![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17283 closed defect (duplicate)
Crash in Modeller tool _update_sequence_menus in Qt call meth_QFormLayout_removeRow()
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.3.2-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: Segmentation fault
Current thread 0x00000002084d8840 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/tool.py", line 349 in _update_sequence_menus
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/widgets.py", line 45 in _items_change
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/manager.py", line 129 in destroy_alignment
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 445 in detach_viewer
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/tool.py", line 511 in delete
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 780 in close_request
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2430 in
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, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.coulombic._esp, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 67)
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"uptime" : 600000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 4012,
"osVersion" : {
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"build" : "24D81",
"releaseType" : "User"
},
"captureTime" : "2025-04-03 20:34:31.5131 -0500",
"codeSigningMonitor" : 1,
"incident" : "55F1EDAA-0D11-45A4-9A1F-480112FB084E",
"pid" : 54547,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-24 09:46:58.3537 -0500",
"procStartAbsTime" : 6467629134207,
"procExitAbsTime" : 14509237358204,
"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"},
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"parentProc" : "launchd",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3C03AB57-DF91-6538-731F-87145E7E925C",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 178,
"sleepWakeUUID" : "9B7638BC-364F-43A9-9DDB-BE7B07419F44",
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"vmRegionInfo" : "0x8ab is not in any region. Bytes before following region: 4373018453\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104a70000-104a74000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000000008ab","rawCodes":[1,2219],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000008ab"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":54547},
"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\nAPFS - (arg = 0x3aad001600200040) cluster_pagein() failed\nVM - (arg = 0x1900000016) Filesystem pagein returned an error in vnode_pagein\n",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
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/kompa012/Desktop/NiP N protein article/Figures/dimer close
> aup.cxs" format session
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.044, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
opened ChimeraX session
> select #1 /z :44-57
283 atoms, 311 bonds, 14 residues, 1 model selected
> show sel atoms
> select #1 /z :54-57
83 atoms, 91 bonds, 4 residues, 1 model selected
> hide sel atoms
> select #1 /z :44-55
240 atoms, 263 bonds, 12 residues, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select #1 /l :178,192,193,196,199,200,258,265,344,349,352
100 atoms, 92 bonds, 11 residues, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> ui mousemode right select
> select clear
> ui mousemode right distance
> distance #1/Z:55@OP2 #1/L:258@OH
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z
U 55 OP2 and /L TYR 258 OH: 2.512Å
> distance #1/L:192@NH1 #1/Z:54@OP2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L
ARG 192 NH1 and /Z U 54 OP2: 2.941Å
> distance #1/L:193@NH2 #1/Z:54@OP2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L
ARG 193 NH2 and /Z U 54 OP2: 3.220Å
> distance #1/L:178@NZ #1/Z:53@OP2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L
LYS 178 NZ and /Z U 53 OP2: 2.995Å
> distance #1/L:344@OG #1/Z:53@N1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L
SER 344 OG and /Z U 53 N1: 4.766Å
> ~distance #1/L:344@OG #1/Z:53@N1
> distance #1/L:344@OG #1/Z:52@O2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L
SER 344 OG and /Z U 52 O2: 2.891Å
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> select add #1.9
6188 atoms, 796 residues, 2 models selected
> select subtract #1.9
3094 atoms, 398 residues, 3 models selected
> transparency (#!1 & sel) 30
> show sel surfaces
> ui mousemode right select
> select clear
> select add #1.6
3094 atoms, 398 residues, 1 model selected
> select subtract #1.6
1 model selected
> select add #1.7
3094 atoms, 398 residues, 1 model selected
> select subtract #1.7
1 model selected
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> hide sel surfaces
> select add #1.9
6188 atoms, 796 residues, 2 models selected
> select subtract #1.8
3094 atoms, 398 residues, 3 models selected
> show sel surfaces
> select clear
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> transparency (#!1 & sel) 20
> select clear
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> select #1 /l :370-400
219 atoms, 219 bonds, 31 residues, 1 model selected
> select #1 /l :260-369
874 atoms, 895 bonds, 1 pseudobond, 110 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #e0b3c7ff
> select #1 /l :261-369
865 atoms, 886 bonds, 1 pseudobond, 109 residues, 2 models selected
> select #1 /l :32-260
1791 atoms, 1818 bonds, 229 residues, 1 model selected
> color (#!1 & sel) #64e0e4ff
> select clear
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> transparency (#!1 & sel) 20
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/dimer close
> aup.cxs"
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Dimer_RNA
> overall.png" width 3000 height 2729 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Monomer_RNA
> overall.png" width 3000 height 2729 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Monomer_44-49
> zoom.png" width 3000 height 2729 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Monomer_49-53
> zoom.png" width 3000 height 2729 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Monomer_44-49
> zoom.png" width 3000 height 2729 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/dimer close
> 44-49.cxs"
> open 2gic fromDatabase pdb format mmcif
Summary of feedback from opening 2gic fetched from pdb
---
note | Fetching compressed mmCIF 2gic from http://files.rcsb.org/download/2gic.cif
2gic title:
Crystal Structure of a vesicular stomatitis virus nucleocapsid-RNA complex
[more info...]
