![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15517 closed defect (can't reproduce)
Crash changing Mac display configuration
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001eab94c00 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, 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, openmm._openmm, openmm.app.internal.compiled, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)
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{
"uptime" : 560000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,6",
"coalitionID" : 91728,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-06-26 17:01:59.6585 -0700",
"codeSigningMonitor" : 1,
"incident" : "4CB256E4-41CE-42CA-94FB-C3880429E8AB",
"pid" : 30283,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-06-26 10:26:58.4428 -0700",
"procStartAbsTime" : 13068033008754,
"procExitAbsTime" : 13624414934767,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"06B671E0-6B9C-5370-85AD-F50D71EB9B2D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5C0C8E13-8B02-E700-C0B3-5F95CBCD57A3",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 15325,
"sleepWakeUUID" : "0F2188B5-C4E6-4681-9CCF-1CD7075F2AFC",
"sip" : "enabled",
"vmRegionInfo" : "0x1eabac6 is not in any region. Bytes before following region: 4263888186\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100108000-10010c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000101, 0x5000000001eabac6","rawCodes":[257,5764607523066395334],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"UNKNOWN_0x101 at 0x5000000001eabac6 -> 0x0000000001eabac6 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":30283},
"ktriageinfo" : "CL - (arg = 0x0) cluster_pagein past EOF\nVM - (arg = 0x0) Filesystem pagein returned an error in vnode_pagein\nVM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\nVM - (arg = 0x0) Filesystem pagein returned an error in vnode_pagein\n",
"vmregioninfo" : "0x1eabac6 is not in any region. Bytes before following region: 4263888186\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100108000-10010c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias cofron cofr centerofview showpivot 4,0.2
> alias cofroff cofr centerofview showpivot false
> alias paulsave save
> /Users/psauer/Documents/Processing/20240530_IVTT15/$1.png
> transparentbackground true format png supersample 3
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias paulclip cofr centerofview; style stick; surface cap false; clip near
> -2 far 6 position cofr; material transparentCastShadows false; lighting
> flat; graphics silhouettes false; transparency 70; volume step 1
> alias paulunclip view all; transparency 0; lighting soft
> alias paullight material transparentCastShadows true; lighting soft;
> transparency 70; style stick; show cartoon
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; #disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.1; transparency 70;
> cofr centerofview; clip near -2 far 6 position cofr; #color ##~num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_30 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 30; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette ^RdYlBu-5;
> lighting soft; view all; transparency 0
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias paulvis lighting soft; material transparentcastshadows false; style
> stick; color /* #2b8cbe; select :ANM; select up; select up; color sel pink;
> ~select; color :IDB* yellow; color byhetero; graphics silhouettes true;
> graphics silhouettes width 1; graphics silhouettes depthJump 0.1;
> transparency 60; hide H
> alias paullabel label /* residues color black height 0.8 bgcolor
> rgba(100%,100%,100%,0.6); ~label :HOH
> alias IDB view :IDB*; paulclip; volume step 1
> alias paulcolor color $*/m #e31a1c; color $*/s,t #a6cee3; color $*/L* &
> nucleic #1f78b4; color $*/L* & protein #a6cee3; color $*/S* & nucleic
> #ff7f00; color $*/S* & protein #fdbf6f; color $*/Pt* #33a02c; color $*/mR
> #b2df8a; color $*:ANM $*/X yellow; color $*/By,NC #fb9a99
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_30
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"
> buttonpanel Shortcuts add IDB command IDB
> buttonpanel Shortcuts add paulvis command paulvis
> buttonpanel Shortcuts add paullabel command paullabel
> buttonpanel Shortcuts add paulclip command paulclip
> buttonpanel Shortcuts add paullight command paullight
> buttonpanel Shortcuts add paulsave command paulsave
> buttonpanel Shortcuts add unclip command paulunclip
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/TI-
> Post_SSU_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/TI-
> Post_P-tRNA_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/TI_uL11_5LZZ.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/TI_uL10_5LZZ.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/TI_eEF2_7LS2.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/SSU_7LS2.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH2_SSU_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH2_PE-
> tRNA_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH2_A-
> tRNA_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH1_SSU_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH1_PE-
> tRNA_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH1_A-
> tRNA_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/Nascent_chain.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/MDsnapshot_1403_Ala35Glu_Ala36_Glu_Ala37Glu.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/LSU_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/LSU_7LS2.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/IDB_1403.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/GTP_eEF2.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/Nascent_chain.cif
---
warnings | Unknown polymer entity '1' on line 146
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening
/Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/MDsnapshot_1403_Ala35Glu_Ala36_Glu_Ala37Glu.cif
---
warnings | Unknown polymer entity '1' on line 165
Unknown polymer entity '2' on line 878
Unknown polymer entity '3' on line 6200
Unknown polymer entity '4' on line 6334
Missing second atom in struct_conn "covale55"
Missing second atom in struct_conn "covale56"
Atom HH31 is not in the residue template for ACE /L:1B
Atom HH31 is not in the residue template for ACE /L:1Q
Atom H is not in the residue template for ALA /L:2
Atom CA is not in the residue template for NMA /L:3A
Atom CA is not in the residue template for NMA /L:3B
Atom HH31 is not in the residue template for ACE /L:4
Atom CA is not in the residue template for NMA /L:5A
Atom HH31 is not in the residue template for ACE /L:66
Atom CA is not in the residue template for NMA /L:73A
