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.61477223 0.78537164 0.07243157 165.16366536
-0.78773169 -0.60685903 -0.10583368 213.30436617
-0.03916303 -0.12212026 0.99174228 149.41963677
Axis -0.01032665 0.07075754 -0.99744009
Axis point 136.36920920 71.86707437 0.00000000
Rotation angle (degrees) 127.94788932
Shift along axis -135.64983094
> fitmap #5 inMap #2
Fit molecule 2o1u.pdb (#5) to map cryosparc_P83_J37_002_volume_map_sharp.mrc
(#2) using 9544 atoms
average map value = 1.633, steps = 96
shifted from previous position = 18.3
rotated from previous position = 0.0379 degrees
atoms outside contour = 3213, contour level = 1.4259
Position of 2o1u.pdb (#5) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.61471519 0.78546900 0.07185771 165.15427460
-0.78774601 -0.60678731 -0.10613779 213.27528673
-0.03976561 -0.12185015 0.99175152 149.41157363
Axis -0.00996188 0.07077092 -0.99744285
Axis point 136.38991539 71.83891769 0.00000000
Rotation angle (degrees) 127.94287619
Shift along axis -135.58106360
> fitmap #5 inMap #2
Fit molecule 2o1u.pdb (#5) to map cryosparc_P83_J37_002_volume_map_sharp.mrc
(#2) using 9544 atoms
average map value = 1.633, steps = 84
shifted from previous position = 17.3
rotated from previous position = 0.0096 degrees
atoms outside contour = 3211, contour level = 1.4259
Position of 2o1u.pdb (#5) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.61467796 0.78551138 0.07171280 165.15335459
-0.78776791 -0.60674856 -0.10619681 213.27115504
-0.03990717 -0.12176989 0.99175569 149.40868293
Axis -0.00987319 0.07076600 -0.99744408
Axis point 136.39810959 71.83108187 0.00000000
Rotation angle (degrees) 127.93996423
Shift along axis -135.56505040
> view matrix models
> #5,0.10351,0.99264,0.062933,86.769,-0.94397,0.07811,0.32065,204.54,0.31337,-0.092598,0.94511,122.32
> view matrix models
> #5,0.047241,0.99862,0.023094,87.469,-0.95742,0.038676,0.2861,206.32,0.28481,-0.035626,0.95792,120.55
> view matrix models
> #5,0.6824,0.46879,0.56086,94.151,-0.19612,-0.62172,0.75829,219,0.70417,-0.62745,-0.33233,187.42
> view matrix models
> #5,0.90848,0.24341,-0.33974,131.29,0.090461,0.6791,0.72845,171.49,0.40803,-0.69251,0.59493,161.98
> fitmap #5 inMap #2
Fit molecule 2o1u.pdb (#5) to map cryosparc_P83_J37_002_volume_map_sharp.mrc
(#2) using 9544 atoms
average map value = 1.633, steps = 88
shifted from previous position = 11.9
rotated from previous position = 4.45 degrees
atoms outside contour = 3211, contour level = 1.4259
Position of 2o1u.pdb (#5) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.61478284 0.78537173 0.07234054 165.16220307
-0.78771913 -0.60686836 -0.10587359 213.30015152
-0.03924894 -0.12207330 0.99174466 149.41876243
Axis -0.01027166 0.07075491 -0.99744084
Axis point 136.37051572 71.86384113 0.00000000
Rotation angle (degrees) 127.94852713
Shift along axis -135.64083266
> fitmap #5 inMap #2
Fit molecule 2o1u.pdb (#5) to map cryosparc_P83_J37_002_volume_map_sharp.mrc
(#2) using 9544 atoms
average map value = 1.633, steps = 84
shifted from previous position = 9.58
rotated from previous position = 0.0128 degrees
atoms outside contour = 3211, contour level = 1.4259
Position of 2o1u.pdb (#5) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.61467539 0.78546867 0.07220102 165.15982202
-0.78779441 -0.60675542 -0.10596070 213.29343732
-0.03942046 -0.12201101 0.99174552 149.41461479
Axis -0.01017581 0.07076746 -0.99744094
Axis point 136.38461498 71.85149338 0.00000000
Rotation angle (degrees) 127.94048977
Shift along axis -135.61865406
> fitmap #5 inMap #2
Fit molecule 2o1u.pdb (#5) to map cryosparc_P83_J37_002_volume_map_sharp.mrc
(#2) using 9544 atoms
average map value = 1.633, steps = 60
shifted from previous position = 7.39
rotated from previous position = 0.008 degrees
atoms outside contour = 3211, contour level = 1.4259
Position of 2o1u.pdb (#5) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.61470101 0.78543707 0.07232659 165.16319985
-0.78778019 -0.60678143 -0.10591756 213.30083765
-0.03930516 -0.12208510 0.99174098 149.41684121
Axis -0.01025042 0.07077593 -0.99743957
Axis point 136.38061602 71.85935028 0.00000000
Rotation angle (degrees) 127.94252995
Shift along axis -135.63069608
> view matrix models
> #5,-0.042315,0.90111,0.43152,86.068,-0.94757,-0.17312,0.2686,215.37,0.31674,-0.39752,0.86119,140.76
> view matrix models
> #5,-0.042315,0.90111,0.43152,-67.952,-0.94757,-0.17312,0.2686,309.97,0.31674,-0.39752,0.86119,-1.9176
> select add #6
19413 atoms, 19337 bonds, 22 pseudobonds, 2880 residues, 5 models selected
> select subtract #5
9869 atoms, 9858 bonds, 9 pseudobonds, 1484 residues, 2 models selected
> view matrix models
> #6,0.77341,0.61322,0.16062,-62.26,-0.61654,0.78658,-0.03429,307.54,-0.14737,-0.07251,0.98642,-80.224
> view matrix models
> #6,0.90683,0.39306,0.15222,-88.581,-0.42076,0.86563,0.27139,223.67,-0.025095,-0.31015,0.95036,-143.33
> select subtract #6
Nothing selected
> select add #1
20294 atoms, 20478 bonds, 2 pseudobonds, 1246 residues, 2 models selected
> view matrix models
> #1,-0.7394,0.63268,-0.23022,245.37,-0.34985,-0.65321,-0.67151,405.73,-0.57523,-0.41597,0.70433,260.85
> select subtract #1
Nothing selected
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 84
shifted from previous position = 18.5
rotated from previous position = 0.0246 degrees
atoms outside contour = 5381, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29798919 0.31303677 -0.90178181 285.74333556
0.50468583 -0.75020105 -0.42718918 179.29758335
-0.81024358 -0.58241426 0.06556658 398.28369148
Axis -0.59006255 -0.34796749 0.72852235
Axis point 295.10397942 199.30222774 0.00000000
Rotation angle (degrees) 172.44182824
Shift along axis 59.16239709
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 84
shifted from previous position = 16.3
rotated from previous position = 0.0118 degrees
