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Opened 12 months ago
Closed 12 months ago
#16492 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 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 0x00000001e6a09ec0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 162 in copy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 65 in combine_cmd
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.dssp._dssp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 60)
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"procRole" : "Foreground",
"version" : 2,
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"captureTime" : "2024-12-18 16:19:10.1229 +0800",
"codeSigningMonitor" : 1,
"incident" : "ED717BEA-B4B7-4D16-BEC8-10611E367DB0",
"pid" : 66043,
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"procLaunch" : "2024-12-17 11:00:08.3598 +0800",
"procStartAbsTime" : 16772164858762,
"procExitAbsTime" : 17536145823270,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "2DB44331-A26E-8CBE-0A9B-01589F89B818",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"vmRegionInfo" : "0x1a is not in any region. Bytes before following region: 105578886070246\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600600000000-600620000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000000000000001a","rawCodes":[1,26],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000001a"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":66043},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x1a is not in any region. Bytes before following region: 105578886070246\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600600000000-600620000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 9d9x
9d9x title:
Mycobacteriophage Bxb1 Capsid - Composite map and model [more info...]
Chain information for 9d9x #1
---
Chain | Description | UniProt
Ha Hb Hc Hd He Hf Pa Pb Pc Pd Pe | Major capsid protein | Q9B0A7_BPMB1 1-397
> select /Ha:2-397
5813 atoms, 5870 bonds, 396 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /Ha
Alignment identifier is 1/Ha
> select /Ha:397
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /Ha:393-397
67 atoms, 66 bonds, 5 residues, 1 model selected
> select /Ha:397
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /Ha:323-397
1002 atoms, 1005 bonds, 75 residues, 1 model selected
> select add #1
62686 atoms, 63306 bonds, 4263 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select /Ha:2-397
5813 atoms, 5870 bonds, 396 residues, 1 model selected
> show sel cartoons
> open 9d9w
Summary of feedback from opening 9d9w fetched from pdb
---
note | Fetching compressed mmCIF 9d9w from http://files.rcsb.org/download/9d9w.cif
9d9w title:
Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model [more
info...]
Chain information for 9d9w #2
---
Chain | Description | UniProt
Aa Ab Ac Ad Ae Af Ba Bb Bc Bd Be Bf Ca Cb Cc Cd Ce Cf Da Db Dc Dd De Df Ea Eb Ec Ed Ee Ef | Major capsid protein | Q9B0A7_BPMB1 1-397
Fa Fb Fc Fd Fe Ff Fg Fh Fi Fj Fk Fl | Portal protein | Q9B0B0_BPMB1 1-488
> select #2/Aa:4-397
5785 atoms, 5841 bonds, 394 residues, 1 model selected
> view clip false
> select add #2
257618 atoms, 260283 bonds, 17270 residues, 1 model selected
> hide sel atoms
> select #2/Aa:4-397
5785 atoms, 5841 bonds, 394 residues, 1 model selected
> show sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #2/Aa
Alignment identifier is 2/Aa
> select #2/Aa:397
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/Aa:107-397
4218 atoms, 4256 bonds, 291 residues, 1 model selected
> open /Users/melvinshen/Downloads/9d9w.cif
9d9w.cif title:
Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model [more
info...]
Chain information for 9d9w.cif #3
---
Chain | Description | UniProt
Aa Ab Ac Ad Ae Af Ba Bb Bc Bd Be Bf Ca Cb Cc Cd Ce Cf Da Db Dc Dd De Df Ea Eb Ec Ed Ee Ef | Major capsid protein | Q9B0A7_BPMB1 1-397
Fa Fb Fc Fd Fe Ff Fg Fh Fi Fj Fk Fl | Portal protein | Q9B0B0_BPMB1 1-488
Compositor returned null texture
Already setting window visible!
> close #3
> close
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/ChimeraX/Cluster L/Douge/Douge_08/Douge_GP08.pdb"
Chain information for Douge_GP08.pdb #1
---
Chain | Description
A | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> rainbow
> lighting flat
> set bgColor white
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-70
545 atoms, 554 bonds, 70 residues, 1 model selected
> close
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /3D/Capsid Assembled.pdb" format
> pdb
Chain information for Capsid Assembled.pdb #1
---
Chain | Description
0 1 2 3 4 5 6 7 8 9 A A0 A1 A2 A4 A6 A7 A8 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Af Ah Ai Aj Al An Ao Ap Ar At Au Av Ax Az B B2 B4 B5 B7 B8 B9 BB BC BD BF BH BI BJ BL BN BO BP BR BT BU BV BX BZ Ba Bb Bd Bf Bg Bh Bj Bl Bm Bn Bp Br Bs Bt Bv Bx By Bz C C0 C2 C4 C5 C6 C8 CA CC CD CE CG CI CJ CK CM CO CP CQ CS CU CV CW CY Ca Cb Cc Ce Cg Ch Cj Cl Cm Cn Cp Cr Cs Ct Cv Cx Cy Cz D D0 D1 D3 D4 D5 D7 D9 DA DB DD DF DG DH DJ DL DM DN DP DR DS DT DV DW DY DZ Da Dc De Df Dg Di Dk Dl Dm Do Dq Dr Ds Du Dw Dx Dy E E1 E2 E3 E5 E7 E8 E9 EB ED EE EF EH EJ EK EL EN EP EQ ER ET EV EW EX EZ Eb Ec Ed Ef Eh Ei Ej El En Eo Ep Er Et Eu Ev Ex Ey F0 F2 F4 F5 F6 F8 FA FC FD FE FG FI FJ FK FM FO FP FQ FS FU FV FW FY Fa Fb Fd Ff Fg Fh Fj Fl Fm Fn Fp Fr Fs Ft Fv Fx Fy Fz G G0 G1 G3 G4 G6 G8 G9 GA GB GD GF GG GH GJ GL GM GN GP GQ GS GT GU GW GY GZ Ga Gc Ge Gf Gg Gi Gk Gl Gm Go Gq Gr Gs Gu Gw Gx Gy H H0 H2 H4 H5 H6 H8 HB HD HE HF HH HJ HK HL HN HP HQ HR HT HV HW HX HZ Hb Hc Hd Hf Hh Hi Hj Hl Hn Ho Hp Hr Hs Ht Hv Hx Hy Hz I0 I1 I2 I3 I4 I5 I6 I7 I8 I9 IA IB ID IF IG IH IJ IL IM IN IO IP IQ IR IS IT IU IV IW IX IY IZ Ib Id Ie If Ih Ii Ij Ik Il Im In Io Ip Iq Ir Is It Iu Iv Iw Ix Iy Iz J J0 J2 J3 J4 J6 J8 J9 JA JC JE JF JG JI JK JL JM JO JQ JR JS JU JW JX JZ Jb Jd Je Jf Jh Jj Jk Jl Jn Jp Jq Jr Jt Jv Jw Jx Jz K0 K1 K2 K3 K4 K5 K6 K7 K8 K9 KB KD KE KF KH KJ KK KL KN KP KQ KR KS KT KU KW KX KZ Kb Kc Ke Kh Ki Kk Kn Ko Kq Kt Ku Kw Kz L LA LB LC LD LE LF M O R S U X Y a d e g j k l m n o p q r s t u v w x y z | No description available
A3 A5 A9 Ae Ag Ak Am Aq As Aw Ay B0 B1 B3 B6 BA BE BG BK BM BQ BS BW BY Bc Be Bi Bk Bo Bq Bu Bw C1 C3 C7 C9 CB CF CH CL CN CR CT CX CZ Cd Cf Ci Ck Co Cq Cu Cw D2 D6 D8 DC DE DI DK DO DQ DU DX Db Dd Dh Dj Dn Dp Dt Dv Dz E0 E4 E6 EA EC EG EI EM EO ES EU EY Ea Ee Eg Ek Em Eq Es Ew Ez F F1 F3 F7 F9 FB FF FH FL FN FR FT FX FZ Fc Fe Fi Fk Fo Fq Fu Fw G2 G5 G7 GC GE GI GK GO GR GV GX Gb Gd Gh Gj Gn Gp Gt Gv Gz H1 H3 H7 H9 HA HC HG HI HM HO HS HU HY Ha He Hg Hk Hm Hq Hu Hw I IC IE II IK Ia Ic Ig J1 J5 J7 JB JD JH JJ JN JP JT JV JY Ja Jc Jg Ji Jm Jo Js Ju Jy K KA KC KG KI KM KO KV KY Ka Kd Kf Kg Kj Kl Km Kp Kr Ks Kv Kx Ky N P Q T V W Z b c f h i | No description available