Atom HH31 is not in the residue template for ACE /L:74
Atom CA is not in the residue template for NMA /L:75A
Atom HH31 is not in the residue template for ACE /L:112A
Atom CA is not in the residue template for NMA /L:115A
Atom HH31 is not in the residue template for ACE /L:131
Atom CA is not in the residue template for NMA /L:133A
Atom HH31 is not in the residue template for ACE /L:134
Atom CA is not in the residue template for NMA /L:135A
Too many hydrogens missing from residue template(s) to warn about
Atom CA is not in the residue template for NMA /L:246A
Atom CA is not in the residue template for NMA /L:250A
Atom CA is not in the residue template for NMA /L:261A
Atom O3' is not in the residue template for ALA /y:39
Atom O is not in the residue template for SPC :27
Atom O is not in the residue template for SPC :28
Atom O is not in the residue template for SPC :30
Atom O is not in the residue template for SPC :32
Atom O is not in the residue template for SPC :31
195 messages similar to the above omitted
Atom O1 is not in the residue template for UNK :900
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening
/Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/IDB_1403.cif
---
warning | Unable to fetch template for '.': will connect using distance criteria
Chain information for TI-Post_SSU_8GLP.cif #1
---
Chain | Description
S2 | 18S rRNA
SA | 40S ribosomal protein SA
SB | 40S ribosomal protein S3a
SC | 40S ribosomal protein S2
SD | 40S ribosomal protein S3
SE | 40S ribosomal protein S4, X isoform
SF | 40S ribosomal protein S5
SG | 40S ribosomal protein S6
SH | 40S ribosomal protein S7
SI | 40S ribosomal protein S8
SJ | 40S ribosomal protein S9
SK | 40S ribosomal protein S10
SL | 40S ribosomal protein S11
SM | 40S ribosomal protein S12
SN | 40S ribosomal protein S13
SO | 40S ribosomal protein S14
SP | 40S ribosomal protein S15
SQ | 40S ribosomal protein S16
SR | 40S ribosomal protein S17
SS | 40S ribosomal protein S18
ST | 40S ribosomal protein S19
SU | 40S ribosomal protein S20
SV | 40S ribosomal protein S21
SW | 40S ribosomal protein S15a
SX | 40S ribosomal protein S23 (uS12)
SY | 40S ribosomal protein S24
SZ | 40S ribosomal protein S25
Sa | 40S ribosomal protein S26
Sb | 40S ribosomal protein S27
Sc | 40S ribosomal protein S28
Sd | 40S ribosomal protein S29
Se | FAU ubiquitin-like and ribosomal protein S30
Sf | Ubiquitin-40S ribosomal protein S27a
Sg | Receptor of activated protein C kinase 1
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for TI-Post_P-tRNA_8GLP.cif #2
---
Chain | Description
Pt | P-site tRNA
Chain information for TI_uL11_5LZZ.cif #3
---
Chain | Description
t | uL11
Chain information for TI_uL10_5LZZ.cif #4
---
Chain | Description
s | uL10
Chain information for TI_eEF2_7LS2.cif #5
---
Chain | Description
m | Elongation factor 2
Chain information for SSU_7LS2.cif #6
---
Chain | Description
A | Isoform 3 of Plasminogen activator inhibitor 1 RNA-binding protein
A3 | 40S ribosomal protein S18
B3 | 40S ribosomal protein S19
C3 | 40S ribosomal protein S20
D3 | 40S ribosomal protein S21
E3 | 40S ribosomal protein S23
F3 | 40S ribosomal protein S26
G3 | 40S ribosomal protein S28
H3 | 40S ribosomal protein S29
I3 | Receptor of activated protein C kinase 1
J3 | 40S ribosomal protein S2
K3 | 40S ribosomal protein S6
L3 | 40S ribosomal protein S9
M3 | 40S ribosomal protein S12
N3 | 40S ribosomal protein S13
O3 | 40S ribosomal protein S14
P3 | 40S ribosomal protein S15a
Q3 | 40S ribosomal protein S24
R3 | 40S ribosomal protein S25
S3 | 40S ribosomal protein S27-like
T3 | 40S ribosomal protein S30
U3 | Ubiquitin-40S ribosomal protein S27a
m2 | 18S rRNA
o2 | 40S ribosomal protein SA
p2 | 40S ribosomal protein S3a
q2 | 40S ribosomal protein S3
r2 | 40S ribosomal protein S4, X isoform
s2 | 40S ribosomal protein S5
t | 40S ribosomal protein S7
u | 40S ribosomal protein S8
v2 | 40S ribosomal protein S10
w2 | 40S ribosomal protein S11
x2 | 40S ribosomal protein S15
y2 | 40S ribosomal protein S16
z2 | 40S ribosomal protein S17
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for PreH2_SSU_8GLP.cif #7
---
Chain | Description
S2 | 18S rRNA
SA | 40S ribosomal protein SA
SB | 40S ribosomal protein S3a
SC | 40S ribosomal protein S2
SD | 40S ribosomal protein S3
SE | 40S ribosomal protein S4, X isoform
SF | 40S ribosomal protein S5
SG | 40S ribosomal protein S6
SH | 40S ribosomal protein S7
SI | 40S ribosomal protein S8
SJ | 40S ribosomal protein S9
SK | 40S ribosomal protein S10
SL | 40S ribosomal protein S11
SM | 40S ribosomal protein S12
SN | 40S ribosomal protein S13
SO | 40S ribosomal protein S14
SP | 40S ribosomal protein S15
SQ | 40S ribosomal protein S16
SR | 40S ribosomal protein S17
SS | 40S ribosomal protein S18
ST | 40S ribosomal protein S19
SU | 40S ribosomal protein S20
SV | 40S ribosomal protein S21
SW | 40S ribosomal protein S15a
SX | 40S ribosomal protein S23 (uS12)
SY | 40S ribosomal protein S24
SZ | 40S ribosomal protein S25
Sa | 40S ribosomal protein S26
Sb | 40S ribosomal protein S27
Sc | 40S ribosomal protein S28
Sd | 40S ribosomal protein S29
Se | FAU ubiquitin-like and ribosomal protein S30
Sf | Ubiquitin-40S ribosomal protein S27a
Sg | Receptor of activated protein C kinase 1
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for PreH2_PE-tRNA_8GLP.cif #8
---
Chain | Description
Pt | P-site tRNA
Chain information for PreH2_A-tRNA_8GLP.cif #9
---
Chain | Description
Pt | P-site tRNA
Chain information for PreH1_SSU_8GLP.cif #10
---
Chain | Description
S2 | 18S rRNA
SA | 40S ribosomal protein SA
SB | 40S ribosomal protein S3a
SC | 40S ribosomal protein S2
SD | 40S ribosomal protein S3
SE | 40S ribosomal protein S4, X isoform
SF | 40S ribosomal protein S5
SG | 40S ribosomal protein S6
SH | 40S ribosomal protein S7
SI | 40S ribosomal protein S8
SJ | 40S ribosomal protein S9
SK | 40S ribosomal protein S10
SL | 40S ribosomal protein S11
SM | 40S ribosomal protein S12
SN | 40S ribosomal protein S13
SO | 40S ribosomal protein S14
SP | 40S ribosomal protein S15
SQ | 40S ribosomal protein S16
SR | 40S ribosomal protein S17
SS | 40S ribosomal protein S18
ST | 40S ribosomal protein S19
SU | 40S ribosomal protein S20
SV | 40S ribosomal protein S21
SW | 40S ribosomal protein S15a
SX | 40S ribosomal protein S23 (uS12)
SY | 40S ribosomal protein S24
SZ | 40S ribosomal protein S25
Sa | 40S ribosomal protein S26
Sb | 40S ribosomal protein S27
Sc | 40S ribosomal protein S28
Sd | 40S ribosomal protein S29
Se | FAU ubiquitin-like and ribosomal protein S30
Sf | Ubiquitin-40S ribosomal protein S27a
Sg | Receptor of activated protein C kinase 1
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for PreH1_PE-tRNA_8GLP.cif #11
---
Chain | Description
Pt | P-site tRNA
Chain information for PreH1_A-tRNA_8GLP.cif #12
---