atoms outside contour = 5378, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29808749 0.31310819 -0.90172452 285.75464565
0.50452060 -0.75025250 -0.42729400 179.34498489
-0.81031033 -0.58230959 0.06567135 398.28357457
Axis -0.59002696 -0.34794463 0.72856209
Axis point 295.10114609 199.29536428 0.00000000
Rotation angle (degrees) 172.45163001
Shift along axis 59.16924455
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 76
shifted from previous position = 7
rotated from previous position = 0.0069 degrees
atoms outside contour = 5378, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29807755 0.31321383 -0.90169112 285.71595467
0.50445695 -0.75025155 -0.42737080 179.34335202
-0.81035361 -0.58225399 0.06563025 398.29013211
Axis -0.59003538 -0.34795489 0.72855037
Axis point 295.09687810 199.28675368 0.00000000
Rotation angle (degrees) 172.45822272
Shift along axis 59.18850390
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 76
shifted from previous position = 13.1
rotated from previous position = 0.0147 degrees
atoms outside contour = 5382, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29805909 0.31299709 -0.90177248 285.74406279
0.50460625 -0.75025325 -0.42719152 179.30791604
-0.81026744 -0.58236835 0.06567951 398.27979723
Axis -0.59003408 -0.34793273 0.72856201
Axis point 295.08835394 199.28772325 0.00000000
Rotation angle (degrees) 172.44382462
Shift along axis 59.18570044
> fitmap #1 inMap #2
Fit molecule Model Yasser Colorized.pdb (#1) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 20294 atoms
average map value = 1.725, steps = 76
shifted from previous position = 15.1
rotated from previous position = 0.0138 degrees
atoms outside contour = 5382, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#1) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.29827683 0.31300974 -0.90169609 285.79733409
0.50450573 -0.75024535 -0.42732410 179.34564890
-0.81024991 -0.58237172 0.06586560 398.26173062
Axis -0.58994471 -0.34794596 0.72862806
Axis point 295.07406216 199.28792109 0.00000000
Rotation angle (degrees) 172.44900210
Shift along axis 59.17745145
> select add #3
7774 atoms, 7833 bonds, 500 residues, 1 model selected
> view matrix models
> #3,0.11895,-0.90419,0.41023,114.59,-0.36204,0.34522,0.86588,323.97,-0.92454,-0.25152,-0.28629,345.73
> volume #2 style surface
> view matrix models
> #3,0.43095,0.18146,0.88394,-124,0.35366,-0.93517,0.019561,425.07,0.83018,0.30418,-0.46719,-41.743
> surface sel
> view matrix models
> #3,0.00044454,0.69339,-0.72056,2.8197,0.99749,0.050756,0.049458,170.67,0.070867,-0.71877,-0.69163,253.12
> view matrix models
> #3,-0.14001,0.9822,0.12521,-70.933,0.7717,0.18748,-0.60772,241.62,-0.62038,0.011535,-0.78422,289.97
> view matrix models
> #3,0.26314,0.77216,0.57838,-150.25,0.96437,-0.22751,-0.13502,227.56,0.027332,0.5933,-0.80452,92.839
> view matrix models
> #3,0.13752,0.57094,0.80939,-116.51,0.98233,0.026126,-0.18534,193.74,-0.12696,0.82058,-0.55726,73.097
> view matrix models
> #3,-0.79715,0.22313,0.56104,121.83,-0.60313,-0.25105,-0.75711,566.8,-0.028079,-0.94191,0.3347,227.5
> view matrix models
> #3,-0.79761,0.054844,0.60067,141.7,-0.52862,-0.54315,-0.65235,584.69,0.29047,-0.83784,0.46221,145.13
> view matrix models
> #3,-0.79761,0.054844,0.60067,284.48,-0.52862,-0.54315,-0.65235,493.57,0.29047,-0.83784,0.46221,171.32
> view matrix models
> #3,-0.79761,0.054844,0.60067,283.79,-0.52862,-0.54315,-0.65235,494.33,0.29047,-0.83784,0.46221,171.86
> view matrix models
> #3,-0.053143,-0.11593,0.99183,134.39,0.5375,-0.8404,-0.069432,283.6,0.84159,0.52942,0.10698,-120.2
> view matrix models
> #3,0.54468,0.20614,0.81292,-96.611,-0.74443,-0.32752,0.58185,473.77,0.38619,-0.92208,-0.024936,175.65
> surface hidePatches (#!3 & sel)
> view matrix models
> #3,0.45549,9.1062e-05,0.89024,7.3181,-0.7225,-0.58421,0.36972,476.84,0.52012,-0.8116,-0.26604,163.02
> fitmap #3 inMap #2
Fit molecule Model Yasser Colorized.pdb (#3) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 7774 atoms
average map value = 1.807, steps = 156
shifted from previous position = 42.5
rotated from previous position = 31.7 degrees
atoms outside contour = 1706, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#3) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.64278703 -0.31437033 0.69856724 51.59412721
-0.60575025 0.34962805 0.71472158 224.37844156
-0.46892595 -0.88257100 0.03430647 410.83119969
Axis -0.79871756 0.58379869 -0.14570296
Axis point 0.00000000 394.45204152 69.44149387
Rotation angle (degrees) 89.23446112
Shift along axis 29.92338203
> fitmap #3 inMap #2
Fit molecule Model Yasser Colorized.pdb (#3) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 7774 atoms
average map value = 1.623, steps = 156
shifted from previous position = 37.4
rotated from previous position = 17.9 degrees
atoms outside contour = 3117, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#3) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.60350781 -0.22286773 0.76557714 56.69369049
-0.52019932 0.61761381 0.58986941 150.80409708
-0.60429386 -0.75424346 0.25679910 393.19770891
Axis -0.69210723 0.70537054 -0.15310123
Axis point 458.91354709 0.00000000 157.34767098
Rotation angle (degrees) 76.17481235
Shift along axis 6.93560026
> view matrix models
> #3,-0.96814,0.20033,0.15022,314.45,-0.20037,-0.26004,-0.94458,340.89,-0.15016,-0.94459,0.2919,302.14
> fitmap #3 inMap #2
Fit molecule Model Yasser Colorized.pdb (#3) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 7774 atoms
average map value = 1.807, steps = 120
shifted from previous position = 23.6
rotated from previous position = 17.9 degrees
atoms outside contour = 1705, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#3) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.64288182 -0.31444108 0.69844816 51.59075845
-0.60566697 0.34952983 0.71484018 224.36652593
-0.46890358 -0.88258470 0.03425979 410.83436200