> hide atoms
> show cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain /0
Alignment identifier is 1/0
> select /0:131-132
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /0:131-149
137 atoms, 139 bonds, 19 residues, 1 model selected
> select /0:410
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /0:135-410
1986 atoms, 2022 bonds, 276 residues, 1 model selected
> view clip false
> ui tool show "Show Sequence Viewer"
> sequence chain /0 /1 /2 /3 /4 /5 /6 /7 /8 /9 /A /A0 /A1 /A2 /A4 /A6 /A7 /A8
> /AA /AB /AC /AD /AE /AF /AG /AH /AI /AJ /AK /AL /AM /AN /AO /AP /AQ /AR /AS
> /AT /AU /AV /AW /AX /AY /AZ /Aa /Ab /Ac /Ad /Af /Ah /Ai /Aj /Al /An /Ao /Ap
> /Ar /At /Au /Av /Ax /Az /B /B2 /B4 /B5 /B7 /B8 /B9 /BB /BC /BD /BF /BH /BI
> /BJ /BL /BN /BO /BP /BR /BT /BU /BV /BX /BZ /Ba /Bb /Bd /Bf /Bg /Bh /Bj /Bl
> /Bm /Bn /Bp /Br /Bs /Bt /Bv /Bx /By /Bz /C /C0 /C2 /C4 /C5 /C6 /C8 /CA /CC
> /CD /CE /CG /CI /CJ /CK /CM /CO /CP /CQ /CS /CU /CV /CW /CY /Ca /Cb /Cc /Ce
> /Cg /Ch /Cj /Cl /Cm /Cn /Cp /Cr /Cs /Ct /Cv /Cx /Cy /Cz /D /D0 /D1 /D3 /D4
> /D5 /D7 /D9 /DA /DB /DD /DF /DG /DH /DJ /DL /DM /DN /DP /DR /DS /DT /DV /DW
> /DY /DZ /Da /Dc /De /Df /Dg /Di /Dk /Dl /Dm /Do /Dq /Dr /Ds /Du /Dw /Dx /Dy
> /E /E1 /E2 /E3 /E5 /E7 /E8 /E9 /EB /ED /EE /EF /EH /EJ /EK /EL /EN /EP /EQ
> /ER /ET /EV /EW /EX /EZ /Eb /Ec /Ed /Ef /Eh /Ei /Ej /El /En /Eo /Ep /Er /Et
> /Eu /Ev /Ex /Ey /F0 /F2 /F4 /F5 /F6 /F8 /FA /FC /FD /FE /FG /FI /FJ /FK /FM
> /FO /FP /FQ /FS /FU /FV /FW /FY /Fa /Fb /Fd /Ff /Fg /Fh /Fj /Fl /Fm /Fn /Fp
> /Fr /Fs /Ft /Fv /Fx /Fy /Fz /G /G0 /G1 /G3 /G4 /G6 /G8 /G9 /GA /GB /GD /GF
> /GG /GH /GJ /GL /GM /GN /GP /GQ /GS /GT /GU /GW /GY /GZ /Ga /Gc /Ge /Gf /Gg
> /Gi /Gk /Gl /Gm /Go /Gq /Gr /Gs /Gu /Gw /Gx /Gy /H /H0 /H2 /H4 /H5 /H6 /H8
> /HB /HD /HE /HF /HH /HJ /HK /HL /HN /HP /HQ /HR /HT /HV /HW /HX /HZ /Hb /Hc
> /Hd /Hf /Hh /Hi /Hj /Hl /Hn /Ho /Hp /Hr /Hs /Ht /Hv /Hx /Hy /Hz /I0 /I1 /I2
> /I3 /I4 /I5 /I6 /I7 /I8 /I9 /IA /IB /ID /IF /IG /IH /IJ /IL /IM /IN /IO /IP
> /IQ /IR /IS /IT /IU /IV /IW /IX /IY /IZ /Ib /Id /Ie /If /Ih /Ii /Ij /Ik /Il
> /Im /In /Io /Ip /Iq /Ir /Is /It /Iu /Iv /Iw /Ix /Iy /Iz /J /J0 /J2 /J3 /J4
> /J6 /J8 /J9 /JA /JC /JE /JF /JG /JI /JK /JL /JM /JO /JQ /JR /JS /JU /JW /JX
> /JZ /Jb /Jd /Je /Jf /Jh /Jj /Jk /Jl /Jn /Jp /Jq /Jr /Jt /Jv /Jw /Jx /Jz /K0
> /K1 /K2 /K3 /K4 /K5 /K6 /K7 /K8 /K9 /KB /KD /KE /KF /KH /KJ /KK /KL /KN /KP
> /KQ /KR /KS /KT /KU /KW /KX /KZ /Kb /Kc /Ke /Kh /Ki /Kk /Kn /Ko /Kq /Kt /Ku
> /Kw /Kz /L /LA /LB /LC /LD /LE /LF /M /O /R /S /U /X /Y /a /d /e /g /j /k /l
> /m /n /o /p /q /r /s /t /u /v /w /x /y /z
Alignment identifier is 1
> close
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/ChimeraX/Cluster L/Douge/Douge_08/gp8-B.pdb"
Summary of feedback from opening /Users/melvinshen/Desktop/Sinica /Protein
Purification/New Phage Proteins/Structure/CryoEM/ChimeraX/Cluster
L/Douge/Douge_08/gp8-B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 25 GLY A 27 1 3
Start residue of secondary structure not found: HELIX 2 2 LYS A 41 ASP A 43 1
3
Start residue of secondary structure not found: HELIX 3 3 ASP A 93 ASP A 99 1
7
Start residue of secondary structure not found: HELIX 4 4 TYR A 103 VAL A 107
1 5
Start residue of secondary structure not found: HELIX 5 5 LEU A 108 GLU A 128
1 21
233 messages similar to the above omitted
Chain information for gp8-B.pdb #1
---
Chain | Description
B | No description available
> rainbow
> close
> close #
Expected a models specifier or a keyword
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /3D/Capsid Assembled.pdb" format
> pdb
Chain information for Capsid Assembled.pdb #1
---
Chain | Description
0 1 2 3 4 5 6 7 8 9 A A0 A1 A2 A4 A6 A7 A8 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Af Ah Ai Aj Al An Ao Ap Ar At Au Av Ax Az B B2 B4 B5 B7 B8 B9 BB BC BD BF BH BI BJ BL BN BO BP BR BT BU BV BX BZ Ba Bb Bd Bf Bg Bh Bj Bl Bm Bn Bp Br Bs Bt Bv Bx By Bz C C0 C2 C4 C5 C6 C8 CA CC CD CE CG CI CJ CK CM CO CP CQ CS CU CV CW CY Ca Cb Cc Ce Cg Ch Cj Cl Cm Cn Cp Cr Cs Ct Cv Cx Cy Cz D D0 D1 D3 D4 D5 D7 D9 DA DB DD DF DG DH DJ DL DM DN DP DR DS DT DV DW DY DZ Da Dc De Df Dg Di Dk Dl Dm Do Dq Dr Ds Du Dw Dx Dy E E1 E2 E3 E5 E7 E8 E9 EB ED EE EF EH EJ EK EL EN EP EQ ER ET EV EW EX EZ Eb Ec Ed Ef Eh Ei Ej El En Eo Ep Er Et Eu Ev Ex Ey F0 F2 F4 F5 F6 F8 FA FC FD FE FG FI FJ FK FM FO FP FQ FS FU FV FW FY Fa Fb Fd Ff Fg Fh Fj Fl Fm Fn Fp Fr Fs Ft Fv Fx Fy Fz G G0 G1 G3 G4 G6 G8 G9 GA GB GD GF GG GH GJ GL GM GN GP GQ GS GT GU GW GY GZ Ga Gc Ge Gf Gg Gi Gk Gl Gm Go Gq Gr Gs Gu Gw Gx Gy H H0 H2 H4 H5 H6 H8 HB HD HE HF HH HJ HK HL HN HP HQ HR HT HV HW HX HZ Hb Hc Hd Hf Hh Hi Hj Hl Hn Ho Hp Hr Hs Ht Hv Hx Hy Hz I0 I1 I2 I3 I4 I5 I6 I7 I8 I9 IA IB ID IF IG IH IJ IL IM IN IO IP IQ IR IS IT IU IV IW IX IY IZ Ib Id Ie If Ih Ii Ij Ik Il Im In Io Ip Iq Ir Is It Iu Iv Iw Ix Iy Iz J J0 J2 J3 J4 J6 J8 J9 JA JC JE JF JG JI JK JL JM JO JQ JR JS JU JW JX JZ Jb Jd Je Jf Jh Jj Jk Jl Jn Jp Jq Jr Jt Jv Jw Jx Jz K0 K1 K2 K3 K4 K5 K6 K7 K8 K9 KB KD KE KF KH KJ KK KL KN KP KQ KR KS KT KU KW KX KZ Kb Kc Ke Kh Ki Kk Kn Ko Kq Kt Ku Kw Kz L LA LB LC LD LE LF M O R S U X Y a d e g j k l m n o p q r s t u v w x y z | No description available
A3 A5 A9 Ae Ag Ak Am Aq As Aw Ay B0 B1 B3 B6 BA BE BG BK BM BQ BS BW BY Bc Be Bi Bk Bo Bq Bu Bw C1 C3 C7 C9 CB CF CH CL CN CR CT CX CZ Cd Cf Ci Ck Co Cq Cu Cw D2 D6 D8 DC DE DI DK DO DQ DU DX Db Dd Dh Dj Dn Dp Dt Dv Dz E0 E4 E6 EA EC EG EI EM EO ES EU EY Ea Ee Eg Ek Em Eq Es Ew Ez F F1 F3 F7 F9 FB FF FH FL FN FR FT FX FZ Fc Fe Fi Fk Fo Fq Fu Fw G2 G5 G7 GC GE GI GK GO GR GV GX Gb Gd Gh Gj Gn Gp Gt Gv Gz H1 H3 H7 H9 HA HC HG HI HM HO HS HU HY Ha He Hg Hk Hm Hq Hu Hw I IC IE II IK Ia Ic Ig J1 J5 J7 JB JD JH JJ JN JP JT JV JY Ja Jc Jg Ji Jm Jo Js Ju Jy K KA KC KG KI KM KO KV KY Ka Kd Kf Kg Kj Kl Km Kp Kr Ks Kv Kx Ky N P Q T V W Z b c f h i | No description available
> hide atoms
> show cartoons
> lighting soft
> lighting full
> lighting soft
> dssp
> hide #1 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /3D/Capsid Assembled.mrc" format
> mrc
Opened Capsid Assembled.mrc as #2, grid size 888,888,1731, pixel
1.06,1.06,1.06, shown at step 1, values float32
> ui tool show "Volume Viewer"
Already setting window visible!