Chain information for 2gic #13
---
Chain | Description | UniProt
A B C D E | Nucleocapsid protein | NCAP_VSVSJ 1-422
R | 45-MER |
Non-standard residues in 2gic #13
---
IUM — uranyl (VI) ion
2gic mmCIF Assemblies
---
1| author_defined_assembly
> hide #!6 models
> show #!10 models
> hide #!10 models
> show #9 models
> rename #9 "6c54 ebola"
> rename #13 "2gic VSV"
> rename #10 "4uft Measles"
> rename #8 "6m7d sendai"
> hide #9 models
> hide #!13 models
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 2 models selected
> select add #5
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 19 models selected
> select add #6
44999 atoms, 45909 bonds, 28 pseudobonds, 5656 residues, 20 models selected
> show #!5 models
> select subtract #6
44999 atoms, 45909 bonds, 5656 residues, 18 models selected
> select clear
> show #!4 models
> hide #!5 models
> select #1 /l :120-140
166 atoms, 165 bonds, 21 residues, 1 model selected
> select add #4
166 atoms, 165 bonds, 21 residues, 5 models selected
> view sel
> select subtract #4
166 atoms, 165 bonds, 21 residues, 2 models selected
> open 8pds fromDatabase pdb format mmcif
Summary of feedback from opening 8pds fetched from pdb
---
note | Fetching compressed mmCIF 8pds from http://files.rcsb.org/download/8pds.cif
8pds title:
Local refinement of dimeric HMPV N-RNA bound to the C-terminal region of P
[more info...]
Chain information for 8pds #14
---
Chain | Description | UniProt
A C | Nucleoprotein | NCAP_HMPVC 1-394
B D | Phosphoprotein | PHOSP_HMPVC 10-16
E | RNA |
> rename #14 "8pds HMPV"
> open "7EV8 " fromDatabase pdb format mmcif
PDB identifiers are either 4 or 8 characters long, got "7EV8 "
> open 7EV8 fromDatabase pdb format mmcif
Summary of feedback from opening 7EV8 fetched from pdb
---
note | Fetching compressed mmCIF 7ev8 from http://files.rcsb.org/download/7ev8.cif
7ev8 title:
Structure of Human Parainfluenza Virus 3 Unassembled Nucleoprotein in Complex
with its viral chaperone [more info...]
Chain information for 7ev8 #15
---
Chain | Description | UniProt
A | Nucleoprotein | NCAP_PI3H4 29-374
B | Phosphoprotein | A0A346TKJ9_9MONO 1-42
> rename #15 "7ev8 HPIV3"
> open 4XJN fromDatabase pdb format mmcif
Summary of feedback from opening 4XJN fetched from pdb
---
notes | Fetching compressed mmCIF 4xjn from http://files.rcsb.org/download/4xjn.cif
Fetching CCD PB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/PB/PB.cif
4xjn title:
Structure of the parainfluenza virus 5 nucleocapsid-RNA complex: an insight
into paramyxovirus polymerase activity [more info...]
Chain information for 4xjn #16
---
Chain | Description | UniProt
A B C D E F G H I J K L M | Nucleocapsid | W5QKM4_9PARA 1-509
N | RNA (78-MER) |
Non-standard residues in 4xjn #16
---
PB — lead (II) ion
> rename #16 "4xjn HPIV5"
> open 7EWQ fromDatabase pdb format mmcif
Summary of feedback from opening 7EWQ fetched from pdb
---
note | Fetching compressed mmCIF 7ewq from http://files.rcsb.org/download/7ewq.cif
7ewq title:
Structure of Mumps virus nucleocapsid ring [more info...]