Chain | Description
Pt | P-site tRNA
Chain information for Nascent_chain.cif #13
---
Chain | Description
By | Nascent protein chain
Chain information for MDsnapshot_1403_Ala35Glu_Ala36_Glu_Ala37Glu.cif #14
---
Chain | Description
L | No description available
L | No description available
P | No description available
y | No description available
Chain information for LSU_8GLP.cif #15
---
Chain | Description
L5 | 28S rRNA
L7 | 5S rRNA
L8 | 5.8S rRNA
LA | 60S ribosomal protein L8 (uL2)
LB | 60S ribosomal protein L3
LC | 60S ribosomal protein L4
LD | 60S ribosomal protein L5
LE | 60S ribosomal protein L6
LF | 60S ribosomal protein L7
LG | 60S ribosomal protein L7a
LH | 60S ribosomal protein L9
LI | 60S ribosomal protein L10
LJ | 60S ribosomal protein L11
LL | 60S ribosomal protein L13
LM | 60S ribosomal protein L14
LN | 60S ribosomal protein L15
LO | 60S ribosomal protein L13a
LP | 60S ribosomal protein L17
LQ | 60S ribosomal protein L18
LR | 60S ribosomal protein L19
LS | 60S ribosomal protein L18a
LT | 60S ribosomal protein L21
LU | 60S ribosomal protein L22
LV | 60S ribosomal protein L23
LW | 60S ribosomal protein L24
LX | 60S ribosomal protein L23a
LY | 60S ribosomal protein L26
LZ | 60S ribosomal protein L27
La | 60S ribosomal protein L27a
Lb | 60S ribosomal protein L29
Lc | 60S ribosomal protein L30
Ld | 60S ribosomal protein L31
Le | 60S ribosomal protein L32
Lf | 60S ribosomal protein L35a
Lg | 60S ribosomal protein L34
Lh | 60S ribosomal protein L35
Li | 60S ribosomal protein L36
Lj | 60S ribosomal protein L37
Lk | 60S ribosomal protein L38
Ll | 60S ribosomal protein L39
Lm | 60S ribosomal protein L40 (eL40)
Ln | 60S ribosomal protein L41
Lo | 60S ribosomal protein L36a
Lp | 60S ribosomal protein L37a
Lr | 60S ribosomal protein L28
124 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for LSU_7LS2.cif #16
---
Chain | Description
A1 | 60S ribosomal protein L7
A2 | 28S rRNA
B1 | 60S ribosomal protein L7a
B2 | 5S rRNA
C1 | 60S ribosomal protein L9
C2 | 5.8S rRNA
D1 | 60S ribosomal protein L10-like
D2 | 60S ribosomal protein L8
E1 | 60S ribosomal protein L11
E2 | 60S ribosomal protein L3
F1 | 60S ribosomal protein L13
F2 | 60S ribosomal protein L4
G1 | 60S ribosomal protein L14
G2 | 60S ribosomal protein L5
H1 | 60S ribosomal protein L15
H2 | 60S ribosomal protein L6
I2 | 60S ribosomal protein L13a
J2 | 60S ribosomal protein L17
K2 | 60S ribosomal protein L18
L2 | 60S ribosomal protein L19
M2 | 60S ribosomal protein L18a
N2 | 60S ribosomal protein L21
O2 | 60S ribosomal protein L22
P2 | 60S ribosomal protein L23
R2 | 60S ribosomal protein L23a
S2 | 60S ribosomal protein L26
T2 | 60S ribosomal protein L27
U2 | 60S ribosomal protein L27a
V2 | 60S ribosomal protein L29
W2 | 60S ribosomal protein L30
X2 | 60S ribosomal protein L31
Y2 | 60S ribosomal protein L32
Z2 | 60S ribosomal protein L35a
a2 | 60S ribosomal protein L34
b2 | 60S ribosomal protein L35
c2 | 60S ribosomal protein L36
d2 | 60S ribosomal protein L37
e2 | 60S ribosomal protein L38
f2 | 60S ribosomal protein L39
g2 | Ubiquitin-60S ribosomal protein L40
h2 | 60S ribosomal protein L41
i2 | 60S ribosomal protein L36a
j2 | 60S ribosomal protein L37a
k2 | 60S ribosomal protein L28
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> paulcolor
> style stick
Changed 606762 atom styles
> lighting soft
> help H
No help found for 'H'
> help H
No help found for 'H'
> hide H
> show cartoons
> hide atoms
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> alias paulcolor
Aliased "paulcolor" to: color $*/m #e31a1c; color $*/s,t #a6cee3; color $*/L*
& nucleic #1f78b4; color $*/L* & protein #a6cee3; color $*/S* & nucleic
#ff7f00; color $*/S* & protein #fdbf6f; color $*/Pt* #33a02c; color $*/mR
#b2df8a; color $*:ANM $*/X yellow; color $*/By,NC #fb9a99
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!16 models
> show #!16 models
> hide #18 models
> show #18 models
> hide #17 models
> hide #18 models
> show #!15 models
> hide #!15 models
> show #!6 models
> show #!5 models
> hide #!5 models
> hide #!16 models
> show #!16 models
> color #16 & nucleic #1f78b4
> color #16 & protein #a6cee3
> color #6 & nucleic #ff7f00
> color #6 & protein #fdbf6f
> color #6A #b2df8a
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> paulcolor
> color #16 & nucleic #1f78b4
> color #16 & protein #a6cee3
> color #6 & nucleic #ff7f00
> color #6 & protein #fdbf6f
> color #6A #b2df8a
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #16 & nucleic #1f78b4
> color #16 & protein #a6cee3
> color #6 & nucleic #ff7f00
> color #6 & protein #fdbf6f
> color #6/A #b2df8a
> hide molecule
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #!16 models
> hide #!6 models
> show #!1 models
> show #!2 models
> show #!15 models
> show #13 models
> alias Post hide #1-18 model; show 1,2,13,15 model
> hide #!2 models
> hide #!1 models
> show #4 models
> show #!6 models
> show #!8 models
> show #!10 models
> hide #13 models
> show #18 models
> Post
> show 1,2,13,15 model
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> alias Post hide #1-18 model; show #1,2,13,15 model
> Post
> save
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_reference_session.cxs
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J110_004_volume_map.mrc
Opened cryosparc_P9_J110_004_volume_map.mrc as #19, grid size 512,512,512,
pixel 0.834, shown at level 0.0803, step 1, values float32
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J110_004_volume_map_sharp.mrc
Opened cryosparc_P9_J110_004_volume_map_sharp.mrc as #20, grid size
512,512,512, pixel 0.834, shown at level 0.128, step 1, values float32
> hide #!20 models
> rename #19 Post_loc-ref_P9_J110_004_volume_map.mrc
> rename #20 Post_loc-ref_P9_J110_004_volume_map_sharp.mrc
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J113_map_locres.mrc
Opened cryosparc_P9_J113_map_locres.mrc as #21, grid size 512,512,512, pixel
0.834, shown at level 2.06, step 1, values float32
> hide #!21 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rename #21 Post_loc-ref_P9_J113_map_locres.mrc
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J99_002_volume_map.mrc
Opened cryosparc_P9_J99_002_volume_map.mrc as #22, grid size 256,256,256,
pixel 1.67, shown at level 0.244, step 1, values float32
> fitmap #22 inMap #19
Fit map cryosparc_P9_J99_002_volume_map.mrc in map Post_loc-
ref_P9_J110_004_volume_map.mrc using 167612 points
correlation = 0.856, correlation about mean = 0.468, overlap = 5917
steps = 60, shift = 2.17, angle = 0.68 degrees
Position of cryosparc_P9_J99_002_volume_map.mrc (#22) relative to Post_loc-
ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99993193 -0.00410130 0.01092291 0.08893679
0.00412466 0.99998925 -0.00211684 -1.88670035
-0.01091411 0.00216175 0.99993810 0.98071294