> volume #2 region 0,0,0,887,887,1730 step 8
> volume #2 change image level -0.02638,0 level 0.2124,0.8 level 0.713,1
> volume #2 step 1
> lighting simple
> show #2.1 models
> hide #2.1 models
> hide #2.2 models
> hide #!2 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/ChimeraX/Cluster L/Douge/Douge_08/Douge_GP08.pdb"
Chain information for Douge_GP08.pdb #3
---
Chain | Description
A | No description available
> view #3 clip false
> close #3
> show #1 models
> view #1 clip false
> close #1
> close
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Fitting/Capsid Map PDB
> Fitting Session 3.cxs" format session
Opened Top Capsid.mrc as #2, grid size 512,512,512, pixel 1.06, shown at level
0.3, step 1, values float32
Opened Middle Capsid Tube 1.mrc as #3, grid size 640,640,640, pixel 1.06,
shown at level 0.3, step 1, values float32
Opened Middle Capsid Tube 2.mrc as #4, grid size 640,640,640, pixel 1.06,
shown at level 0.3, step 1, values float32
Opened Middle Capsid Tube 2.mrc as #6, grid size 640,640,640, pixel 1.06,
shown at level 0.3, step 1, values float32
Opened Bottom Capsid.mrc as #7, grid size 512,512,512, pixel 1.06, shown at
level 0.3, step 1, values float32
Opened Middle Capsid Tube 2.mrc as #11, grid size 640,640,640, pixel 1.06,
shown at level 0.3, step 1, values float32
opened ChimeraX session
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> hide #!3 models
> show #!9 models
> hide #!9 models
> show #12 models
> hide #12 models
> show #13 models
> hide #13 models
> show #!11 models
> hide #!11 models
> close
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Fitting/Capsid Map PDB
> Fitting Session 3.cxs"
Opened Top Capsid.mrc as #2, grid size 512,512,512, pixel 1.06, shown at level
0.3, step 1, values float32
Opened Middle Capsid Tube 1.mrc as #3, grid size 640,640,640, pixel 1.06,
shown at level 0.3, step 1, values float32
Opened Middle Capsid Tube 2.mrc as #4, grid size 640,640,640, pixel 1.06,
shown at level 0.3, step 1, values float32
Opened Middle Capsid Tube 2.mrc as #6, grid size 640,640,640, pixel 1.06,
shown at level 0.3, step 1, values float32
Opened Bottom Capsid.mrc as #7, grid size 512,512,512, pixel 1.06, shown at
level 0.3, step 1, values float32
Opened Middle Capsid Tube 2.mrc as #11, grid size 640,640,640, pixel 1.06,
shown at level 0.3, step 1, values float32
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!7 models
> view #9 clip false
> ui tool show "Fit in Map"
> fitmap #9 inMap #7
Fit molecule combination (#9) to map Bottom Capsid.mrc (#7) using 363465 atoms
average map value = 0.4198, steps = 44
shifted from previous position = 0.00309
rotated from previous position = 0.00347 degrees
atoms outside contour = 129201, contour level = 0.3
Position of combination (#9) relative to Bottom Capsid.mrc (#7) coordinates:
Matrix rotation and translation
-0.79798322 -0.60171776 -0.03403710 655.88079370
0.60263000 -0.79736902 -0.03224491 327.64098187
-0.00773779 -0.04624268 0.99890027 7.32060934
Axis -0.01161914 -0.02183030 0.99969417
Axis point 273.11788948 273.77086671 0.00000000
Rotation angle (degrees) 142.96102844
Shift along axis -7.45489709
> hide #!7 models
> view #1 clip false
> hide #!2 models
> ui tool show Distances
> select add #1.1.1
1 atom, 1 residue, 1 model selected
> select add #9.1
2 atoms, 2 residues, 2 models selected
> distance #1.1.1 #9.1
Distance already exists; modify distance properties with 'distance style'
Compositor returned null texture
> select clear
> select add #1
363466 atoms, 370125 bonds, 50446 residues, 33 models selected
> select add #2
363466 atoms, 370125 bonds, 50446 residues, 35 models selected
> show #!2 models
> hide #!2 models
> select subtract #2
363466 atoms, 370125 bonds, 50446 residues, 33 models selected
> select subtract #1
Nothing selected
> select add #9
363466 atoms, 370125 bonds, 50446 residues, 2 models selected
> select add #7
363466 atoms, 370125 bonds, 50446 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.87866,-0.47745,0.00095559,636.4,-0.47745,0.87866,0.00013041,154.53,-0.0009019,-0.00034166,-1,1780.6,#9,0.41342,0.90936,0.046257,-96.317,0.9105,-0.41333,-0.011951,129.26,0.0082516,0.047058,-0.99886,1772.6
> view matrix models
> #7,-0.87866,-0.47745,0.00095559,637.1,-0.47745,0.87866,0.00013041,158.66,-0.0009019,-0.00034166,-1,1812.6,#9,0.41342,0.90936,0.046257,-95.619,0.9105,-0.41333,-0.011951,133.4,0.0082516,0.047058,-0.99886,1804.6
> ~distance #9.1 #1.1.1
> undo
> select clear
> select add #9.1
1 atom, 1 residue, 1 model selected
> view matrix models
> #9.1,1,4.3872e-16,1.0408e-17,104.7,-1.816e-16,1,3.4694e-17,46.269,-1.3878e-17,2.0817e-17,1,-290.12
> undo
> ui mousemode right translate
> undo
> select add #1.1.1
1 atom, 1 residue, 1 model selected
> select add #9.1
2 atoms, 2 residues, 2 models selected
> distance #1.1.1 #9.1
Distance between centroid #1.1.1 and centroid #9.1: 1681.917Å
> select clear
> select add #9
363466 atoms, 370125 bonds, 50446 residues, 2 models selected
> select subtract #9
Nothing selected
> select add #7
2 models selected
> select add #9
363466 atoms, 370125 bonds, 50446 residues, 4 models selected
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.87866,-0.47745,0.00095559,639.93,-0.47745,0.87866,0.00013041,164.27,-0.0009019,-0.00034166,-1,1826.6,#9,0.41342,0.90936,0.046257,-92.794,0.9105,-0.41333,-0.011951,139.01,0.0082516,0.047058,-0.99886,1818.5
> select subtract #9
2 models selected
> select clear
> select add #6
2 models selected
> view matrix models
> #6,0.99998,-0.0057225,0.00026554,-69.16,0.0057225,0.99998,-1.4237e-05,-45.575,-0.00026546,1.5757e-05,1,758.84
> fitmap #6 inMap #7
Fit map Middle Capsid Tube 2.mrc in map Bottom Capsid.mrc using 1387970 points
correlation = 0.4237, correlation about mean = 0.07855, overlap = 3.263e+04
steps = 1556, shift = 338, angle = 24.2 degrees
Position of Middle Capsid Tube 2.mrc (#6) relative to Bottom Capsid.mrc (#7)
coordinates:
Matrix rotation and translation
-0.91952236 -0.35195044 -0.17495580 767.55665772
-0.39247461 0.84603727 0.36081107 -15.53569280
0.02103152 0.40043956 -0.91608179 559.19370164
Axis 0.19423941 -0.96063381 -0.19862963
Axis point 367.04381144 0.00000000 301.35922684
Rotation angle (degrees) 174.14510869
Shift along axis 52.94142600
> view clip false
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.28832,0.95656,-0.04322,61.087,-0.95078,-0.29135,-0.10551,719.93,-0.11352,0.010671,0.99348,1132.5
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.28832,0.95656,-0.04322,70.234,-0.95078,-0.29135,-0.10551,762.6,-0.11352,0.010671,0.99348,833.89
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.30038,0.95308,-0.037488,73.55,-0.95379,-0.29979,0.020449,723.5,0.0082506,0.041898,0.99909,780.02
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.30038,0.95308,-0.037488,71.186,-0.95379,-0.29979,0.020449,683.18,0.0082506,0.041898,0.99909,783.64