Chain information for 7ewq #17
---
Chain | Description | UniProt
A | Nucleoprotein | NCAP_MUMPJ 1-549
B | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') |
7ewq mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
> rename #17 "7ewq MuV"
> open 6JC3 fromDatabase pdb format mmcif
Summary of feedback from opening 6JC3 fetched from pdb
---
note | Fetching compressed mmCIF 6jc3 from http://files.rcsb.org/download/6jc3.cif
6jc3 title:
The Cryo-EM structure of nucleoprotein-RNA complex of Newcastle disease virus
[more info...]
Chain information for 6jc3 #18
---
Chain | Description | UniProt
A | Nucleocapsid | D6R3F6_9MONO 1-398
N | polyU |
> rename #18 "6jc3 NDV"
> open 8C4H fromDatabase pdb format mmcif
Summary of feedback from opening 8C4H fetched from pdb
---
note | Fetching compressed mmCIF 8c4h from http://files.rcsb.org/download/8c4h.cif
8c4h title:
CryoEM structure of the Hendra henipavirus nucleocapsid sauronoid assembly
multimer [more info...]
Chain information for 8c4h #19
---
Chain | Description | UniProt
1 2 | RNA (84-MER) |
A B C D E F G H I J K L M N a b c d e f g h i j k l m n | Nucleocapsid | A0A1L7B858_9MONO 1-532
> rename #19 "8c4h HEV"
> show #!13 models
> show #!10 models
> show #9 models
> show #8 models
> select add #8
3446 atoms, 3513 bonds, 439 residues, 3 models selected
> select add #9
9110 atoms, 9276 bonds, 1159 residues, 4 models selected
> select add #10
12183 atoms, 12412 bonds, 2 pseudobonds, 1542 residues, 6 models selected
> select add #13
29615 atoms, 30295 bonds, 5 pseudobonds, 3688 residues, 8 models selected
> select add #14
35671 atoms, 36466 bonds, 5 pseudobonds, 4446 residues, 9 models selected
> select add #15
38379 atoms, 39164 bonds, 6 pseudobonds, 4851 residues, 11 models selected
> select add #16
80708 atoms, 82414 bonds, 38 pseudobonds, 10078 residues, 14 models selected
> select add #17
83796 atoms, 85575 bonds, 38 pseudobonds, 10458 residues, 15 models selected
> select add #18
86950 atoms, 88789 bonds, 39 pseudobonds, 10855 residues, 17 models selected
> select add #19
174702 atoms, 178359 bonds, 39 pseudobonds, 22055 residues, 18 models selected
> hide sel atoms
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> hide #!4 models
> select add #1
219535 atoms, 224103 bonds, 65 pseudobonds, 27690 residues, 87 models selected
> hide sel atoms
> show sel cartoons
> select add #6
219535 atoms, 224103 bonds, 67 pseudobonds, 27690 residues, 102 models
selected
> select subtract #6
219535 atoms, 224103 bonds, 39 pseudobonds, 27690 residues, 100 models
selected
> select subtract #1
174536 atoms, 178194 bonds, 39 pseudobonds, 22034 residues, 98 models selected
> select subtract #8
171256 atoms, 174846 bonds, 39 pseudobonds, 21616 residues, 82 models selected
> select subtract #9
165592 atoms, 169083 bonds, 39 pseudobonds, 20896 residues, 79 models selected
> select subtract #10
162519 atoms, 165947 bonds, 37 pseudobonds, 20513 residues, 75 models selected
> select add #13
162519 atoms, 165947 bonds, 37 pseudobonds, 20513 residues, 76 models selected
> select subtract #13
145087 atoms, 148064 bonds, 34 pseudobonds, 18367 residues, 71 models selected
> select subtract #14
139031 atoms, 141893 bonds, 34 pseudobonds, 17609 residues, 64 models selected
> select add #15
139031 atoms, 141893 bonds, 34 pseudobonds, 17609 residues, 60 models selected
> select add #16
139031 atoms, 141893 bonds, 34 pseudobonds, 17609 residues, 71 models selected
> select subtract #17
135943 atoms, 138732 bonds, 34 pseudobonds, 17229 residues, 70 models selected
> select subtract #18
132789 atoms, 135518 bonds, 33 pseudobonds, 16832 residues, 66 models selected
> select subtract #19
45037 atoms, 45948 bonds, 33 pseudobonds, 5632 residues, 63 models selected
> select subtract #16
2708 atoms, 2698 bonds, 1 pseudobond, 405 residues, 19 models selected
> select subtract #15
2 models selected
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> ui tool show Matchmaker
> hide #!19 models
> show #!9 models
> hide #!9 models
> show #!19 models
> matchmaker #19/G to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8c4h HEV, chain G (#19), sequence alignment score = 1842.5
RMSD between 351 pruned atom pairs is 0.701 angstroms; (across all 392 pairs:
1.916)