Axis 0.18034892 0.92046114 0.34673557
Axis point 133.88729797 0.00000000 -30.10218853
Rotation angle (degrees) 0.67965850
Shift along axis -1.38054665
> hide #!19 models
> volume #22 level 0.1379
> close #22
> open
> "/Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J99_002_volume_map
> (1).mrc"
Opened cryosparc_P9_J99_002_volume_map (1).mrc as #22, grid size 256,256,256,
pixel 1.67, shown at level 0.62, step 1, values float32
> fitmap #22 inMap #19
Fit map cryosparc_P9_J99_002_volume_map (1).mrc in map Post_loc-
ref_P9_J110_004_volume_map.mrc using 167714 points
correlation = 0.9011, correlation about mean = 0.581, overlap = 1.558e+04
steps = 112, shift = 2.26, angle = 0.638 degrees
Position of cryosparc_P9_J99_002_volume_map (1).mrc (#22) relative to
Post_loc-ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99993911 -0.00387364 0.01033267 0.22157189
0.00388955 0.99999128 -0.00151964 -1.97559423
-0.01032669 0.00155973 0.99994546 0.99364306
Axis 0.13818990 0.92711052 0.34838145
Axis point 145.51180047 0.00000000 -40.04310273
Rotation angle (degrees) 0.63839120
Shift along axis -1.45480839
> rename #22 PreH1_P9_J99_002_volume_map.mrc
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!22 models
> Post
> show #3 models
> show #4 models
> hide #3 models
> hide #4 models
> fitmap #1,2,15 inMap #19
Fit molecules TI-Post_SSU_8GLP.cif (#1), TI-Post_P-tRNA_8GLP.cif (#2),
LSU_8GLP.cif (#15) to map Post_loc-ref_P9_J110_004_volume_map.mrc (#19) using
220518 atoms
average map value = 0.1059, steps = 80
shifted from previous position = 1.27
rotated from previous position = 0.745 degrees
atoms outside contour = 89418, contour level = 0.080308
Position of TI-Post_SSU_8GLP.cif (#1) relative to Post_loc-
ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99991608 -0.00731537 0.01069177 0.63243717
0.00730267 0.99997258 0.00122708 -2.07212631
-0.01070045 -0.00114890 0.99994209 2.69991550
Axis -0.09131926 0.82219434 0.56183384
Axis point 265.45523551 0.00000000 -54.97964275
Rotation angle (degrees) 0.74539452
Shift along axis -0.24454032
Position of TI-Post_P-tRNA_8GLP.cif (#2) relative to Post_loc-
ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99991608 -0.00731537 0.01069177 0.63243717
0.00730267 0.99997258 0.00122708 -2.07212631
-0.01070045 -0.00114890 0.99994209 2.69991550
Axis -0.09131926 0.82219434 0.56183384
Axis point 265.45523551 0.00000000 -54.97964275
Rotation angle (degrees) 0.74539452
Shift along axis -0.24454032
Position of LSU_8GLP.cif (#15) relative to Post_loc-
ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99991608 -0.00731537 0.01069177 0.63243717
0.00730267 0.99997258 0.00122708 -2.07212631
-0.01070045 -0.00114890 0.99994209 2.69991550
Axis -0.09131926 0.82219434 0.56183384
Axis point 265.45523551 0.00000000 -54.97964275
Rotation angle (degrees) 0.74539452
Shift along axis -0.24454032
> show #!22 models
> hide #!22 models
> show #!22 models
> show #!10 models
> hide #!10 models
> hide #13 models
> hide #!15 models
> hide #!19 models
> hide #!2 models
> hide #!1 models
> show #!10 models
> show #!11 models
> show #!12 models
> show #!15 models
> fitmap #10,11,12 inMap #22
Fit molecules PreH1_SSU_8GLP.cif (#10), PreH1_PE-tRNA_8GLP.cif (#11), PreH1_A-
tRNA_8GLP.cif (#12) to map PreH1_P9_J99_002_volume_map.mrc (#22) using 78591
atoms
average map value = 0.5012, steps = 64
shifted from previous position = 1.97
rotated from previous position = 0.926 degrees
atoms outside contour = 54992, contour level = 0.61986
Position of PreH1_SSU_8GLP.cif (#10) relative to
PreH1_P9_J99_002_volume_map.mrc (#22) coordinates:
Matrix rotation and translation
0.99997059 -0.00761563 0.00090089 1.51549784
0.00761584 0.99997097 -0.00022345 -0.90592439
-0.00089916 0.00023030 0.99999957 0.41648558
Axis 0.02957131 0.11731184 0.99265476
Axis point 125.12564239 197.14846141 0.00000000
Rotation angle (degrees) 0.43958262
Shift along axis 0.35196599
Position of PreH1_PE-tRNA_8GLP.cif (#11) relative to
PreH1_P9_J99_002_volume_map.mrc (#22) coordinates:
Matrix rotation and translation
0.99997059 -0.00761563 0.00090089 1.51549784
0.00761584 0.99997097 -0.00022345 -0.90592439
-0.00089916 0.00023030 0.99999957 0.41648558
Axis 0.02957131 0.11731184 0.99265476
Axis point 125.12564239 197.14846141 0.00000000
Rotation angle (degrees) 0.43958262
Shift along axis 0.35196599
Position of PreH1_A-tRNA_8GLP.cif (#12) relative to
PreH1_P9_J99_002_volume_map.mrc (#22) coordinates:
Matrix rotation and translation
0.99997059 -0.00761563 0.00090089 1.51549784
0.00761584 0.99997097 -0.00022345 -0.90592439
-0.00089916 0.00023030 0.99999957 0.41648558
Axis 0.02957131 0.11731184 0.99265476
Axis point 125.12564239 197.14846141 0.00000000
Rotation angle (degrees) 0.43958262
Shift along axis 0.35196599
> alias Post
Aliased "Post" to: hide #1-18 model; show #1,2,13,15 model
> alias PreH1 hide #1-18 model; show #10,11,12,15 model
> Post
> PreH1
> alias Post
Aliased "Post" to: hide #1-18 model; show #1,2,13,15 model
> alias Post volume hide; hide #1-18 model; show #1,2,13,15 model; volume #19
> unhide
> Post
> volume #19 unhide
Expected a keyword
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume show
> volume hide
> alias Post volume hide; hide #1-18 model; show #1,2,13,15 model; volume #19
> show
> Post
> PreH1
> alias PreH1
Aliased "PreH1" to: hide #1-18 model; show #10,11,12,15 model
> alias PreH1 hide #1-18 model; show #10,11,12,15 model ; volume hide; volume
> #22 show
> PreH1
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J100_002_volume_map.mrc
Opened cryosparc_P9_J100_002_volume_map.mrc as #23, grid size 256,256,256,
pixel 1.67, shown at level 0.656, step 1, values float32
Window position QRect(1848,950 712x373) outside any known screen, using
primary screen
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Window position QRect(1848,128 712x1174) outside any known screen, using
primary screen
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #23 inMap #19
Fit map cryosparc_P9_J100_002_volume_map.mrc in map Post_loc-
ref_P9_J110_004_volume_map.mrc using 167750 points
correlation = 0.8986, correlation about mean = 0.569, overlap = 1.698e+04
steps = 92, shift = 2.35, angle = 0.742 degrees
Position of cryosparc_P9_J100_002_volume_map.mrc (#23) relative to Post_loc-
ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99991729 -0.00472081 0.01196342 0.15337496
0.00473893 0.99998767 -0.00148701 -2.21520023
-0.01195625 0.00154358 0.99992733 1.34288143
Axis 0.11700987 0.92353134 0.36523767
Axis point 159.44285093 0.00000000 -26.75469307
Rotation angle (degrees) 0.74200734
Shift along axis -1.53738957
> show #!7 models
> show #!8 models
> show #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!22 models
> fitmap #7,8,9 inMap #23