> fitmap #6 inMap #7
Fit map Middle Capsid Tube 2.mrc in map Bottom Capsid.mrc using 1387970 points
correlation = 0.2744, correlation about mean = -0.09997, overlap = 1.318e+04
steps = 2000, shift = 89.1, angle = 3.34 degrees
Position of Middle Capsid Tube 2.mrc (#6) relative to Bottom Capsid.mrc (#7)
coordinates:
Matrix rotation and translation
0.69138011 -0.72248835 -0.00203301 283.31097819
-0.72248991 -0.69138147 -0.00004616 751.89992711
-0.00137223 0.00150074 -0.99999794 937.58416588
Axis 0.91961412 -0.39282185 -0.00092603
Axis point 0.00000000 436.24507563 469.10343845
Rotation angle (degrees) 179.95181071
Shift along axis -35.69417001
> hide #!3 models
> hide #!4 models
> view matrix models
> #6,-0.26254,0.96492,0.00085277,8.3726,-0.96492,-0.26254,0.00079969,692.01,0.00099552,-0.00061291,1,688.03
> hide #!6 models
> select subtract #6
Nothing selected
> hide #!3 models
> view orient
> turn x 90
> view orient
> turn x 90
> ui mousemode right translate
> view #1 clip false
> hide #!1 models
> show #!2 models
> show #!3 models
> select add #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99996,0.0086538,0.00011096,-72.435,-0.0086538,0.99996,4.2866e-05,-78.843,-0.00011058,-4.3825e-05,1,331.4
> fitmap #3 inMap #2
Fit map Middle Capsid Tube 1.mrc in map Top Capsid.mrc using 1387970 points
correlation = 0.2192, correlation about mean = -0.142, overlap = 9043
steps = 2000, shift = 25.1, angle = 0.941 degrees
Position of Middle Capsid Tube 1.mrc (#3) relative to Top Capsid.mrc (#2)
coordinates:
Matrix rotation and translation
0.99996994 -0.00774775 0.00030549 -65.57741764
0.00774803 0.99996955 -0.00093058 -70.32656495
-0.00029827 0.00093292 0.99999952 310.17252724
Axis 0.11930955 0.03865556 0.99210432
Axis point 10507.95042710 -13081.19191036 0.00000000
Rotation angle (degrees) 0.44745904
Shift along axis 297.18097862
> ui mousemode right translate
> select subtract #3
Nothing selected
> show #!4 models
> select add #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99998,0.006414,0.00018089,-64.961,-0.006414,0.99998,7.9058e-05,-56.309,-0.00018038,-8.0217e-05,1,722.21
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!9 models
> view #4 clip false
> view matrix models
> #4,0.99998,0.006414,0.00018089,-68.371,-0.006414,0.99998,7.9058e-05,-51.252,-0.00018038,-8.0217e-05,1,770.7
> view matrix models
> #4,0.99998,0.006414,0.00018089,-69.504,-0.006414,0.99998,7.9058e-05,-51.498,-0.00018038,-8.0217e-05,1,769.2
> fitmap #4 inMap #3
Fit map Middle Capsid Tube 2.mrc in map Middle Capsid Tube 1.mrc using 1387970
points
correlation = 0.2907, correlation about mean = -0.1311, overlap = 1.086e+04
steps = 288, shift = 50.7, angle = 1.51 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Middle Capsid Tube 1.mrc
(#3) coordinates:
Matrix rotation and translation
0.99992625 -0.01214411 0.00008859 4.12603081
0.01214412 0.99992625 -0.00012508 -4.09021939
-0.00008707 0.00012615 0.99999999 410.18463007
Axis 0.01034261 0.00723177 0.99992036
Axis point 580.97825438 -13.09209856 0.00000000
Rotation angle (degrees) 0.69587920
Shift along axis 410.16505854
> view matrix models
> #4,0.9998,-0.019891,0.00039505,-61.589,0.019891,0.9998,-0.001055,-71.073,-0.00037399,0.0010626,1,765.49
> fitmap #4 inMap #3
Fit map Middle Capsid Tube 2.mrc in map Middle Capsid Tube 1.mrc using 1387970
points
correlation = 0.2964, correlation about mean = -0.135, overlap = 1.116e+04
steps = 1480, shift = 46.8, angle = 5.39 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Middle Capsid Tube 1.mrc
(#3) coordinates:
Matrix rotation and translation
0.99435617 -0.10609315 -0.00023038 37.98502166
0.10609318 0.99435619 0.00011475 -34.11396059
0.00021690 -0.00013855 0.99999997 408.64772838
Axis -0.00119375 -0.00210793 0.99999707
Axis point 331.77936944 344.98333300 0.00000000
Rotation angle (degrees) 6.09016999
Shift along axis 408.67309458
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99942,0.031811,-0.012555,-74.303,-0.031884,0.99948,-0.005648,-55.419,0.012369,0.006045,0.99991,712.84
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99942,0.031811,-0.012555,-73.948,-0.031884,0.99948,-0.005648,-50.871,0.012369,0.006045,0.99991,763.22
> fitmap #4 inMap #3
Fit map Middle Capsid Tube 2.mrc in map Middle Capsid Tube 1.mrc using 1387970
points
correlation = 0.2907, correlation about mean = -0.1311, overlap = 1.086e+04
steps = 872, shift = 49.1, angle = 3.07 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Middle Capsid Tube 1.mrc
(#3) coordinates:
Matrix rotation and translation
0.99992638 -0.01213391 0.00006115 4.12332398
0.01213392 0.99992637 -0.00013708 -4.08671479
-0.00005948 0.00013781 0.99999999 410.16715724
Axis 0.01132614 0.00497028 0.99992350
Axis point 504.53136200 -46.10016983 0.00000000
Rotation angle (degrees) 0.69529228
Shift along axis 410.16217052
> view matrix models
> #4,0.9998,-0.019881,0.0003677,-58.349,0.019881,0.9998,-0.0010672,-77.18,-0.00034641,0.0010743,1,808.48
> fitmap #4 inMap #7
Fit map Middle Capsid Tube 2.mrc in map Bottom Capsid.mrc using 1387970 points
correlation = 0.2316, correlation about mean = -0.1074, overlap = 8449
steps = 2000, shift = 57, angle = 1.81 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Bottom Capsid.mrc (#7)
coordinates:
Matrix rotation and translation
-0.90206401 -0.43159933 -0.00159814 725.19472780
-0.43160029 0.90206492 0.00029092 111.51049452
0.00131606 0.00095219 -0.99999868 959.89216945
Axis 0.22128602 -0.97520890 -0.00031866
Axis point 374.88118997 0.00000000 480.20127974
Rotation angle (degrees) 179.91439194
Shift along axis 51.42354515
> hide #!3 models
> show #!3 models
> select subtract #4
Nothing selected
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99928,0.037311,-0.0062285,-77.689,-0.037344,0.99929,-0.0053163,-51.792,0.0060257,0.0055451,0.99997,861.64
> view matrix models
> #4,0.9518,0.30532,-0.02939,-144.58,-0.30596,0.95182,-0.020428,60.714,0.021736,0.028436,0.99936,848.74
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.9518,0.30532,-0.02939,-142.31,-0.30596,0.95182,-0.020428,58.487,0.021736,0.028436,0.99936,817.54
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.95069,0.31014,0.001083,-153.97,-0.31011,0.95056,0.016577,47.699,0.0041118,-0.016096,0.99986,838.46
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.95069,0.31014,0.001083,-149.75,-0.31011,0.95056,0.016577,45.24,0.0041118,-0.016096,0.99986,791.01
> view matrix models
> #4,0.95069,0.31014,0.001083,-149.21,-0.31011,0.95056,0.016577,44.971,0.0041118,-0.016096,0.99986,807.1
> view matrix models
> #4,0.95069,0.31014,0.001083,-149,-0.31011,0.95056,0.016577,44.868,0.0041118,-0.016096,0.99986,813.3
> fitmap #4 inMap #7
Fit map Middle Capsid Tube 2.mrc in map Bottom Capsid.mrc using 1387970 points
correlation = 0.2334, correlation about mean = -0.1093, overlap = 8840
steps = 2000, shift = 57.6, angle = 1.83 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Bottom Capsid.mrc (#7)