Axis -0.79878345 0.58372776 -0.14562589
Axis point 0.00000000 394.41392540 69.46941184
Rotation angle (degrees) 89.23589689
Shift along axis 29.93100483
> view matrix models
> #3,0.16199,-0.15243,0.97495,44.678,-0.42624,-0.90188,-0.070189,440.57,0.88999,-0.40419,-0.21107,29.363
> fitmap #3 inMap #2
Fit molecule Model Yasser Colorized.pdb (#3) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 7774 atoms
average map value = 1.807, steps = 96
shifted from previous position = 15.5
rotated from previous position = 0.0333 degrees
atoms outside contour = 1707, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#3) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.64280251 -0.31394909 0.69874241 51.56002313
-0.60591848 0.34971238 0.71453770 224.40593523
-0.46868733 -0.88268753 0.03456843 410.76267600
Axis -0.79868582 0.58376838 -0.14599808
Axis point 0.00000000 394.46657040 69.32655660
Rotation angle (degrees) 89.22409642
Shift along axis 29.85026940
> view matrix models
> #3,0.44294,-0.33477,0.8317,36.342,0.057138,-0.91525,-0.39882,378.06,0.89473,0.22418,-0.38627,-65.304
> fitmap #3 inMap #2
Fit molecule Model Yasser Colorized.pdb (#3) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 7774 atoms
average map value = 1.807, steps = 104
shifted from previous position = 18.9
rotated from previous position = 0.0232 degrees
atoms outside contour = 1706, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#3) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.64282318 -0.31430437 0.69856365 51.58272844
-0.60571406 0.34969402 0.71471997 224.36053086
-0.46892313 -0.88256836 0.03441284 410.81798266
Axis -0.79871655 0.58379630 -0.14571806
Axis point 0.00000000 394.45800075 69.43063400
Rotation angle (degrees) 89.22848781
Shift along axis 29.91727141
> view matrix models
> #3,-0.3388,0.51916,0.78466,65.589,-0.89394,-0.4377,-0.096384,474.95,0.2934,-0.73409,0.61239,154.75
> fitmap #3 inMap #2
Fit molecule Model Yasser Colorized.pdb (#3) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 7774 atoms
average map value = 1.807, steps = 108
shifted from previous position = 19.9
rotated from previous position = 0.0123 degrees
atoms outside contour = 1707, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#3) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.64294248 -0.31431680 0.69844826 51.57769422
-0.60567555 0.34952399 0.71483576 224.36747355
-0.46880931 -0.88263128 0.03434982 410.80909149
Axis -0.79880530 0.58368124 -0.14569247
Axis point 0.00000000 394.40247315 69.43956762
Rotation angle (degrees) 89.23174686
Shift along axis 29.90675789
> view matrix models
> #3,0.86276,0.31038,0.39913,-116.07,-0.15857,-0.58347,0.7965,315.06,0.4801,-0.75048,-0.45418,172.25
> fitmap #3 inMap #2
Fit molecule Model Yasser Colorized.pdb (#3) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 7774 atoms
average map value = 1.807, steps = 136
shifted from previous position = 34.1
rotated from previous position = 0.0317 degrees
atoms outside contour = 1706, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#3) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.64279685 -0.31389619 0.69877139 51.52209505
-0.60599974 0.34962430 0.71451188 224.43615036
-0.46859001 -0.88274123 0.03451638 410.77010842
Axis -0.79869898 0.58373363 -0.14606502
Axis point 0.00000000 394.44983500 69.32759247
Rotation angle (degrees) 89.22827313
Shift along axis 29.86114000
> view matrix models
> #3,-0.89437,0.20777,0.39614,65.181,-0.44413,-0.30689,-0.84176,524.33,-0.053319,-0.92879,0.36675,244.27
> view matrix models
> #3,0.15576,0.88792,-0.43283,-161.22,0.98544,-0.16994,0.006017,178.96,-0.068211,-0.42746,-0.90146,271.55
> view matrix models
> #3,0.15576,0.88792,-0.43283,100.18,0.98544,-0.16994,0.006017,-1.6062,-0.068211,-0.42746,-0.90146,290.51
> view matrix models
> #3,-0.64631,-0.38619,-0.65814,324.47,-0.26602,0.9224,-0.28002,200.64,0.71521,-0.0058978,-0.69889,104.56
> fitmap #3 inMap #2
Fit molecule Model Yasser Colorized.pdb (#3) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 7774 atoms
average map value = 1.814, steps = 128
shifted from previous position = 16.9
rotated from previous position = 30.3 degrees
atoms outside contour = 1583, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#3) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.58856991 0.67559007 -0.44403105 237.58723871
0.07394530 0.59192493 0.80259393 62.62803550
0.80505753 0.43954861 -0.39834590 35.94655259
Axis -0.25331480 -0.87155130 -0.41979751
Axis point 114.18896031 0.00000000 52.46276429
Rotation angle (degrees) 134.22640520
Shift along axis -129.85818248
> fitmap #3 inMap #2
Fit molecule Model Yasser Colorized.pdb (#3) to map
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) using 7774 atoms
average map value = 1.742, steps = 260
shifted from previous position = 52.6
rotated from previous position = 97.6 degrees
atoms outside contour = 2239, contour level = 1.4259
Position of Model Yasser Colorized.pdb (#3) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.72254317 -0.69119401 0.01350108 410.81275461
-0.69037559 0.72243598 0.03831256 209.80161765
-0.03623508 0.01836166 -0.99917462 226.89277632
Axis -0.37225508 0.92800483 0.01527045
Axis point 249.11901069 0.00000000 108.63242627
Rotation angle (degrees) 178.46444067
Shift along axis 45.23453604
> view matrix models
> #3,0.45861,-0.78955,-0.40778,16.739,-0.87548,-0.32277,-0.35965,524.15,0.15234,0.52194,-0.83927,83.863
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> select subtract #3
1 model selected
> select add #2
2 models selected
> view matrix models
> #2,0.52036,-0.84914,0.090519,99.019,0.73774,0.5004,0.45314,-91.487,-0.43007,-0.16902,0.88683,7.4362
> select subtract #2
Nothing selected
> save /Users/linda_cmmc/Desktop/image4.png supersample 3
> open /Users/linda_cmmc/Downloads/7kw7.pdb
7kw7.pdb title:
Atomic cryoem structure of HSP90-HSP70-hop-GR [more info...]