Fit molecules PreH2_SSU_8GLP.cif (#7), PreH2_PE-tRNA_8GLP.cif (#8), PreH2_A-
tRNA_8GLP.cif (#9) to map cryosparc_P9_J100_002_volume_map.mrc (#23) using
78591 atoms
average map value = 0.5413, steps = 48
shifted from previous position = 1.73
rotated from previous position = 0.849 degrees
atoms outside contour = 53310, contour level = 0.65553
Position of PreH2_SSU_8GLP.cif (#7) relative to
cryosparc_P9_J100_002_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.99999050 -0.00434553 -0.00032855 0.62570456
0.00434561 0.99999053 0.00023051 -0.24093287
0.00032755 -0.00023194 0.99999992 0.30672488
Axis -0.05298415 -0.07517037 0.99576207
Axis point 50.74102676 147.41780288 0.00000000
Rotation angle (degrees) 0.25004315
Shift along axis 0.29038359
Position of PreH2_PE-tRNA_8GLP.cif (#8) relative to
cryosparc_P9_J100_002_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.99999050 -0.00434553 -0.00032855 0.62570456
0.00434561 0.99999053 0.00023051 -0.24093287
0.00032755 -0.00023194 0.99999992 0.30672488
Axis -0.05298415 -0.07517037 0.99576207
Axis point 50.74102676 147.41780288 0.00000000
Rotation angle (degrees) 0.25004315
Shift along axis 0.29038359
Position of PreH2_A-tRNA_8GLP.cif (#9) relative to
cryosparc_P9_J100_002_volume_map.mrc (#23) coordinates:
Matrix rotation and translation
0.99999050 -0.00434553 -0.00032855 0.62570456
0.00434561 0.99999053 0.00023051 -0.24093287
0.00032755 -0.00023194 0.99999992 0.30672488
Axis -0.05298415 -0.07517037 0.99576207
Axis point 50.74102676 147.41780288 0.00000000
Rotation angle (degrees) 0.25004315
Shift along axis 0.29038359
> alias PreH1
Aliased "PreH1" to: hide #1-18 model; show #10,11,12,15 model ; volume hide;
volume #22 show
> alias PreH2 hide #1-18 model; show #7,8,9,15 model ; volume hide; volume #23
> show
> PreH2
> Post
> PreH1
> PreH2
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J65_005_volume_map.mrc
Opened cryosparc_P9_J65_005_volume_map.mrc as #24, grid size 256,256,256,
pixel 1.67, shown at level 0.612, step 1, values float32
> fitmap #24 inMap #19
Fit map cryosparc_P9_J65_005_volume_map.mrc in map Post_loc-
ref_P9_J110_004_volume_map.mrc using 167682 points
correlation = 0.9227, correlation about mean = 0.6502, overlap = 1.602e+04
steps = 72, shift = 2.15, angle = 0.646 degrees
Position of cryosparc_P9_J65_005_volume_map.mrc (#24) relative to Post_loc-
ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99993838 -0.00336469 0.01057858 -0.01040071
0.00338581 0.99999231 -0.00197888 -1.75524526
-0.01057184 0.00201458 0.99994209 0.99296319
Axis 0.17703197 0.93760740 0.29925246
Axis point 132.26541933 0.00000000 -20.84572927
Rotation angle (degrees) 0.64624876
Shift along axis -1.35042553
> hide #!23 models
> volume #24 level 0.3603
> show #!5 models
> volume #24 level 0.4915
> show #3 models
> show #4 models
> hide #!15 models
> show #!15 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!16 models
> hide #!16 models
> show #!6 models
> hide #4 models
> show #4 models
> volume #24 level 0.3026
> fitmap #3,4,5,6 inMap #24
Fit molecules TI_uL11_5LZZ.cif (#3), TI_uL10_5LZZ.cif (#4), TI_eEF2_7LS2.cif
(#5), SSU_7LS2.cif (#6) to map cryosparc_P9_J65_005_volume_map.mrc (#24) using
85459 atoms
average map value = 0.5001, steps = 64
shifted from previous position = 1.95
rotated from previous position = 0.582 degrees
atoms outside contour = 14033, contour level = 0.30257
Position of TI_uL11_5LZZ.cif (#3) relative to
cryosparc_P9_J65_005_volume_map.mrc (#24) coordinates:
Matrix rotation and translation
0.99999616 -0.00185907 -0.00205576 0.84648926
0.00186685 0.99999109 0.00378658 -0.71430714
0.00204871 -0.00379041 0.99999072 0.86752649
Axis -0.80706855 -0.43719047 0.39686880
Axis point 0.00000000 231.18771316 192.25595738
Rotation angle (degrees) 0.26895561
Shift along axis -0.02659239
Position of TI_uL10_5LZZ.cif (#4) relative to
cryosparc_P9_J65_005_volume_map.mrc (#24) coordinates:
Matrix rotation and translation
0.99999616 -0.00185907 -0.00205576 0.84648926
0.00186685 0.99999109 0.00378658 -0.71430714
0.00204871 -0.00379041 0.99999072 0.86752649
Axis -0.80706855 -0.43719047 0.39686880
Axis point 0.00000000 231.18771316 192.25595738
Rotation angle (degrees) 0.26895561
Shift along axis -0.02659239
Position of TI_eEF2_7LS2.cif (#5) relative to
cryosparc_P9_J65_005_volume_map.mrc (#24) coordinates:
Matrix rotation and translation
0.99999616 -0.00185907 -0.00205576 0.84648926
0.00186685 0.99999109 0.00378658 -0.71430714
0.00204871 -0.00379041 0.99999072 0.86752649
Axis -0.80706855 -0.43719047 0.39686880
Axis point 0.00000000 231.18771316 192.25595738
Rotation angle (degrees) 0.26895561
Shift along axis -0.02659239
Position of SSU_7LS2.cif (#6) relative to cryosparc_P9_J65_005_volume_map.mrc
(#24) coordinates:
Matrix rotation and translation
0.99999616 -0.00185907 -0.00205576 0.84648926
0.00186685 0.99999109 0.00378658 -0.71430714
0.00204871 -0.00379041 0.99999072 0.86752649
Axis -0.80706855 -0.43719047 0.39686880
Axis point 0.00000000 231.18771316 192.25595738
Rotation angle (degrees) 0.26895561
Shift along axis -0.02659239
> show #18 models
> fitmap #3,4,5,6,18 inMap #24
Fit molecules TI_uL11_5LZZ.cif (#3), TI_uL10_5LZZ.cif (#4), TI_eEF2_7LS2.cif
(#5), SSU_7LS2.cif (#6), GTP_eEF2.cif (#18) to map
cryosparc_P9_J65_005_volume_map.mrc (#24) using 85503 atoms
average map value = 0.5, steps = 40
shifted from previous position = 0.0147
rotated from previous position = 0.00972 degrees
atoms outside contour = 14051, contour level = 0.30257
Position of TI_uL11_5LZZ.cif (#3) relative to
cryosparc_P9_J65_005_volume_map.mrc (#24) coordinates:
Matrix rotation and translation
0.99999612 -0.00196259 -0.00197903 0.86036920
0.00197029 0.99999047 0.00389684 -0.76713098
0.00197136 -0.00390073 0.99999045 0.92194563
Axis -0.81350442 -0.41213637 0.41030983
Axis point 0.00000000 236.44263774 198.01643742
Rotation angle (degrees) 0.27459561
Shift along axis -0.00546821
Position of TI_uL10_5LZZ.cif (#4) relative to
cryosparc_P9_J65_005_volume_map.mrc (#24) coordinates:
Matrix rotation and translation
0.99999612 -0.00196259 -0.00197903 0.86036920
0.00197029 0.99999047 0.00389684 -0.76713098
0.00197136 -0.00390073 0.99999045 0.92194563
Axis -0.81350442 -0.41213637 0.41030983
Axis point 0.00000000 236.44263774 198.01643742
Rotation angle (degrees) 0.27459561
Shift along axis -0.00546821
Position of TI_eEF2_7LS2.cif (#5) relative to
cryosparc_P9_J65_005_volume_map.mrc (#24) coordinates:
Matrix rotation and translation
0.99999612 -0.00196259 -0.00197903 0.86036920
0.00197029 0.99999047 0.00389684 -0.76713098
0.00197136 -0.00390073 0.99999045 0.92194563
Axis -0.81350442 -0.41213637 0.41030983
Axis point 0.00000000 236.44263774 198.01643742
Rotation angle (degrees) 0.27459561
Shift along axis -0.00546821