coordinates:
Matrix rotation and translation
-0.66831486 -0.74387648 0.00174298 750.31801583
-0.74387843 0.66831410 -0.00107223 297.75954811
-0.00036726 -0.00201315 -0.99999791 960.91794335
Axis -0.40723730 0.91332200 -0.00084466
Axis point 441.84623948 0.00000000 480.36382374
Rotation angle (degrees) 179.93380872
Shift along axis -34.41879168
> view orient
> turn x 90
> zoom 1.5
> zoom 0.2
> color #3 #ffffb24d models
> color #4 #b2ffff4d models
> view #4 clip false
> view orient
> turn x 90
> zoom 0.8
> color #4 #b2ffffff models
> view matrix models
> #4,0.94238,0.33453,-0.0019751,-161.91,-0.33453,0.94238,-0.0019047,67.788,0.0012242,0.0024557,1,807.55
> fitmap #4 inMap #7
Fit map Middle Capsid Tube 2.mrc in map Bottom Capsid.mrc using 1387970 points
correlation = 0.2754, correlation about mean = -0.09788, overlap = 1.338e+04
steps = 2000, shift = 81.3, angle = 1.09 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Bottom Capsid.mrc (#7)
coordinates:
Matrix rotation and translation
-0.65428059 -0.75625147 -0.00079974 751.00842591
-0.75625170 0.65427929 0.00141111 305.40781979
-0.00054391 0.00152807 -0.99999869 935.82205233
Axis 0.41576472 -0.90947185 -0.00080893
Axis point 445.27656811 0.00000000 467.80369755
Rotation angle (degrees) 179.99194145
Shift along axis 33.72598599
> ui mousemode right translate
> zoom 0.8
> view orient
> turn x 90
> zoom 0.6
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.93596,0.3521,-0.00092663,-154.53,-0.3521,0.93596,0.0014913,78.006,0.0013924,-0.0010695,1,799.98
> view matrix models
> #4,0.93596,0.3521,-0.00092663,-153.6,-0.3521,0.93596,0.0014913,78.204,0.0013924,-0.0010695,1,792.24
> fitmap #4 inMap #7
Fit map Middle Capsid Tube 2.mrc in map Bottom Capsid.mrc using 1387970 points
correlation = 0.2763, correlation about mean = -0.1002, overlap = 1.349e+04
steps = 1108, shift = 102, angle = 3.1 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Bottom Capsid.mrc (#7)
coordinates:
Matrix rotation and translation
-0.61243642 -0.79051980 0.00029486 747.78176793
-0.79051985 0.61243634 -0.00031699 332.23225528
0.00007000 -0.00042723 -0.99999991 932.95081579
Axis -0.44020572 0.89789692 -0.00020849
Axis point 455.36401635 0.00000000 466.48838654
Rotation angle (degrees) 179.99282581
Shift along axis -31.06200709
> view matrix models
> #4,0.91556,0.40219,-0.0010633,-165.92,-0.40219,0.91556,-0.00054972,104.22,0.00075245,0.00093096,1,802.6
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.75886,0.65114,0.012301,-201.72,-0.65059,0.7588,-0.030953,252.15,-0.029489,0.015486,0.99945,808.12
> view matrix models
> #4,0.75757,0.65275,-0.0010179,-197.28,-0.65269,0.75749,-0.014445,247.68,-0.0086578,0.011607,0.9999,802.21
> fitmap #4 inMap #7
Fit map Middle Capsid Tube 2.mrc in map Bottom Capsid.mrc using 1387970 points
correlation = 0.2577, correlation about mean = -0.1094, overlap = 1.115e+04
steps = 2000, shift = 77, angle = 2.27 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Bottom Capsid.mrc (#7)
coordinates:
Matrix rotation and translation
-0.31953169 -0.94757531 -0.00073114 701.98132908
-0.94757549 0.31953119 0.00072100 484.43833524
-0.00044958 0.00092320 -0.99999948 946.58377401
Axis 0.58329644 -0.81225920 -0.00050764
Axis point 524.88166192 0.00000000 473.17747181
Rotation angle (degrees) 179.99006942
Shift along axis 15.49319221
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.73318,0.68004,-0.00065741,-203.53,-0.68004,0.73318,0.00085219,251.9,0.0010615,-0.00017775,1,802.59
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.54504,0.83839,-0.0059832,-191.53,-0.83841,0.54503,-0.0044227,371.33,-0.00044694,0.0074269,0.99997,800.53
> fitmap #4 inMap #7
Fit map Middle Capsid Tube 2.mrc in map Bottom Capsid.mrc using 1387970 points
correlation = 0.2738, correlation about mean = -0.1033, overlap = 1.292e+04
steps = 2000, shift = 84.8, angle = 0.449 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Bottom Capsid.mrc (#7)
coordinates:
Matrix rotation and translation
-0.08398531 -0.99646643 0.00106116 637.71926982
-0.99646688 0.08398576 0.00038556 581.16429238
-0.00047332 -0.00102503 -0.99999937 939.21223904
Axis -0.67676222 0.73620164 -0.00021748
Axis point 586.31315569 0.00000000 469.46721371
Rotation angle (degrees) 179.94028863
Shift along axis -3.93446105
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.54956,0.83545,-0.0020721,-201.82,-0.83546,0.54956,-0.00029828,369.56,0.00088952,0.0018951,1,765.77
> view matrix models
> #4,0.54956,0.83545,-0.0020721,-200.73,-0.83546,0.54956,-0.00029828,367.94,0.00088952,0.0018951,1,765.75
> fitmap #4 inMap #3
Fit map Middle Capsid Tube 2.mrc in map Middle Capsid Tube 1.mrc using 1387970
points
correlation = 0.3667, correlation about mean = -0.1008, overlap = 1.792e+04
steps = 420, shift = 89.7, angle = 2.5 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Middle Capsid Tube 1.mrc
(#3) coordinates:
Matrix rotation and translation
0.50597373 0.86254889 -0.00004998 -125.12036142
-0.86254877 0.50597363 -0.00055377 460.68296276
-0.00045237 0.00032330 0.99999985 366.72002933
Axis 0.00050842 0.00023326 -0.99999984
Axis point 339.77414561 339.44892241 0.00000000
Rotation angle (degrees) 59.60399666
Shift along axis -366.67612815
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.068115,-0.33089,-0.94121,727.98,-0.88268,0.4597,-0.097733,448.02,0.46501,0.82413,-0.32339,691.12
> view matrix models
> #4,-0.79599,-0.59711,0.099281,710.47,-0.60125,0.79891,-0.015591,209.3,-0.070007,-0.072103,-0.99494,1406.1
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.79599,-0.59711,0.099281,711.23,-0.60125,0.79891,-0.015591,212.24,-0.070007,-0.072103,-0.99494,1495.8
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.7983,-0.60208,0.014573,742.61,-0.60214,0.79839,0.00044666,207.25,-0.011904,-0.0084183,-0.99989,1456.1
> fitmap #4 inMap #3
Fit map Middle Capsid Tube 2.mrc in map Middle Capsid Tube 1.mrc using 1387970
points
correlation = 0.2963, correlation about mean = -0.1176, overlap = 1.121e+04
steps = 652, shift = 49.1, angle = 0.848 degrees
Position of Middle Capsid Tube 2.mrc (#4) relative to Middle Capsid Tube 1.mrc
(#3) coordinates:
Matrix rotation and translation
-0.80336057 -0.59549290 0.00009981 814.40664071
-0.59549291 0.80336056 -0.00016098 269.03731759
0.00001568 -0.00018876 -0.99999999 1089.89491006
Axis -0.31355910 0.94956868 -0.00009950
Axis point 451.63572569 0.00000000 544.95205245
Rotation angle (degrees) 179.99746182
Shift along axis -0.00365326
> hide #!3 models
> show #!3 models
> select subtract #4
Nothing selected
> hide #!4 models
> show #!4 models
> show #5 models
> hide #5 models
> show #!6 models
> select add #6
2 models selected
> view matrix models
> #6,-0.66884,0.74326,0.014455,216.95,-0.74228,-0.66664,-0.067836,776.91,-0.040784,-0.056101,0.99759,721.87