Chain information for 7kw7.pdb #7
---
Chain | Description | UniProt
A B | heat shock protein HSP 90-α | HS90A_HUMAN 1-732
C D | heat shock 70 kda protein 1A | HS71A_HUMAN 1-641
E | stress-induced-phosphoprotein 1 | STIP1_HUMAN 1-543
F | glucocorticoid receptor | GCR_HUMAN 1-777
Non-standard residues in 7kw7.pdb #7
---
ADP — adenosine-5'-diphosphate
K — potassium ion
MG — magnesium ion
> hide #2,7 target a
> cartoon #2,7
> select #1/A,B:1-225
4588 atoms, 4610 bonds, 292 residues, 1 model selected
> color (#!1 & sel) red
> select #1/A,B:226-280
1760 atoms, 1774 bonds, 110 residues, 1 model selected
> color (#!1 & sel) light gray
> select #1/A,B:281-544
7208 atoms, 7294 bonds, 2 pseudobonds, 432 residues, 2 models selected
> color (#!1 & sel) cyan
> select #1/A,B:545-554
306 atoms, 308 bonds, 20 residues, 1 model selected
> color (#!1 & sel) light gray
> select #1/A,B:555-695
4616 atoms, 4660 bonds, 282 residues, 1 model selected
> color (#!1 & sel) blue
> select #1/A,B:696-732
1198 atoms, 1202 bonds, 74 residues, 1 model selected
> color (#!1 & sel) light gray
> select #1/C,D:1-381
Nothing selected
> color (#!1 & sel) forest green
> select #1/C,D:1-381
Nothing selected
> color (#!1 & sel) forest green
> select #1/C,D:382-396
Nothing selected
> color (#!1 & sel) light gray
> select #1/C,D:396-611
Nothing selected
> color (#!1 & sel) light green
> select #1/C,D:612-641
Nothing selected
> color (#!1 & sel) light gray
> cartoon hide #1/E,F
> select #7/A,B:1-225
6540 atoms, 6592 bonds, 416 residues, 1 model selected
> color (#!7 & sel) red
> select #7/A,B:226-280
Nothing selected
> color (#!7 & sel) light gray
> select #7/A,B:281-544
8744 atoms, 8826 bonds, 520 residues, 1 model selected
> color (#!7 & sel) cyan
> select #7/A,B:545-554
304 atoms, 304 bonds, 20 residues, 1 model selected
> color (#!7 & sel) light gray
> select #7/A,B:555-695
4612 atoms, 4638 bonds, 282 residues, 1 model selected
> color (#!7 & sel) blue
> select #7/A,B:696-732
190 atoms, 187 bonds, 1 pseudobond, 13 residues, 2 models selected
> color (#!7 & sel) light gray
> select #7/C,D:1-381
11750 atoms, 11846 bonds, 756 residues, 1 model selected
> color (#!7 & sel) forest green
> select #7/C,D:1-381
11750 atoms, 11846 bonds, 756 residues, 1 model selected
> color (#!7 & sel) forest green
> select #7/C,D:382-396
237 atoms, 235 bonds, 16 residues, 1 model selected
> color (#!7 & sel) light gray
> select #7/C,D:396-611
1702 atoms, 1713 bonds, 112 residues, 1 model selected
> color (#!7 & sel) light green
> select #7/C,D:612-641
106 atoms, 106 bonds, 7 residues, 1 model selected
> color (#!7 & sel) light gray
> cartoon hide #1/E,F
> cartoon hide #7/E,F
> select add #7
43804 atoms, 44165 bonds, 8 pseudobonds, 2733 residues, 3 models selected
> select subtract #7
Nothing selected
> select add #7
43804 atoms, 44165 bonds, 8 pseudobonds, 2733 residues, 3 models selected
> view matrix models
> #7,0.99581,0.068626,0.060463,-277.2,-0.070544,0.99705,0.030177,125.45,-0.058214,-0.034316,0.99771,-124.95
> view matrix models
> #7,-0.16423,0.92027,0.35514,-279.31,0.36362,0.39115,-0.84545,303.89,-0.91696,-0.0097103,-0.39887,248.31
> view matrix models
> #7,-0.56852,0.75345,0.3303,-180.63,-0.57293,-0.074492,-0.81621,531.12,-0.59037,-0.65327,0.47403,155.05
> view matrix models
> #7,-0.7293,0.60236,0.32447,-127.84,-0.4291,-0.033304,-0.90264,515.18,-0.53291,-0.79753,0.28276,202.17
> view matrix models
> #7,-0.65271,0.68041,0.33318,-155.01,-0.5013,-0.058143,-0.86332,524.57,-0.56804,-0.73052,0.37904,180.41
> view matrix models
> #7,-0.65271,0.68041,0.33318,-175.25,-0.5013,-0.058143,-0.86332,544.51,-0.56804,-0.73052,0.37904,191.52
> view matrix models
> #7,-0.59635,0.77874,0.19476,-30.535,-0.41067,-0.087502,-0.90758,447.68,-0.68972,-0.62121,0.37199,220.35
> view matrix models
> #7,0.075838,-0.22582,0.97121,-87.157,-0.83005,0.52541,0.18698,217.29,-0.55251,-0.82033,-0.14759,320.53
> fitmap #7 inMap #2
Fit molecule 7kw7.pdb (#7) to map cryosparc_P83_J37_002_volume_map_sharp.mrc
(#2) using 43804 atoms
average map value = 1.332, steps = 112
shifted from previous position = 23.6
rotated from previous position = 17.2 degrees
atoms outside contour = 22038, contour level = 1.4259
Position of 7kw7.pdb (#7) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.27781880 0.40218585 -0.87238925 311.83742644
0.53466684 -0.68974091 -0.48825055 306.91740562
-0.79809011 -0.60208286 -0.02341245 424.49000042
Axis -0.59970439 -0.39143120 0.69795148
Axis point 327.97487086 282.89444549 0.00000000
Rotation angle (degrees) 174.55403127
Shift along axis -10.87389912
> fitmap #7 inMap #2
Fit molecule 7kw7.pdb (#7) to map cryosparc_P83_J37_002_volume_map_sharp.mrc
(#2) using 43804 atoms
average map value = 1.332, steps = 84
shifted from previous position = 16.5
rotated from previous position = 0.0277 degrees
atoms outside contour = 22044, contour level = 1.4259
Position of 7kw7.pdb (#7) relative to
cryosparc_P83_J37_002_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.27760306 0.40188919 -0.87259462 311.92686722
0.53497503 -0.68976537 -0.48787826 306.79712260
-0.79795865 -0.60225291 -0.02351971 424.51221890
Axis -0.59978329 -0.39139277 0.69790523
Axis point 328.02096396 282.88838277 0.00000000
Rotation angle (degrees) 174.52872814