Position of SSU_7LS2.cif (#6) relative to cryosparc_P9_J65_005_volume_map.mrc
(#24) coordinates:
Matrix rotation and translation
0.99999612 -0.00196259 -0.00197903 0.86036920
0.00197029 0.99999047 0.00389684 -0.76713098
0.00197136 -0.00390073 0.99999045 0.92194563
Axis -0.81350442 -0.41213637 0.41030983
Axis point 0.00000000 236.44263774 198.01643742
Rotation angle (degrees) 0.27459561
Shift along axis -0.00546821
Position of GTP_eEF2.cif (#18) relative to cryosparc_P9_J65_005_volume_map.mrc
(#24) coordinates:
Matrix rotation and translation
0.99993954 0.00328243 -0.01049492 0.04032191
-0.00326031 0.99999243 0.00212395 1.70008200
0.01050182 -0.00208961 0.99994267 -0.94205928
Axis -0.18816824 -0.93766800 -0.29218392
Axis point 126.49623613 0.00000000 -20.66913443
Rotation angle (degrees) 0.64151160
Shift along axis -1.32644521
> hide #!15 models
> show #!16 models
> fitmap #3,4,5,6,18,16 inMap #24
Fit molecules TI_uL11_5LZZ.cif (#3), TI_uL10_5LZZ.cif (#4), TI_eEF2_7LS2.cif
(#5), SSU_7LS2.cif (#6), GTP_eEF2.cif (#18), LSU_7LS2.cif (#16) to map
cryosparc_P9_J65_005_volume_map.mrc (#24) using 221726 atoms
average map value = 0.5916, steps = 52
shifted from previous position = 0.804
rotated from previous position = 0.412 degrees
atoms outside contour = 28314, contour level = 0.30257
Position of TI_uL11_5LZZ.cif (#3) relative to
cryosparc_P9_J65_005_volume_map.mrc (#24) coordinates:
Matrix rotation and translation
0.99996671 -0.00814582 0.00047052 2.44867349
0.00814253 0.99994500 0.00661076 -2.81766521
-0.00052435 -0.00660670 0.99997804 2.15813778
Axis -0.62940178 0.04737482 0.77563460
Axis point 348.05900501 299.12384154 0.00000000
Rotation angle (degrees) 0.60161773
Shift along axis -0.00075950
Position of TI_uL10_5LZZ.cif (#4) relative to
cryosparc_P9_J65_005_volume_map.mrc (#24) coordinates:
Matrix rotation and translation
0.99996671 -0.00814582 0.00047052 2.44867349
0.00814253 0.99994500 0.00661076 -2.81766521
-0.00052435 -0.00660670 0.99997804 2.15813778
Axis -0.62940178 0.04737482 0.77563460
Axis point 348.05900501 299.12384154 0.00000000
Rotation angle (degrees) 0.60161773
Shift along axis -0.00075950
Position of TI_eEF2_7LS2.cif (#5) relative to
cryosparc_P9_J65_005_volume_map.mrc (#24) coordinates:
Matrix rotation and translation
0.99996671 -0.00814582 0.00047052 2.44867349
0.00814253 0.99994500 0.00661076 -2.81766521
-0.00052435 -0.00660670 0.99997804 2.15813778
Axis -0.62940178 0.04737482 0.77563460
Axis point 348.05900501 299.12384154 0.00000000
Rotation angle (degrees) 0.60161773
Shift along axis -0.00075950
Position of SSU_7LS2.cif (#6) relative to cryosparc_P9_J65_005_volume_map.mrc
(#24) coordinates:
Matrix rotation and translation
0.99996671 -0.00814582 0.00047052 2.44867349
0.00814253 0.99994500 0.00661076 -2.81766521
-0.00052435 -0.00660670 0.99997804 2.15813778
Axis -0.62940178 0.04737482 0.77563460
Axis point 348.05900501 299.12384154 0.00000000
Rotation angle (degrees) 0.60161773
Shift along axis -0.00075950
Position of GTP_eEF2.cif (#18) relative to cryosparc_P9_J65_005_volume_map.mrc
(#24) coordinates:
Matrix rotation and translation
0.99996353 -0.00289645 -0.00803436 1.60880176
0.00293496 0.99998424 0.00478526 -0.36064720
0.00802037 -0.00480866 0.99995627 0.28949931
Axis -0.48971355 -0.81949957 0.29765937
Axis point -50.21021108 0.00000000 175.71364051
Rotation angle (degrees) 0.56124655
Shift along axis -0.40612961
Position of LSU_7LS2.cif (#16) relative to cryosparc_P9_J65_005_volume_map.mrc
(#24) coordinates:
Matrix rotation and translation
0.99996321 -0.00279280 -0.00811059 1.59485858
0.00283078 0.99998506 0.00467541 -0.30776497
0.00809741 -0.00469820 0.99995618 0.23517946
Axis -0.47947717 -0.82906904 0.28765634
Axis point -43.81777146 0.00000000 170.71439381
Rotation angle (degrees) 0.56006508
Shift along axis -0.44188901
> alias PreH1
Aliased "PreH1" to: hide #1-18 model; show #10,11,12,15 model ; volume hide;
volume #22 show
> alias Hiber hide #1-18 model; show #3-6,16,18 model ; volume hide; volume
> #24 show
> H1
Expected fewer arguments
> PreH1
> PreH2
> rename #23 PreH2_P9_J100_002_volume_map.mrc
> rename #24 Hibernating_P9_J65_005_volume_map.mrc
> Hibwe
Unknown command: Hibwe
> Hibwe
Unknown command: Hibwe
> Hiber
> volume #24 level 0.4233
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J68_004_volume_map.mrc
Opened cryosparc_P9_J68_004_volume_map.mrc as #25, grid size 256,256,256,
pixel 1.67, shown at level 0.609, step 1, values float32
> hide #!24 models
> fitmap #25 inMap #19
Fit map cryosparc_P9_J68_004_volume_map.mrc in map Post_loc-
ref_P9_J110_004_volume_map.mrc using 167705 points
correlation = 0.9398, correlation about mean = 0.6996, overlap = 1.715e+04
steps = 72, shift = 2.27, angle = 0.71 degrees
Position of cryosparc_P9_J68_004_volume_map.mrc (#25) relative to Post_loc-
ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99992483 -0.00262420 0.01197668 -0.25657065
0.00264605 0.99999486 -0.00180918 -1.62079789
-0.01197187 0.00184073 0.99992664 1.29072458
Axis 0.14722281 0.96598898 0.21258112
Axis point 131.37668314 0.00000000 5.90960865
Rotation angle (degrees) 0.71024928
Shift along axis -1.32906228
> hide #!25 models
> hide #!5 models
> hide #3 models
> hide #4 models
> hide #!6 models
> hide #18 models
> hide #!16 models
> show #!25 models
> show #!15 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!7 models
> hide #!7 models
> show #!10 models
> hide #!10 models
> volume #25 level 0.4279
> hide #!15 models
> show #!10 models
> show #!1 models
> show #!6 models
> hide #!1 models
> hide #!10 models
> Post
> alias Post
Aliased "Post" to: volume hide; hide #1-18 model; show #1,2,13,15 model;
volume #19 show
> show #!25 models
> hide #!19 models
> hide #13 models
> hide #!2 models
> hide #!1 models
> show #!6 models
> alias empty hide #1-18 model; show #6,15 model; volume #25 show
> Post
> color zone #19 near #1,2,13,15 r 4
Expected a keyword
> color zone #19 near #1,2,13,15 distance 4
> color zone #19 near #1,2,13,15 & protein & nucleic distance 4
color zone: No atoms specified.
> color zone #19 near ((#1,2,13,15 & (protein & nucleic) d 4
Invalid "near" argument: invalid atoms specifier
> color zone #19 near #1,2,13,15 & (protein & nucleic) distance 4
color zone: No atoms specified.
> color zone #19 near #1,2,13,15 & @@c distance 4
color zone: No atoms specified.
> color zone #19 near #1,2,13,15 & @c distance 4
> color zone #19 near #1,2,13,15 & nucleic distance 4
> color zone #19 near #1,2,13,15 & nucleic, protein d 4
Expected a keyword
> color zone #19 near #1,2,13,15 & nucleic || protein d 4
Expected a keyword
> color zone #19 near #1,2,13,15 & @c* distance 4
> color zone #19 near #1,2,13,15 & @c* distance 5
> PreH1
> color zone #12 near #10,11,12,15 & @c* distance 5
color zone: No surfaces specified.