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.66884,0.74326,0.014455,565.64,-0.74228,-0.66664,-0.067836,1023.1,-0.040784,-0.056101,0.99759,965.75
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.66957,0.74249,0.01989,564.3,-0.74195,-0.66735,-0.064462,1022.1,-0.034589,-0.057918,0.99772,964.22
> view matrix models
> #6,-0.62732,0.77717,-0.049872,561.98,-0.77861,-0.62462,0.060189,977.49,0.015626,0.076589,0.99694,901.79
> view matrix models
> #6,-0.62953,0.77684,-0.014348,550.73,-0.77504,-0.62656,0.082083,969.47,0.054775,0.062794,0.99652,893.32
> view matrix models
> #6,-0.6278,0.77715,-0.043683,560.05,-0.77805,-0.62493,0.06402,976.1,0.022454,0.074179,0.99699,900.28
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.6278,0.77715,-0.043683,681.31,-0.77805,-0.62493,0.06402,1052.2,0.022454,0.074179,0.99699,909.51
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.65475,0.75441,-0.046631,699.18,-0.7556,-0.65172,0.065725,1053.1,0.019193,0.078268,0.99675,909.32
> view matrix models
> #6,-0.65539,0.75436,-0.037577,696.33,-0.75472,-0.65215,0.071319,1051,0.029294,0.075101,0.99675,906.96
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> hide #14 models
> show #14 models
> hide #!10 models
> hide #!7 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> volume erase #6 center 714.83,598.69,1155 radius 254.3
Opened Middle Capsid Tube 2.mrc copy as #15, grid size 640,640,640, pixel
1.06, shown at step 1, values float32
> volume erase #15 center 714.83,598.69,1155 radius 254.3
> hide #14 models
Already setting window visible!
> show #!2 models
> show #!3 models
> show #!4 models
> show #!7 models
> show #!6 models
> hide #!6 models
> select subtract #6
Nothing selected
> select add #15
2 models selected
> select subtract #15
Nothing selected
> show #14 models
> hide #14 models
> select add #15
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.65539,0.75436,-0.037577,558.21,-0.75472,-0.65215,0.071319,984.23,0.029294,0.075101,0.99675,807.9
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.71521,0.69877,-0.014387,586.33,-0.69861,-0.71414,0.044124,999.21,0.020558,0.041609,0.99892,821.2
> view matrix models
> #15,-0.71508,0.69799,-0.038326,597.98,-0.699,-0.71458,0.027894,1007.2,-0.0079169,0.046736,0.99888,829.16
> view matrix models
> #15,-0.72118,0.69228,-0.025272,595.76,-0.69264,-0.72123,0.0089639,1016.4,-0.012021,0.023969,0.99964,837.92
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.72118,0.69228,-0.025272,578.78,-0.69264,-0.72123,0.0089639,1005.5,-0.012021,0.023969,0.99964,874.41
> view matrix models
> #15,-0.72118,0.69228,-0.025272,645.54,-0.69264,-0.72123,0.0089639,1053.7,-0.012021,0.023969,0.99964,833.9
> show #14 models
> view matrix models
> #15,-0.72118,0.69228,-0.025272,649.55,-0.69264,-0.72123,0.0089639,1056.3,-0.012021,0.023969,0.99964,841.85
> ui mousemode right "map eraser"
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.72134,0.69249,-0.010976,642.71,-0.69255,-0.72109,0.020245,1050.8,0.0061048,0.022205,0.99973,836.25
> ui mousemode right "map eraser"
> hide #!4 models
> hide #!2 models
> hide #!3 models
> hide #!7 models
Already setting window visible!
> volume erase #15 center 641.99,560.24,1130.6 radius 254.3
Already setting window visible!
> ~distance #1.1.1 #9.1
Exactly two atoms must be selected!
> hide #14 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!7 models
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.72134,0.69249,-0.010976,302.71,-0.69255,-0.72109,0.020245,722.5,0.0061048,0.022205,0.99973,823.29
> fitmap #15 inMap #7
Fit map Middle Capsid Tube 2.mrc copy in map Bottom Capsid.mrc using 285222
points
correlation = 0.558, correlation about mean = -0.00785, overlap = 7914
steps = 304, shift = 65.8, angle = 5.26 degrees
Position of Middle Capsid Tube 2.mrc copy (#15) relative to Bottom Capsid.mrc
(#7) coordinates:
Matrix rotation and translation
0.96607857 -0.25821818 -0.00394699 28.17062841
-0.25787019 -0.96372444 -0.06883438 695.50687598
0.01397047 0.06751723 -0.99762030 900.58484289
Axis 0.99147324 -0.13028588 0.00253041
Axis point 0.00000000 333.96850978 462.19310290
Rotation angle (degrees) 176.05710939
Shift along axis -60.40545093
> view matrix models
> #15,-0.72572,0.68708,0.03538,285.8,-0.68783,-0.72349,-0.058728,761.6,-0.014754,-0.066955,0.99765,860.69
> fitmap #15 inMap #6
Fit map Middle Capsid Tube 2.mrc copy in map Middle Capsid Tube 2.mrc using
285222 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of Middle Capsid Tube 2.mrc copy (#15) relative to Middle Capsid Tube
2.mrc (#6) coordinates:
Matrix rotation and translation
0.99431924 0.09377117 0.05036077 486.11851116
-0.09998834 0.98510238 0.13991297 -124.42041478
-0.03649071 -0.14415365 0.98888227 -51.33598639
Axis -0.80096734 0.24489042 -0.54633323
Axis point 0.00000000 -1841.54482720 7.43805132
Rotation angle (degrees) 10.21411647
Shift along axis -391.78786405
> view matrix models
> #15,-0.72572,0.68708,0.03538,267.66,-0.68783,-0.72349,-0.058728,793.27,-0.014754,-0.066955,0.99765,848.2
> view matrix models
> #15,-0.72572,0.68708,0.03538,9.5444,-0.68783,-0.72349,-0.058728,1230.8,-0.014754,-0.066955,0.99765,788.72
> select subtract #15
Nothing selected
> hide #!3 models
> hide #!2 models
> hide #!4 models
> hide #!7 models
> show #14 models
> ui mousemode right "map eraser"
> volume erase #15 center 37.369,758.8,1073.9 radius 254.3
> close #15
> show #!6 models
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.65539,0.75436,-0.037577,72.33,-0.75472,-0.65215,0.071319,1086.1,0.029294,0.075101,0.99675,918.64
> show #!7 models
> show #5 models
> close #5
> show #!4 models
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.65488,0.75573,-0.0030474,59.907,-0.75572,-0.65488,-0.004156,1113.1,-0.0051365,-0.0004187,0.99999,954.85
> view matrix models
> #6,-0.82316,0.56762,0.014916,174.76,-0.56763,-0.82327,0.0033074,1103.8,0.014157,-0.0057442,0.99988,950.14
> view matrix models
> #6,-0.82336,0.5675,0.0039057,178.63,-0.56721,-0.82312,0.027371,1095.4,0.018748,0.020321,0.99962,939.82
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.82336,0.5675,0.0039057,186.4,-0.56721,-0.82312,0.027371,1078.8,0.018748,0.020321,0.99962,819.5
> view matrix models
> #6,-0.82336,0.5675,0.0039057,165.54,-0.56721,-0.82312,0.027371,1124.4,0.018748,0.020321,0.99962,822.18
> view matrix models
> #6,-0.82336,0.5675,0.0039057,142.73,-0.56721,-0.82312,0.027371,1174.3,0.018748,0.020321,0.99962,822.36
> select subtract #6
Nothing selected
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> hide #!4 models
> hide #!7 models
> volume erase #6 center 63.967,703.22,1102.7 radius 254.3
Opened Middle Capsid Tube 2.mrc copy as #5, grid size 640,640,640, pixel 1.06,
shown at step 1, values float32
> hide #14 models
> show #!7 models
> show #!3 models
> show #!4 models
> select add #5
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.82336,0.5675,0.0039057,476.54,-0.56721,-0.82312,0.027371,912.78,0.018748,0.020321,0.99962,815.84