Shift along axis -10.89739921
> view matrix models
> #7,-0.53006,0.84703,0.039716,-170.69,-0.27218,-0.12559,-0.95402,552.07,-0.80309,-0.5165,0.29711,193.28
> view matrix models
> #7,-0.53006,0.84703,0.039716,-171.41,-0.27218,-0.12559,-0.95402,556.76,-0.80309,-0.5165,0.29711,202.06
> surface (#!7 & sel)
> surface hidePatches patches #7/E,F
Expected an objects specifier or a keyword
> surface hidePatches (#7/E,F)
> movie record
> wait 10
> turn y 1 360 models #2 center #2
> turn y 1 360 models #7 center #7
> wait 360
> wait 30
> turn x 1 90 models #2 center #2
> turn x 1 90 models #7 center #7
> wait 90
> surface hidePatches (#7/A,B:466-732)
> wait 30
> movie encode P83-J37_withReference.mp4
Movie saved to P83-J37_withReference.mp4
> turn x -1 90 models #2 center #2
> turn x -1 90 models #7 center #7
> surface (#!7 & sel)
> surface hidePatches (#7/E,F)
> movie record
> wait 10
> turn y 1 360 models #2 center #2
> turn y 1 360 models #7 center #7
> wait 360
> wait 30
> turn x 1 90 models #2 center #2
> turn x 1 90 models #7 center #7
> wait 90
> wait 30
> movie encode P83-J37_withReference.mp4
Movie saved to P83-J37_withReference.mp4
> turn x -1 90 models #2 center #2
> turn x -1 90 models #7 center #7
> hide #!7 models
> select subtract #7
6 models selected
> open /Users/linda_cmmc/Downloads/cryosparc_P83_J70_003_volume_map_sharp.mrc
Opened cryosparc_P83_J70_003_volume_map_sharp.mrc as #8, grid size
200,200,200, pixel 1.89, shown at level 0.793, step 1, values float32
> select add #8
2 models selected
> view matrix models #8,1,0,0,-269.87,0,1,0,121,0,0,1,-157.6
> volume #8 level 1.379
> view matrix models
> #8,-0.50533,0.84464,0.17669,-165.01,-0.8143,-0.53452,0.22628,516.86,0.28557,-0.029528,0.9579,-199.75
> view matrix models
> #8,-0.075338,0.9891,0.12654,-265.4,-0.98098,-0.096282,0.16853,479.89,0.17888,-0.11144,0.97754,-167.77
> view matrix models
> #8,-0.17106,0.90744,0.38378,-279.58,-0.98497,-0.167,-0.044147,532.93,0.024029,-0.38556,0.92237,-77.537
> volume #8 level 1.239
> view matrix models
> #8,-0.86009,0.26517,0.43582,-38.278,-0.29556,-0.95532,-0.0020389,535.17,0.41581,-0.13057,0.90003,-195.97
> view matrix models
> #8,-0.87143,0.28964,0.39588,-33.149,-0.30075,-0.95305,0.035257,528.86,0.38751,-0.088338,0.91762,-201.44
> view matrix models
> #8,-0.8662,0.27824,0.41506,-35.633,-0.29814,-0.95436,0.017562,531.87,0.401,-0.10853,0.90962,-198.89
> view matrix models
> #8,-0.91704,-0.34725,0.19608,128.91,0.34383,-0.93757,-0.052337,417.14,0.20201,0.019423,0.97919,-196.5
> volume #8 level 1.339
> tile
2 models tiled
> view matrix models
> #8,-0.84347,0.33145,0.42273,-70.803,-0.3676,-0.92997,-0.0043244,569.21,0.39169,-0.15904,0.90625,-185.99
> volume #8 level 1.519
> view matrix models
> #8,-0.87832,0.35234,0.32312,-49.901,-0.33259,-0.93586,0.11642,541.39,0.34342,-0.005207,0.93917,-210.83
> view matrix models
> #8,-0.87832,0.35234,0.32312,89.974,-0.33259,-0.93586,0.11642,452.77,0.34342,-0.005207,0.93917,-183.81
> volume #2 style mesh
> view matrix models
> #8,0.14711,0.88241,0.44688,-209.21,-0.885,-0.084356,0.45789,327.35,0.44175,-0.46285,0.76852,-87.72
> view matrix models
> #8,-0.66745,0.49445,0.55681,-8.1508,-0.62665,-0.77689,-0.061271,505.03,0.40228,-0.38981,0.82838,-104.29
> view matrix models
> #8,-0.9604,0.18231,0.21072,169.56,-0.23285,-0.94047,-0.24759,493.19,0.15304,-0.28685,0.94567,-96.573
> view matrix models
> #8,-0.92563,-0.0049212,0.37839,165.97,-0.17046,-0.88731,-0.42851,504.91,0.33786,-0.46114,0.82049,-77.346
> view matrix models
> #8,0.10551,0.5373,0.83676,-217.75,-0.98941,-0.027631,0.1425,400.39,0.099685,-0.84294,0.5287,91.049
> view matrix models
> #8,0.15145,0.66322,0.73294,-230.41,-0.96171,-0.072475,0.26431,380.67,0.22842,-0.7449,0.62685,30.083
> view matrix models
> #8,0.15145,0.66322,0.73294,-214.38,-0.96171,-0.072475,0.26431,368.4,0.22842,-0.7449,0.62685,28.719
> view matrix models
> #8,0.97814,-0.15776,0.13551,-126.06,-0.044861,0.47617,0.87821,-14.686,-0.20307,-0.86509,0.45868,163.64
> view matrix models
> #8,-0.0040353,-0.81769,-0.57565,304.29,0.78522,-0.35904,0.5045,53.544,-0.6192,-0.44997,0.64352,131.39
> view matrix models
> #8,-0.93833,0.24969,0.23916,139.4,-0.28512,-0.95007,-0.12676,485.34,0.19557,-0.18713,0.96267,-133.3
> view matrix models
> #8,-0.92422,0.16417,0.34476,132.73,-0.25211,-0.94045,-0.22802,495.94,0.28679,-0.29766,0.91058,-121.13
> view matrix models
> #8,-0.92422,0.16417,0.34476,138.99,-0.25211,-0.94045,-0.22802,492.87,0.28679,-0.29766,0.91058,-118.05
> view matrix models
> #8,-0.92743,0.19318,0.32024,138.85,-0.28583,-0.91832,-0.27383,503.83,0.24119,-0.34549,0.9069,-99.813
> view matrix models
> #8,-0.92323,0.16546,0.3468,138.14,-0.27695,-0.91217,-0.30206,506.34,0.26637,-0.37492,0.88797,-95.618
> view matrix models
> #8,-0.92323,0.16546,0.3468,139.17,-0.27695,-0.91217,-0.30206,505.92,0.26637,-0.37492,0.88797,-94.93
> view matrix models
> #8,0.18325,0.73064,0.65771,-224.09,-0.90914,-0.12859,0.39615,348.42,0.37402,-0.67055,0.64068,-14.33
> view matrix models
> #8,0.96065,-0.24878,-0.12352,-58.038,0.23972,0.51798,0.82112,-65.954,-0.1403,-0.81842,0.55723,126.65
> view matrix models
> #8,0.96065,-0.24878,-0.12352,-59.35,0.23972,0.51798,0.82112,-65.225,-0.1403,-0.81842,0.55723,126.18
> view matrix models