> color zone #22 near #10,11,12,15 & @c* distance 5
> PreH2
> color zone #23 near #7-9,15 & @c* distance 5
> Hiber
> color zone #24 near #3-6,16,18 & @c* distance 5
> volume #24 level 0.46
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> cofron
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!16 models
> hide #!24 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> show #!15 models
> Hiber
> color zone #24 near #3-6,16,18,15/LW & @c* distance 5
> color zone #24 near #3-6,16,18 #15/LW & @c* distance 5
> color zone #24 near #3-6,16,18 #15/LW & @c* distance 10
> empty
> alias empty
Aliased "empty" to: hide #1-18 model; show #6,15 model; volume #25 show
> alias Post
Aliased "Post" to: volume hide; hide #1-18 model; show #1,2,13,15 model;
volume #19 show
> alias empty hide #1-18 model; show #6,15 model; volume hide; volume #25 show
> empty
> color zone #25 near #6,15 & @c* distance 10
> volume #25 level 0.5308
> hide #!6,15 atoms
> hide #!6,15 cartoons
> PreH1
> PreH2
> select ~sel & ##selected
Nothing selected
> PreH1
> PreH2
> Post
> hide #13#!1-2,15 atoms
> hide #13#!1-2,15 cartoons
> alias paulsave
Aliased "paulsave" to: save
/Users/psauer/Documents/Processing/20240530_IVTT15/$1.png
transparentbackground true format png supersample 3
> alias paulsave save
> /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/$1.png transparentbackground true format png
> supersample 3
> Post
> hide cartoons
> paulsave test1
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/test1.png transparentBackground true format png
> supersample 3
> set bgColor white
> set bgColor #ffffff00
> paulsave test1
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/test1.png transparentBackground true format png
> supersample 3
> volume #19 level 0.06562
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J106_003_volume_map.mrc
Opened cryosparc_P9_J106_003_volume_map.mrc as #26, grid size 512,512,512,
pixel 0.834, shown at level 0.0839, step 1, values float32
> close #26
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J106_003_volume_map_sharp.mrc
Opened cryosparc_P9_J106_003_volume_map_sharp.mrc as #26, grid size
512,512,512, pixel 0.834, shown at level 0.114, step 1, values float32
> fitmap #26 inMap #19
Fit map cryosparc_P9_J106_003_volume_map_sharp.mrc in map Post_loc-
ref_P9_J110_004_volume_map.mrc using 1339758 points
correlation = 0.9677, correlation about mean = 0.8052, overlap = 3.728e+04
steps = 76, shift = 2.16, angle = 0.398 degrees
Position of cryosparc_P9_J106_003_volume_map_sharp.mrc (#26) relative to
Post_loc-ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99997600 -0.00174376 0.00670536 0.46541289
0.00173983 0.99999831 0.00059141 -1.78554549
-0.00670638 -0.00057973 0.99997734 0.61893540
Axis -0.08421685 0.96444497 0.25050633
Axis point 152.45243860 0.00000000 -48.68999598
Rotation angle (degrees) 0.39838576
Shift along axis -1.60620874
> hide #!19 models
> volume #26 level 0.09095
> color zone #26 near #1,2,13,15 & @c* distance 5
> ui tool show "Hide Dust"
> surface dust #26 size 5
> surface undust #26
> volume #26 level 0.07271
> surface dust #26 size 5
> close #26
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J106_003_volume_map.mrc
Opened cryosparc_P9_J106_003_volume_map.mrc as #26, grid size 512,512,512,
pixel 0.834, shown at level 0.0839, step 1, values float32
> fitmap #26 inMap #19
Fit map cryosparc_P9_J106_003_volume_map.mrc in map Post_loc-
ref_P9_J110_004_volume_map.mrc using 1341680 points
correlation = 0.9918, correlation about mean = 0.9203, overlap = 2.305e+04
steps = 92, shift = 2.15, angle = 0.402 degrees
Position of cryosparc_P9_J106_003_volume_map.mrc (#26) relative to Post_loc-
ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99997563 -0.00170905 0.00676889 0.44305550
0.00170482 0.99999835 0.00062968 -1.77812984
-0.00676995 -0.00061813 0.99997689 0.65373391
Axis -0.08901339 0.96580004 0.24353006
Axis point 154.18134963 0.00000000 -43.89122331
Rotation angle (degrees) 0.40159683
Shift along axis -1.59755189
> color zone #26 near #1,2,13,15 & @c* distance 5
> volume #26 level 0.07179
> rename #25 empty_P9_J68_004_volume_map.mrc
> rename #26 Post_global_P9_J106_003_volume_map.mrc
> show #3 models
> hide #3 models
> show #13#!1-2,15 cartoons
> show #3 models
> hide #3 models
> show #4 models
> show #!5 models
> show #3 models
> select add #3
1160 atoms, 1174 bonds, 153 residues, 1 model selected
> select add #4
2667 atoms, 2704 bonds, 349 residues, 2 models selected
> select add #5
9316 atoms, 9482 bonds, 1 pseudobond, 1200 residues, 4 models selected
> show sel cartoons
> select subtract #5
2667 atoms, 2704 bonds, 349 residues, 2 models selected
> select subtract #4
1160 atoms, 1174 bonds, 153 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #!5 models
> color zone #26 near #1,2,3,4,13,15 & @c* distance 5
> hide #4 models
> hide #3 models
> hide #13#!1-2,15 cartoons
> paulsave Post
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/Post.png transparentBackground true format png
> supersample 3
> PreH1
> volume #22 level 0.5001
> color zone #22 near #10,11,3,4,12,15 & @c* distance 5
> volume #22 level 0.4602
> Post
> hide #!19 models
> show #!26 models
> view name v1
> paulsave Post
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/Post.png transparentBackground true format png
> supersample 3
> PreH1
> paulsave PreH1
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/PreH1.png transparentBackground true format png
> supersample 3
> PreH2
> volume #23 level 0.5
> view v1
> paulsave PreH2
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/PreH2.png transparentBackground true format png
> supersample 3
> Hiber
> hide #3-4,18#!5-6,16 cartoons
> volume #24 level 0.3761
> volume #24 level 0.3971
> hide #18 models
> paulsave Hiber
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/Hiber.png transparentBackground true format png
> supersample 3
> empty
> volume #25 level 0.4867
> color zone #25 near #6,15,3,4 & @c* distance 10
> paulsave empty
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/empty.png transparentBackground true format png
> supersample 3
> Post
> open /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_final_map_model/20240530_RNC-PS2_50A-PTC_model_temp4.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
PS2_final_map_model/20240530_RNC-PS2_50A-PTC_model_temp4.cif
---
warnings | Unknown polymer entity '1' on line 254
Unknown polymer entity '2' on line 41808
Unknown polymer entity '3' on line 42360
Unknown polymer entity '4' on line 43018
Unknown polymer entity '5' on line 43976
24 messages similar to the above omitted
Atom H1 is not in the residue template for OMG /L5:1316
Atom H61 is not in the residue template for 1MA /L5:1322
Atom H41 is not in the residue template for OMC /L5:1340
Atom H1 is not in the residue template for OMG /L5:1522
Atom H1 is not in the residue template for PSU /L5:1536
Atom H1 is not in the residue template for PSU /L5:1582
Atom H1 is not in the residue template for OMG /L5:1625
Atom H1 is not in the residue template for PSU /L5:1677
1 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 20240530_RNC-PS2_50A-PTC_model_temp4.cif #27
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LF | No description available
LI | No description available
LL | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LS | No description available
LT | No description available
LV | No description available
La | No description available
Lb | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lj | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
NC | No description available
Pt | No description available
mR | No description available
> paulcolor
> help H
> hide H
> style #13#!1-2,15,27 stick
Changed 279331 atom styles
> save /Users/psauer/Documents/Processing/20240530_IVTT15/IVTT15_session.cxs
> includeMaps true
> hide #!27 models
> hide #13 models
> hide #!15 models
> hide #!19 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #1 cartoons
> hide #!1 models
> show #!10 models
> show #!11 models
> show #!12 models
> select add #10
75301 atoms, 79736 bonds, 1975 pseudobonds, 7021 residues, 4 models selected
> select add #11
76946 atoms, 81573 bonds, 2049 pseudobonds, 7098 residues, 6 models selected
> select add #12
78591 atoms, 83410 bonds, 2123 pseudobonds, 7175 residues, 8 models selected
> show sel cartoons
> select clear
> ui tool show "Side View"
> hide #!11 models
> hide #!12 models
> paulsave SSU
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/SSU.png transparentBackground true format png
> supersample 3
> hide #!10 models
> Post
> paulunclip
> view
> set bgColor black
> set bgColor transparent
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J62_006_volume_map.mrc
Opened cryosparc_P9_J62_006_volume_map.mrc as #28, grid size 256,256,256,
pixel 1.67, shown at level 0.0653, step 1, values float32
> hide #!1 models
> hide #!2 models
> hide #13 models
> hide #!15 models
> hide #!19 models
> volume #28 level 0.04729
> open
> /Users/psauer/Documents/Processing/20240530_IVTT15/cryosparc_P9_J67_005_volume_map.mrc
Opened cryosparc_P9_J67_005_volume_map.mrc as #29, grid size 256,256,256,
pixel 1.67, shown at level 0.1, step 1, values float32
> hide #!28 models
> hide #!29 models
> show #!27 models
> show #!19 models
> open /Users/psauer/Documents/Processing/20240327_RNC-
> PS2_IDB-1403/20240327_RNC-PS2_IDB-1403_final_map_model/20240327_RNC-