> view matrix models
> #5,-0.82336,0.5675,0.0039057,374.16,-0.56721,-0.82312,0.027371,727.25,0.018748,0.020321,0.99962,814.99
> view matrix models
> #5,-0.82336,0.5675,0.0039057,357.04,-0.56721,-0.82312,0.027371,729.17,0.018748,0.020321,0.99962,811.24
> view matrix models
> #5,-0.82336,0.5675,0.0039057,-44.96,-0.56721,-0.82312,0.027371,814.76,0.018748,0.020321,0.99962,830.43
> view matrix models
> #5,-0.82336,0.5675,0.0039057,-42.593,-0.56721,-0.82312,0.027371,813,0.018748,0.020321,0.99962,816.05
> view matrix models
> #5,-0.82336,0.5675,0.0039057,-102.73,-0.56721,-0.82312,0.027371,831.1,0.018748,0.020321,0.99962,818.77
> show #14 models
> ui mousemode right "map eraser"
> hide #!3 models
> hide #!4 models
> hide #!7 models
> volume erase #5 center -182.48,543.5,1047.7 radius 254.3
> volume erase #5 center -96.65,545.7,1044.3 radius 254.3
> volume erase #5 center -325.1,522.03,1042.9 radius 254.3
> select subtract #5
Nothing selected
> select add #5
2 models selected
> hide #14 models
> show #!3 models
> show #!7 models
> show #!4 models
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.82336,0.5675,0.0039057,321.03,-0.56721,-0.82312,0.027371,653.72,0.018748,0.020321,0.99962,821.72
> fitmap #5 inMap #4
Fit map Middle Capsid Tube 2.mrc copy in map Middle Capsid Tube 2.mrc using
310234 points
correlation = 0.5433, correlation about mean = 0.01493, overlap = 5275
steps = 796, shift = 30.5, angle = 13.7 degrees
Position of Middle Capsid Tube 2.mrc copy (#5) relative to Middle Capsid Tube
2.mrc (#4) coordinates:
Matrix rotation and translation
0.97204456 0.07993909 -0.22076933 155.29813442
0.11108681 -0.98494194 0.13247296 530.53499892
-0.20685521 -0.15329418 -0.96628764 699.31193241
Axis -0.99294973 -0.04834715 0.10822840
Axis point 0.00000000 287.36589385 338.98108226
Rotation angle (degrees) 171.72652467
Shift along axis -104.16768242
> view matrix models
> #5,-0.84319,0.52882,0.096822,343.34,-0.49631,-0.83491,0.2379,582.35,0.20665,0.15254,0.96645,697.04
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.85397,0.51965,-0.026628,412.86,-0.51974,-0.84945,0.091089,669.84,0.024715,0.091626,0.99549,764.31
> view matrix models
> #5,-0.86319,0.50307,0.042729,386.3,-0.50209,-0.86422,0.031939,698.95,0.052995,0.0061159,0.99858,782.08
> fitmap #5 inMap #6
Fit map Middle Capsid Tube 2.mrc copy in map Middle Capsid Tube 2.mrc using
310234 points
correlation = 0.002138, correlation about mean = -0.002119, overlap = 0.00137
steps = 168, shift = 9.53, angle = 2.91 degrees
Position of Middle Capsid Tube 2.mrc copy (#5) relative to Middle Capsid Tube
2.mrc (#6) coordinates:
Matrix rotation and translation
0.99268322 0.11607236 -0.03327517 64.34557277
-0.11650399 0.99312555 -0.01133374 556.43448548
0.03173089 0.01512751 0.99938196 -60.70927796
Axis 0.10892287 -0.26758548 -0.95735773
Axis point 4603.93237365 -342.74724922 0.00000000
Rotation angle (degrees) 6.97682330
Shift along axis -83.76458708
> view matrix models
> #5,-0.93916,0.34171,0.034756,461.83,-0.34025,-0.93941,0.041722,661.66,0.046907,0.027358,0.99852,777.78
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.93916,0.34171,0.034756,465.58,-0.34025,-0.93941,0.041722,684.91,0.046907,0.027358,0.99852,780.86
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.93844,0.34462,0.02388,469.88,-0.34514,-0.93827,-0.022834,719.01,0.014537,-0.02967,0.99945,810.59
> view matrix models
> #5,-0.94574,0.32375,-0.027675,505.62,-0.32342,-0.94612,-0.015831,710.76,-0.03131,-0.0060218,0.99949,818.07
> fitmap #5 inMap #6
Fit map Middle Capsid Tube 2.mrc copy in map Middle Capsid Tube 2.mrc using
310234 points
correlation = 0.005303, correlation about mean = -0.001527, overlap = 0.005378
steps = 2000, shift = 21.3, angle = 3.48 degrees
Position of Middle Capsid Tube 2.mrc copy (#5) relative to Middle Capsid Tube
2.mrc (#6) coordinates:
Matrix rotation and translation
0.97428482 0.22097823 0.04401935 -27.50630076
-0.22062275 0.97527473 -0.01283731 591.07187846
-0.04576772 0.00279553 0.99894820 -9.20242827
Axis 0.03466974 0.19912528 -0.97936057
Axis point 2516.62220472 437.06395247 0.00000000
Rotation angle (degrees) 13.02956046
Shift along axis 125.75621155
> view matrix models
> #5,-0.99712,0.060351,-0.045828,632.57,-0.057216,-0.99612,-0.066875,660.26,-0.049686,-0.064061,0.99671,862.56
> view matrix models
> #5,-0.9982,0.057144,0.018273,601.41,-0.058407,-0.99522,-0.078286,666.16,0.013712,-0.079213,0.99676,846.24
> view orient
> turn x 90
> zoom 0.8
> view matrix models
> #5,-0.99681,0.054079,0.058756,581.39,-0.055692,-0.99811,-0.026167,639.72,0.057229,-0.029356,0.99793,814.1
> view matrix models
> #5,-0.99746,0.065087,-0.028796,622.42,-0.066206,-0.99701,0.039777,609.36,-0.026121,0.041583,0.99879,817.85
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.99746,0.065087,-0.028796,615.59,-0.066206,-0.99701,0.039777,600.63,-0.026121,0.041583,0.99879,820.37
> view matrix models
> #5,-0.99746,0.065087,-0.028796,600.99,-0.066206,-0.99701,0.039777,605.71,-0.026121,0.041583,0.99879,822.08
> fitmap #5 inMap #6
Fit map Middle Capsid Tube 2.mrc copy in map Middle Capsid Tube 2.mrc using
310234 points
correlation = 0.008719, correlation about mean = 0.003084, overlap = 0.03407
steps = 2000, shift = 91.1, angle = 27.3 degrees
Position of Middle Capsid Tube 2.mrc copy (#5) relative to Middle Capsid Tube
2.mrc (#6) coordinates:
Matrix rotation and translation
0.81147617 0.55597864 0.17998382 -114.71380942
-0.57756711 0.71611223 0.39191773 591.61260747
0.08900927 -0.42198463 0.90222299 54.53670004
Axis -0.58200661 0.06505423 -0.81057772
Axis point 812.08817274 417.79171065 0.00000000
Rotation angle (degrees) 44.36452913
Shift along axis 61.04486264
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.99062,0.014552,-0.13588,657.28,0.0030027,-0.99176,-0.1281,645.99,-0.13663,-0.12731,0.98241,837.88
> view matrix models
> #5,-0.99871,-0.042702,0.027313,596.36,0.043065,-0.99899,0.01285,563.22,0.026737,0.01401,0.99954,726.23
> view matrix models
> #5,-0.99846,-0.042916,0.035198,592.34,0.043044,-0.99907,0.0029021,568.31,0.035041,0.0044127,0.99938,726.76
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.99846,-0.042916,0.035198,587.46,0.043044,-0.99907,0.0029021,577.81,0.035041,0.0044127,0.99938,819.08
> view matrix models
> #5,-0.99846,-0.042916,0.035198,605.49,0.043044,-0.99907,0.0029021,598.67,0.035041,0.0044127,0.99938,817.04
> view matrix models
> #5,-0.99846,-0.042916,0.035198,608.24,0.043044,-0.99907,0.0029021,600.58,0.035041,0.0044127,0.99938,811.32
> fitmap #5 inMap #6
Fit map Middle Capsid Tube 2.mrc copy in map Middle Capsid Tube 2.mrc using
310234 points
correlation = 0.007192, correlation about mean = 0.0003181, overlap = 0.009341
steps = 2000, shift = 21.1, angle = 7.79 degrees
Position of Middle Capsid Tube 2.mrc copy (#5) relative to Middle Capsid Tube