> #8,0.95596,-0.26099,-0.13429,-54.221,0.25586,0.51682,0.81697,-67.368,-0.14382,-0.81534,0.56083,125.63
> view matrix models
> #8,0.95623,-0.24789,-0.1555,-52.737,0.26387,0.50066,0.82445,-67.352,-0.12652,-0.82939,0.54416,127.94
> volume #8 level 1.319
> view matrix models
> #8,0.95623,-0.24789,-0.1555,-54.557,0.26387,0.50066,0.82445,-66.484,-0.12652,-0.82939,0.54416,126.99
> view matrix models
> #8,0.95623,-0.24789,-0.1555,-53.235,0.26387,0.50066,0.82445,-67.019,-0.12652,-0.82939,0.54416,127.88
> view matrix models
> #8,0.13323,-0.87586,-0.46381,267.02,0.91988,-0.064901,0.3868,-2.8137,-0.36888,-0.47819,0.79703,62.357
> view matrix models
> #8,-0.91129,0.28183,0.30022,122.76,-0.31987,-0.94363,-0.085103,481.88,0.25931,-0.17358,0.95007,-141.48
> view matrix models
> #8,0.25722,0.81937,0.51232,-228.32,-0.83531,-0.078044,0.5442,299.18,0.48589,-0.56792,0.66436,-58.257
> view matrix models
> #8,-0.6816,0.56806,-0.46123,161.2,0.43055,-0.19832,-0.88051,343.96,-0.59165,-0.79874,-0.10941,317.15
> view matrix models
> #8,-0.88267,0.39229,0.25886,108.49,-0.41706,-0.90769,-0.046539,486.19,0.21671,-0.14904,0.96479,-136.39
> view matrix models
> #8,0.38931,0.74258,0.54499,-247.07,-0.82944,0.025302,0.55803,277.26,0.40059,-0.66928,0.62577,-16.432
> view matrix models
> #8,-0.89522,0.26987,0.35461,111.94,-0.32839,-0.93744,-0.11561,488.44,0.30122,-0.21994,0.92784,-135.93
> view matrix models
> #8,0.15383,0.8069,0.5703,-214.68,-0.8507,-0.18545,0.49185,330.91,0.50264,-0.56082,0.65791,-59.592
> view matrix models
> #8,-0.83505,0.33156,0.43905,80.318,-0.39723,-0.91547,-0.064176,484.53,0.38066,-0.22799,0.89617,-141.24
> view matrix models
> #8,0.061841,0.80003,0.59677,-202.27,-0.86031,-0.26041,0.43825,357.87,0.50601,-0.54051,0.67216,-66.172
> view matrix models
> #8,-0.7758,0.38279,0.5016,47.532,-0.45366,-0.89091,-0.021753,483.43,0.43856,-0.24443,0.86483,-143.63
> view matrix models
> #8,0.27363,0.79494,0.54148,-230.74,-0.81573,-0.10648,0.56854,296.18,0.50961,-0.59727,0.61932,-46.313
> view matrix models
> #8,-0.72444,0.42272,0.54452,26.329,-0.49413,-0.86922,0.017385,477.59,0.48065,-0.25647,0.83857,-143.86
> view matrix models
> #8,0.51561,0.72379,0.45856,-252.56,-0.72783,0.087572,0.68015,225.38,0.45213,-0.68444,0.57195,-10.551
> view matrix models
> #8,-0.79739,0.2999,0.52367,63.523,-0.38517,-0.92095,-0.059073,482.4,0.46456,-0.2488,0.84987,-144.22
> view matrix models
> #8,0.25469,0.77702,0.57566,-228.78,-0.80452,-0.16003,0.57196,302.63,0.53655,-0.6088,0.58436,-41.99
> view matrix models
> #8,-0.88949,0.093479,0.44729,128.73,-0.17248,-0.97513,-0.13921,469.11,0.42315,-0.20098,0.88349,-151.14
> view matrix models
> #8,0.13274,0.79133,0.59681,-213.63,-0.81908,-0.25148,0.51562,334.06,0.55811,-0.55728,0.61478,-61.057
> view matrix models
> #8,-0.13207,0.85734,0.49752,-155.95,0.26103,-0.45412,0.85184,99.367,0.95625,0.24238,-0.16381,-140.02
> view matrix models
> #8,-0.84369,0.40974,0.34683,91.596,-0.49313,-0.84687,-0.19909,511.81,0.21214,-0.33901,0.91655,-89.669
> view matrix models
> #8,-0.84369,0.40974,0.34683,84.499,-0.49313,-0.84687,-0.19909,515.74,0.21214,-0.33901,0.91655,-92.232
> view matrix models
> #8,-0.35777,0.7705,0.52756,-112.14,-0.06562,-0.58431,0.80887,200.44,0.9315,0.25478,0.25961,-218.83
> view matrix models
> #8,0.38103,0.67392,0.63296,-255.48,-0.92139,0.22007,0.32034,308,0.076586,-0.70526,0.7048,38.16
> view matrix models
> #8,0.95529,-0.22016,-0.19737,-49.977,0.29512,0.75077,0.59096,-74.801,0.018071,-0.62279,0.78218,20.132
> view matrix models
> #8,0.95529,-0.22016,-0.19737,-53.947,0.29512,0.75077,0.59096,-72.751,0.018071,-0.62279,0.78218,18.383
> view matrix models
> #8,0.31122,0.89769,0.31192,-224.99,-0.79475,0.065879,0.60336,259.6,0.52108,-0.43568,0.73394,-104.26
> view matrix models
> #8,-0.4241,0.29287,0.85695,-76.746,0.25539,-0.86918,0.42344,262.72,0.86886,0.39843,0.29382,-242.26
> view matrix models
> #8,-0.4241,0.29287,0.85695,-76.645,0.25539,-0.86918,0.42344,263.79,0.86886,0.39843,0.29382,-239.85
> view matrix models
> #8,-0.45466,0.29275,0.84118,-67.776,0.26828,-0.85556,0.44276,255.23,0.8493,0.42698,0.31045,-244.35
> view matrix models
> #8,-0.50154,0.29233,0.81425,-53.626,0.18826,-0.88175,0.43253,277.42,0.8444,0.37022,0.3872,-247.25
> view matrix models
> #8,-0.53081,0.29846,0.7932,-45.173,0.13173,-0.89551,0.42511,292.26,0.83719,0.33014,0.43602,-247.58
> view matrix models
> #8,-0.49487,0.38602,0.77852,-65.399,0.10873,-0.86136,0.49622,277.33,0.86214,0.33021,0.38429,-242.85
> view matrix models
> #8,-0.51645,0.40632,0.75378,-60.337,0.04886,-0.86484,0.49966,288.93,0.85492,0.29488,0.4268,-242.87
> view matrix models
> #8,-0.49896,0.4406,0.74627,-68.594,0.040226,-0.84842,0.5278,282.4,0.86569,0.29337,0.4056,-240.76
> view matrix models
> #8,0.55599,0.79295,0.24921,-245.74,-0.73621,0.33063,0.59049,202.8,0.38583,-0.51178,0.76761,-75.531
> view matrix models
> #8,0.63759,0.71838,0.27822,-247.78,-0.69731,0.38465,0.60482,179.08,0.32748,-0.57963,0.74618,-47.128
> view matrix models
> #8,-0.73898,0.4418,0.50865,23.994,-0.43007,-0.89048,0.14863,446.3,0.51861,-0.10892,0.84805,-189.36
> view matrix models
> #8,-0.73898,0.4418,0.50865,-149.66,-0.43007,-0.89048,0.14863,561,0.51861,-0.10892,0.84805,-213.04
> volume #8 level 1.339
> volume #8 style mesh