> PS2_IDB-1403_50A-PTC_model.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20240327_RNC-PS2_IDB-1403/20240327_RNC-
PS2_IDB-1403_final_map_model/20240327_RNC-PS2_IDB-1403_50A-PTC_model.cif
---
warnings | Unknown polymer entity '1' on line 257
Unknown polymer entity '2' on line 41799
Unknown polymer entity '3' on line 42351
Unknown polymer entity '4' on line 43009
Unknown polymer entity '5' on line 43967
24 messages similar to the above omitted
Atom H1 is not in the residue template for OMG /L5:1316
Atom H61 is not in the residue template for 1MA /L5:1322
Atom H41 is not in the residue template for OMC /L5:1340
Atom H1 is not in the residue template for OMG /L5:1522
Atom H1 is not in the residue template for PSU /L5:1536
Atom H1 is not in the residue template for PSU /L5:1582
Atom H1 is not in the residue template for OMG /L5:1625
Atom H1 is not in the residue template for PSU /L5:1677
1 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
Unable to fetch template for 'IDB-1403': will connect using distance criteria
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 20240327_RNC-PS2_IDB-1403_50A-PTC_model.cif #30
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LF | No description available
LI | No description available
LL | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LS | No description available
LT | No description available
LV | No description available
La | No description available
Lb | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lj | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
NC | No description available
Pt | No description available
mR | No description available
> paulcolor
> hide #!19 models
> style #!27,30 stick
Changed 117299 atom styles
> hide H
> mmaker #30 to #27
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20240530_RNC-PS2_50A-PTC_model_temp4.cif, chain L5 (#27) with
20240327_RNC-PS2_IDB-1403_50A-PTC_model.cif, chain L5 (#30), sequence
alignment score = 6135.2
RMSD between 1034 pruned atom pairs is 0.306 angstroms; (across all 1034
pairs: 0.306)
> open /Users/psauer/Documents/Processing/20240327_RNC-
> PS2_IDB-1403/20240327_RNC-PS2_IDB-1403_final_map_model/20240327_RNC-
> PS2_IDB-1403_50A-PTC_map.mrc
Opened 20240327_RNC-PS2_IDB-1403_50A-PTC_map.mrc as #31, grid size
165,175,206, pixel 0.832,0.832,0.832, shown at level 0.179, step 1, values
float32
> fitmap #31 to #19
Expected a keyword
> fitmap #31 inMap #19
Fit map 20240327_RNC-PS2_IDB-1403_50A-PTC_map.mrc in map Post_loc-
ref_P9_J110_004_volume_map.mrc using 59461 points
correlation = 0.9866, correlation about mean = 0.6081, overlap = 2947
steps = 56, shift = 1.46, angle = 1.28 degrees
Position of 20240327_RNC-PS2_IDB-1403_50A-PTC_map.mrc (#31) relative to
Post_loc-ref_P9_J110_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99988388 -0.00746291 0.01328633 0.51247391
0.00767955 0.99983717 -0.01632960 1.34963624
-0.01316230 0.01642974 0.99977838 -0.03162179
Axis 0.73215541 0.59111419 0.33842647
Axis point 0.00000000 26.40991549 40.31237300
Rotation angle (degrees) 1.28191964
Shift along axis 1.16229802
> volume #31 level 0.1418
> color #31 #b2b2b2
> cofroff
> cofron
> paulclip
Changed 724061 atom styles
> surface cap false
> hide #!31 models
> show #!19 models
> hide #!30 models
> hide :HOH
> volume #19 level 0.05583
> paulclip
Changed 724061 atom styles
> paulvis
Changed 724061 atom styles
Nothing selected
> paulcolor
> alias paulvis lighting soft; material transparentcastshadows false; style
> stick; color byhetero; graphics silhouettes true; graphics silhouettes width
> 1; graphics silhouettes depthJump 0.1; transparency 60; hide H
> paulvis
Changed 724061 atom styles
> show #!30 models
> hide #!27 models
> ui tool show "Side View"
> paulclip
Changed 724061 atom styles
> hide #!19 models
> show #!31 models
> volume #31 level 0.03848
> volume #31 level 0.04474
> cofroff
> paulvis
Changed 724061 atom styles
> surface transform
Missing or invalid "surfaces" argument: empty atom specifier
> surfacec t
Unknown command: surfacec t
> surface caps
Expected an atoms specifier or a keyword
> surfacecaps
Unknown command: surfacecaps
> surface close t
Expected an objects specifier or a keyword
> surface cap true
> set bgColor white
> set bgColor #ffffff00
> paullabel
> ui tool show "Hide Dust"
> surface dust #31 size 4.99
> volume #31 level 0.04682
> volume #31 level 0.05
> volume #31 level 0.04
> view name v2
> view v2
> view name v2
> paulsave IDB1403comparison_view-v1
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/IDB1403comparison_view-v1.png transparentBackground
> true format png supersample 3
> hide #!30 models
> hide #!31 models
> show #!27 models
> show #!19 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface dust #19 size 5
> paulsave PTC_view-v1
> save /Users/psauer/Documents/Processing/20240530_IVTT15/20240530_RNC-
> PS2_report/report_files/PTC_view-v1.png transparentBackground true format
> png supersample 3
> paulclip
Changed 724061 atom styles
> surface cap false
> set bgColor black
> set bgColor transparent
> ~label
> show #!30 models
> cofron
> hide #!30 models
> volume #19 level 0.05485
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> surface cap true
> paulvis
Changed 724061 atom styles
> set bgColor white
> set bgColor #ffffff00
> cofroff
> paullabel
> lighting simple
> paulvis
Changed 724061 atom styles
> view name v2
> hide #!19 models
> show #!19 models
> show #!30 models
> hide #!30 models
> paulclip
Changed 724061 atom styles
> surface cap false
> cofron
> set bgColor black
> set bgColor transparent
> show #!30 models
> hide #30 atoms
> show #30:IDB* atoms
> hide H
> lighting simple
> lighting flat
> graphics silhouettes false
> surface cap false
> ~label
> hide #!30 models
> show #!30 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias cofron cofr centerofview showpivot 4,0.2
> alias cofroff cofr centerofview showpivot false
> alias paulsave save
> /Users/psauer/Documents/Processing/20240530_IVTT15/$1.png
> transparentbackground true format png supersample 3
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias paulclip cofr centerofview; style stick; surface cap false; clip near
> -2 far 6 position cofr; material transparentCastShadows false; lighting
> flat; graphics silhouettes false; transparency 70; volume step 1
> alias paulunclip view all; transparency 0; lighting soft
> alias paullight material transparentCastShadows true; lighting soft;
> transparency 70; style stick; show cartoon
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; #disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.1; transparency 70;
> cofr centerofview; clip near -2 far 6 position cofr; #color ##~num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_30 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 30; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette ^RdYlBu-5;
> lighting soft; view all; transparency 0
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias paulvis lighting soft; material transparentcastshadows false; style
> stick; color byhetero; graphics silhouettes true; graphics silhouettes width
> 1; graphics silhouettes depthJump 0.1; transparency 60; hide H; ###color /*
> #2b8cbe; select :ANM; select up; select up; color sel pink; ~select; color
> :IDB* yellow;
> alias paullabel label /* residues color black height 0.8 bgcolor
> rgba(100%,100%,100%,0.6); ~label :HOH
> alias IDB view :IDB*; paulclip; volume step 1
> alias paulcolor color $*/m #e31a1c; color $*/s,t #a6cee3; color $*/L* &
> nucleic #1f78b4; color $*/L* & protein #a6cee3; color $*/S* & nucleic
> #ff7f00; color $*/S* & protein #fdbf6f; color $*/Pt* #33a02c; color $*/mR
> #b2df8a; color $*:ANM $*/X yellow; color $*/By,NC #fb9a99
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_30
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"
> buttonpanel Shortcuts add IDB command IDB
> buttonpanel Shortcuts add paulvis command paulvis
> buttonpanel Shortcuts add paullabel command paullabel
> buttonpanel Shortcuts add paulclip command paulclip
> buttonpanel Shortcuts add paullight command paullight
> buttonpanel Shortcuts add paulsave command paulsave
> buttonpanel Shortcuts add unclip command paulunclip
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,6
Model Number: MNXA3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 64 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 37 days, 40 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
32GK650F:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 144.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
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: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 16 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash changing Mac display configuration |
comment:2 by , 16 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Did this ChimeraX crash happen after you unplugged an external display or plugged in an internal display?
The crash trace shows it was trying to reconfigure display in _NSCGSDisplayConfigurationDidReconfigureNotificationHandler. This is a Qt window toolkit bug. If we knew how to reproduce it we might find a way to work around it. I would suggest being careful to save your ChimeraX work before connecting or disconnecting external displays because of this Qt problem.
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Reported by Paul Sauer