2.mrc (#6) coordinates:
Matrix rotation and translation
0.79654924 0.59682177 -0.09650437 -17.63938388
-0.58234245 0.80030932 0.14276644 692.91319881
0.16243947 -0.05752191 0.98504043 -61.17073466
Axis -0.16366598 -0.21159641 -0.96355612
Axis point 1021.54291014 401.04139449 0.00000000
Rotation angle (degrees) 37.72566818
Shift along axis -84.78954507
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.99813,-0.047565,-0.0383,660.91,0.044463,-0.99595,0.078125,549.11,-0.041861,0.076277,0.99621,803.77
> fitmap #5 inMap #6
Fit map Middle Capsid Tube 2.mrc copy in map Middle Capsid Tube 2.mrc using
310234 points
correlation = 0.00951, correlation about mean = 0.008119, overlap = 0.09119
steps = 2000, shift = 80.7, angle = 22.9 degrees
Position of Middle Capsid Tube 2.mrc copy (#5) relative to Middle Capsid Tube
2.mrc (#6) coordinates:
Matrix rotation and translation
0.69999298 0.69467153 0.16565415 -122.33951405
-0.71060320 0.65443104 0.25838556 735.81357197
0.07108387 -0.29858245 0.95173295 -6.20041900
Axis -0.36773748 0.06243992 -0.92783102
Axis point 798.52304322 469.78606166 -0.00000000
Rotation angle (degrees) 49.22588936
Shift along axis 96.68590800
> view matrix models
> #5,-0.9823,-0.18369,-0.036776,681.71,0.18479,-0.98235,-0.02905,525.62,-0.03079,-0.035332,0.9989,762.85
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.9823,-0.18369,-0.036776,757.52,0.18479,-0.98235,-0.02905,177.97,-0.03079,-0.035332,0.9989,851.66
> close #5
> show #!6 models
> show #14 models
> ui mousemode right "map eraser"
> select add #6
2 models selected
> select add #14
3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.82336,0.5675,0.0039057,134.93,-0.56721,-0.82312,0.027371,1292.4,0.018748,0.020321,0.99962,829.13,#14,1,0,0,39.314,0,1,0,845.75,0,0,1,1021.1
> select subtract #6
1 model selected
> select subtract #14
Nothing selected
> ui mousemode right "map eraser"
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> hide #!3 models
> volume erase #6 center 44.548,820.94,1006.9 radius 339.52
Opened Middle Capsid Tube 2.mrc copy as #5, grid size 640,640,640, pixel 1.06,
shown at step 1, values float32
> hide #14 models
> select add #5
2 models selected
> show #!4 models
> show #!7 models
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.82336,0.5675,0.0039057,282.04,-0.56721,-0.82312,0.027371,718.19,0.018748,0.020321,0.99962,812.65
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.82394,0.56656,0.011677,278.55,-0.56662,-0.82397,-0.0027816,733.81,0.0080459,-0.0089085,0.99993,825.98
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.82394,0.56656,0.011677,278.9,-0.56662,-0.82397,-0.0027816,732.24,0.0080459,-0.0089085,0.99993,824.73
> view matrix models
> #5,-0.82394,0.56656,0.011677,349.63,-0.56662,-0.82397,-0.0027816,759.47,0.0080459,-0.0089085,0.99993,831.52
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.84517,0.53447,-0.0057485,376.62,-0.53419,-0.84425,0.043456,731.55,0.018373,0.039798,0.99904,812.03
> view matrix models
> #5,-0.84503,0.53309,-0.041592,395.5,-0.53437,-0.84473,0.029676,738.87,-0.019314,0.047303,0.99869,822.4
> view matrix models
> #5,-0.84538,0.53402,-0.012296,380.21,-0.5341,-0.84541,0.0047562,751.84,-0.0078551,0.010588,0.99991,830.31
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.84538,0.53402,-0.012296,387.59,-0.5341,-0.84541,0.0047562,745.58,-0.0078551,0.010588,0.99991,829.18
> view matrix models
> #5,-0.84538,0.53402,-0.012296,386.25,-0.5341,-0.84541,0.0047562,741.07,-0.0078551,0.010588,0.99991,829.25
> view matrix models
> #5,-0.84538,0.53402,-0.012296,382.05,-0.5341,-0.84541,0.0047562,736.96,-0.0078551,0.010588,0.99991,832.21
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.845,0.53459,0.013712,368.33,-0.53405,-0.84492,0.030018,723.77,0.027633,0.018043,0.99946,817.94
> view matrix models
> #5,-0.83999,0.54197,0.026268,357.68,-0.5417,-0.8404,0.017107,731.48,0.031348,0.00014034,0.99951,822.71
> fitmap #5 inMap #6
Fit map Middle Capsid Tube 2.mrc copy in map Middle Capsid Tube 2.mrc using
318698 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of Middle Capsid Tube 2.mrc copy (#5) relative to Middle Capsid Tube
2.mrc (#6) coordinates:
Matrix rotation and translation
0.99945721 0.03044173 -0.01259322 134.63548650
-0.03017126 0.99932123 0.02113687 587.97863169
0.01322811 -0.02074544 0.99969728 -20.90249357
Axis -0.53647652 -0.33074914 -0.77640064
Axis point 16735.72692050 289.78872914 0.00000000
Rotation angle (degrees) 2.23708690
Shift along axis -250.47349478
> fitmap #5 inMap #4
Fit map Middle Capsid Tube 2.mrc copy in map Middle Capsid Tube 2.mrc using
318698 points
correlation = 0.7407, correlation about mean = 0.1822, overlap = 1.408e+04
steps = 276, shift = 55.3, angle = 3.31 degrees
Position of Middle Capsid Tube 2.mrc copy (#5) relative to Middle Capsid Tube
2.mrc (#4) coordinates:
Matrix rotation and translation
0.99259696 0.12145218 -0.00079758 -38.33268518
0.12145209 -0.99259727 -0.00016716 635.34106936
-0.00081197 0.00006905 -0.99999966 622.70056428
Axis 0.99814748 0.06083960 -0.00040097
Axis point 0.00000000 318.82031725 311.36141129
Rotation angle (degrees) 179.99322058
Shift along axis 0.14253772
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.86589,0.50024,0.00094206,392.22,-0.50024,-0.86589,-0.00042399,735.34,0.00060362,-0.00083839,1,815.68
> fitmap #5 inMap #7
Fit map Middle Capsid Tube 2.mrc copy in map Bottom Capsid.mrc using 318698
points
correlation = 0.5386, correlation about mean = -0.1091, overlap = 9690
steps = 280, shift = 56.4, angle = 0.224 degrees
Position of Middle Capsid Tube 2.mrc copy (#5) relative to Bottom Capsid.mrc
(#7) coordinates:
Matrix rotation and translation
0.99956315 -0.02955504 -0.00007097 -57.69897547
-0.02955504 -0.99956316 0.00000233 620.99978390
-0.00007101 -0.00000023 -1.00000000 954.43230807
Axis -0.99988968 0.01485297 -0.00014503
Axis point 0.00000000 310.07164981 477.22013978
Rotation angle (degrees) 179.99992657
Shift along axis 66.77788552
> view matrix models
> #5,-0.86416,0.50321,-0.00089434,394.68,-0.50321,-0.86416,-9.4473e-05,737.96,-0.0008204,0.0003684,1,834.36
> show #!3 models
> show #!2 models
> select subtract #5
Nothing selected
> rename #6 id #15
> rename #7 id #6
> vop add #2-6
Opened volume sum as #7, grid size 898,898,1725, pixel 1.06, shown at step 1,
values float32
> show #!1 models
> rename #2 id #21
> rename #3 id #22
> rename #4 id #23
> rename #5 id #24
> rename #6 id #25
> show #8 models
> hide #8 models
> combine #1
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16U0000PTA/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 43 days, 1 hour, 6 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403220040
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 12 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 12 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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