> volume #8 style surface
> volume #2 style surface
> select subtract #8
Nothing selected
> color #2 silver models
> color #8 silver models
> select add #8
2 models selected
> view matrix models
> #8,-0.70182,0.45099,0.55141,-166.54,-0.53762,-0.84317,0.005346,598.62,0.46734,-0.2927,0.83422,-169.4
> select subtract #8
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,-0.63574,0.45321,0.62485,39.914,-0.47723,-0.86702,0.14331,413.22,0.6067,-0.20709,0.76748,-164.57
> select subtract #8
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,0.46922,-0.87882,0.08666,9.7322,0.72231,0.4384,0.53486,-25.655,-0.50803,-0.18837,0.84049,11.833
> tile
2 models tiled
> select subtract #2
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,0.46922,-0.87882,0.08666,-98.247,0.72231,0.4384,0.53486,44.188,-0.50803,-0.18837,0.84049,-6.0089
> select subtract #2
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,-0.63574,0.45321,0.62485,-121.5,-0.47723,-0.86702,0.14331,515.61,0.6067,-0.20709,0.76748,-193.96
> select subtract #8
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,0.52276,-0.85247,-0.0041346,-131.92,0.76579,0.46746,0.44164,69.557,-0.37455,-0.23403,0.89718,-38.734
> select subtract #2
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,-0.80187,0.34997,0.48429,-188.28,-0.37825,-0.92475,0.041979,621.12,0.46254,-0.14952,0.8739,-215.02
> view matrix models
> #8,-0.80187,0.34997,0.48429,-189.1,-0.37825,-0.92475,0.041979,621.4,0.46254,-0.14952,0.8739,-215.68
> view matrix models
> #8,0.35411,0.7404,0.57133,-497.55,-0.7934,-0.085581,0.60265,442.96,0.4951,-0.66669,0.55713,-68.66
> view matrix models
> #8,-0.38645,-0.82147,-0.41934,104.34,0.91706,-0.3907,-0.079757,300.05,-0.09832,-0.41538,0.90432,-65.057
> view matrix models
> #8,0.31919,0.69794,0.64109,-497.49,-0.82195,-0.13283,0.55385,466.9,0.47171,-0.70373,0.53128,-53.369
> view matrix models
> #8,-0.67604,-0.42587,0.60133,-92.167,0.72869,-0.50765,0.45969,252.13,0.1095,0.74895,0.65352,-270.83
> volume #2 style mesh
> view matrix models
> #8,-0.36327,-0.84884,-0.38407,106.8,0.91153,-0.40909,0.041969,276.03,-0.19274,-0.33485,0.92235,-64.269
> view matrix models
> #8,-0.36327,-0.84884,-0.38407,104.76,0.91153,-0.40909,0.041969,277.01,-0.19274,-0.33485,0.92235,-65.31
> view matrix models
> #8,-0.36327,-0.84884,-0.38407,103.89,0.91153,-0.40909,0.041969,278.39,-0.19274,-0.33485,0.92235,-63.742
> view matrix models
> #8,-0.34643,-0.87958,-0.32608,95.497,0.92901,-0.3699,0.010789,273.63,-0.13011,-0.2992,0.94528,-86.632
> view matrix models
> #8,0.29324,0.84544,0.44637,-486.24,-0.76825,-0.069519,0.63637,432.02,0.56904,-0.52953,0.62912,-121.61
> view matrix models
> #8,0.24316,0.84207,0.48144,-482.41,-0.78546,-0.12029,0.60711,450.04,0.56914,-0.52578,0.63217,-122.87
> view matrix models
> #8,0.1084,0.87112,0.47896,-460.15,-0.71424,-0.26687,0.64702,454.93,0.69145,-0.41223,0.59326,-159.99
> view matrix models
> #8,0.053878,0.86445,0.49983,-452.23,-0.71581,-0.31556,0.62292,468.58,0.69621,-0.39135,0.60178,-166.3
> view matrix models
> #8,0.061063,0.86344,0.50074,-453.6,-0.71167,-0.31409,0.62839,466.49,0.69986,-0.39473,0.5953,-165.19
> view matrix models
> #8,0.067996,0.85259,0.51814,-456.19,-0.72211,-0.3163,0.61523,471.36,0.68843,-0.41599,0.59416,-158.89
> view matrix models
> #8,0.54771,0.71965,0.42675,-508.01,-0.68556,0.093638,0.72197,369.72,0.47961,-0.68799,0.54465,-59.615
> view matrix models
> #8,0.54771,0.71965,0.42675,-508.15,-0.68556,0.093638,0.72197,369.5,0.47961,-0.68799,0.54465,-60.275
> view matrix models
> #8,0.55524,0.67343,0.48806,-512.52,-0.7262,0.10652,0.67918,382.95,0.40539,-0.73154,0.54818,-38.596
> view matrix models
> #8,0.55524,0.67343,0.48806,-506.77,-0.7262,0.10652,0.67918,378.97,0.40539,-0.73154,0.54818,-38.202
> view matrix models
> #8,-0.87163,0.083585,0.48298,-126.05,-0.14796,-0.98426,-0.09668,612.47,0.46729,-0.15573,0.87028,-215.47
> view matrix models
> #8,-0.014996,-0.88907,-0.45752,52.809,0.96765,-0.12816,0.21732,186.19,-0.25185,-0.43946,0.86223,-23.898
> view matrix models
> #8,0.89393,0.31978,0.31404,-479.71,-0.44426,0.5396,0.71516,240.41,0.059242,-0.77883,0.62444,20.983
> view matrix models
> #8,-0.62164,-0.71344,-0.32338,113.66,0.7595,-0.64999,-0.025999,365.84,-0.19164,-0.26177,0.94591,-85.3
> view matrix models
> #8,0.24714,0.73052,0.6366,-491.76,-0.16838,-0.61461,0.77065,389.45,0.95424,-0.29765,-0.028889,-118.92
> view matrix models
> #8,-0.22374,-0.88428,-0.40987,87.879,0.94502,-0.29972,0.13077,234.63,-0.23848,-0.35808,0.90272,-49.158
> view matrix models
> #8,-0.22374,-0.88428,-0.40987,83.428,0.94502,-0.29972,0.13077,238.27,-0.23848,-0.35808,0.90272,-48.283
> view matrix models
> #8,0.31095,0.88684,0.3418,-482.52,-0.70821,-0.023635,0.70561,401.96,0.63384,-0.46147,0.62072,-146.31
> view matrix models
> #8,0.31095,0.88684,0.3418,-480.15,-0.70821,-0.023635,0.70561,399.83,0.63384,-0.46147,0.62072,-147.18
> view matrix models
> #8,-0.72452,0.44676,0.52486,-109.54,-0.34493,-0.89429,0.28507,482.75,0.59674,0.0255,0.80203,-249.37
> volume #2 style surface
> select subtract #8
Nothing selected
> movie record
> wait 30
> turn x 1 90 models #2 center #2
> turn x 1 90 models #8 center #8
> wait 90
> wait 30
> movie encode P83-J37_P83-J70.mp4
Movie saved to P83-J37_P83-J70.mp4
> turn x -1 90 models #2 center #2
> turn x -1 90 models #8 center #8
> open "/Users/linda_cmmc/Desktop/BiP+GRP94/Model Yasser Colorized.pdb"
Chain information for Model Yasser Colorized.pdb #9
---
Chain | Description
A B | No description available
C | No description available
> show #!1 models
> select add #1
20294 atoms, 20478 bonds, 2 pseudobonds, 1246 residues, 2 models selected
> view matrix models
> #1,-0.65695,0.74722,-0.10039,-179.11,-0.33475,-0.4084,-0.84921,536.54,-0.67555,-0.52428,0.51843,40.927
> view matrix models
> #1,-0.65695,0.74722,-0.10039,-129.23,-0.33475,-0.4084,-0.84921,498.69,-0.67555,-0.52428,0.51843,37.386
> select subtract #1
Nothing selected
> select add #5
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> select subtract #5
Nothing selected
> show #!5 models
> select add #5
9544 atoms, 9479 bonds, 13 pseudobonds, 1396 residues, 3 models selected
> view matrix models
> #5,0.34551,0.9129,0.21735,-104.51,-0.86551,0.22049,0.44975,267.37,0.36265,-0.34351,0.86631,-126.47
> select subtract #5
Nothing selected
> hide #!5 models
> open /Users/linda_cmmc/Desktop/Test_GRP94open_BiPNBD_0956.pdb
Chain information for Test_GRP94open_BiPNBD_0956.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select add #10
24827 atoms, 25045 bonds, 7 pseudobonds, 1533 residues, 2 models selected
> select subtract #10
Nothing selected
> hide #!10 models
> show #!10 models
> select add #10
24827 atoms, 25045 bonds, 7 pseudobonds, 1533 residues, 2 models selected
> view matrix models #10,1,0,0,184.37,0,1,0,-140.64,0,0,1,-14.647
> view matrix models #10,1,0,0,17.495,0,1,0,-57.435,0,0,1,-94.413
> view matrix models #10,1,0,0,-100.1,0,1,0,16.892,0,0,1,-117.5
> view matrix models #10,1,0,0,-280.98,0,1,0,71.356,0,0,1,-279.32
> select subtract #10
Nothing selected
> hide #!10 models
> show #!10 models
> select #10/A,B:86-285
5386 atoms, 5420 bonds, 3 pseudobonds, 336 residues, 2 models selected
> color (#!10 & sel) red
> select #10/A,B:330-338
306 atoms, 312 bonds, 18 residues, 1 model selected
> color (#!10 & sel) light gray
> select #10/A,B:339-595
8130 atoms, 8221 bonds, 2 pseudobonds, 488 residues, 2 models selected
> color (#!10 & sel) cyan
> select #10/A,B:596-749
5040 atoms, 5078 bonds, 308 residues, 1 model selected
> color (#!10 & sel) blue
> select #10/C
5951 atoms, 5996 bonds, 382 residues, 1 model selected
> color (#!10 & sel) forest green
> select #10/C
5951 atoms, 5996 bonds, 382 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #10
18876 atoms, 19049 bonds, 7 pseudobonds, 1151 residues, 2 models selected
> view matrix models
> #10,0.70372,-0.28126,0.65243,-283.12,0.044365,0.93391,0.35474,15.789,-0.70909,-0.2207,0.66969,-50.761
> tile
5 models tiled
> hide #!9 models
> tile
4 models tiled
> select subtract #10
Nothing selected
> select add #10
18876 atoms, 19049 bonds, 7 pseudobonds, 1151 residues, 2 models selected
> view matrix models
> #10,0.74602,-0.21193,0.6313,-598.21,0.027011,0.95686,0.2893,184.87,-0.66537,-0.19877,0.71956,-183.94
> select subtract #10
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,-0.81586,0.36341,0.44979,-202.26,-0.35656,-0.92853,0.10346,531.74,0.45524,-0.075969,0.88712,-418.16
> select subtract #8
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,0.63624,-0.75928,-0.13669,-139.9,0.74106,0.55221,0.38197,63.535,-0.21455,-0.34432,0.91401,-51.368
> select subtract #2
Nothing selected
> select add #1
20294 atoms, 20478 bonds, 2 pseudobonds, 1246 residues, 2 models selected
> view matrix models
> #1,-0.63664,0.74998,-0.1795,-292.71,-0.2717,-0.43599,-0.85796,659.35,-0.72171,-0.49744,0.48134,138.74
> view matrix models
> #1,-0.63664,0.74998,-0.1795,-288.93,-0.2717,-0.43599,-0.85796,660.13,-0.72171,-0.49744,0.48134,146.17
> select subtract #1
Nothing selected
> movie record
> wait 30
> turn x 1 90 models #1 center #1
> turn x 1 90 models #2 center #2
> turn x 1 90 models #10 center #10
> turn x 1 90 models #8 center #8
> wait 90
> wait 30
> movie encode P83-J37_P83-J70_reference.mp4
Movie saved to P83-J37_P83-J70_reference.mp4
> turn x -1 90 models #1 center #1
> turn x -1 90 models #2 center #2
> turn x -1 90 models #3 center #3
> turn x -1 90 models #8 center #8
> turn x -1 90 models #10 center #10
> movie record
> wait 30
> turn x 1 90 models #1 center #1
> turn x 1 90 models #2 center #2
> turn x 1 90 models #10 center #10
> turn x 1 90 models #8 center #8
> wait 90
> wait 20
> cartoon hide #1,10/A,B:466-749
> wait 30
> movie encode P83-J37_P83-J70_reference.mp4
Movie saved to P83-J37_P83-J70_reference.mp4
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
OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
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: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
OS Loader Version: 564.40.4~66
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 12 days, 8 hours, 27 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL S2722DC:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 72JVGD3
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
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: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 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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