> select add #19.30
3014 atoms, 394 residues, 1 model selected
> select add #19.29
6028 atoms, 788 residues, 2 models selected
> select add #19.28
9042 atoms, 1182 residues, 3 models selected
> select add #19.27
12056 atoms, 1576 residues, 4 models selected
> select add #19.26
15070 atoms, 1970 residues, 5 models selected
> select add #19.25
18084 atoms, 2364 residues, 6 models selected
> select add #19.24
21098 atoms, 2758 residues, 7 models selected
> select add #19.23
24112 atoms, 3152 residues, 8 models selected
> select add #19.22
27126 atoms, 3546 residues, 9 models selected
> select add #19.21
30140 atoms, 3940 residues, 10 models selected
> select add #19.20
33154 atoms, 4334 residues, 11 models selected
> select add #19.19
36168 atoms, 4728 residues, 12 models selected
> select add #19.18
39182 atoms, 5122 residues, 13 models selected
> select add #19.17
42196 atoms, 5516 residues, 14 models selected
> hide sel cartoons
> select add #19.2
43876 atoms, 5600 residues, 15 models selected
> hide sel cartoons
> select add #19.9
46890 atoms, 5994 residues, 16 models selected
> select add #19
87752 atoms, 89570 bonds, 11200 residues, 17 models selected
> select subtract #19.9
84738 atoms, 86503 bonds, 10806 residues, 31 models selected
> hide sel cartoons
> select add #19
87752 atoms, 89570 bonds, 11200 residues, 30 models selected
> select subtract #19
30 models selected
> show #!18 models
> matchmaker #18/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 6jc3 NDV, chain A (#18), sequence alignment score = 777.2
RMSD between 297 pruned atom pairs is 1.174 angstroms; (across all 386 pairs:
2.470)
> show #!17 models
> matchmaker #17/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 7ewq MuV, chain A (#17), sequence alignment score = 744.5
RMSD between 264 pruned atom pairs is 1.064 angstroms; (across all 362 pairs:
3.250)
> show #!16 models
> matchmaker #16/G to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 4xjn HPIV5, chain G (#16), sequence alignment score = 779.6
RMSD between 286 pruned atom pairs is 1.105 angstroms; (across all 388 pairs:
3.030)
> select add #16
42329 atoms, 43250 bonds, 32 pseudobonds, 5227 residues, 3 models selected
> select subtract #16.9
39194 atoms, 40055 bonds, 31 pseudobonds, 4832 residues, 17 models selected
> hide sel cartoons
> matchmaker #15/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 7ev8 HPIV3, chain A (#15), sequence alignment score = 585.1
RMSD between 191 pruned atom pairs is 1.179 angstroms; (across all 315 pairs:
3.242)
> select add #16
42329 atoms, 43250 bonds, 32 pseudobonds, 5227 residues, 16 models selected
> select subtract #16
14 models selected
> show #!15 models
> show #!14 models
> matchmaker #14/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8pds HMPV, chain A (#14), sequence alignment score = 358
RMSD between 91 pruned atom pairs is 1.358 angstroms; (across all 335 pairs:
9.905)
> matchmaker #14/B to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8pds HMPV, chain B (#14), sequence alignment score = 10.6
RMSD between 6 pruned atom pairs is 0.841 angstroms; (across all 7 pairs:
2.165)
> select add #14
6056 atoms, 6171 bonds, 758 residues, 1 model selected
> hide #!1 models
> hide #!14 models
> show #!14 models
> matchmaker #14/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8pds HMPV, chain A (#14), sequence alignment score = 358
RMSD between 91 pruned atom pairs is 1.358 angstroms; (across all 335 pairs:
9.905)
> matchmaker #14/C to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8pds HMPV, chain C (#14), sequence alignment score = 351.4
RMSD between 97 pruned atom pairs is 1.371 angstroms; (across all 335 pairs:
9.996)
> matchmaker #14/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8pds HMPV, chain A (#14), sequence alignment score = 358
RMSD between 91 pruned atom pairs is 1.358 angstroms; (across all 335 pairs:
9.905)
> matchmaker #14/C to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8pds HMPV, chain C (#14), sequence alignment score = 351.4
RMSD between 97 pruned atom pairs is 1.371 angstroms; (across all 335 pairs:
9.996)
> select subtract #14
5 models selected
> select add #14
6056 atoms, 6171 bonds, 758 residues, 1 model selected
> select subtract #14.3
3229 atoms, 3300 bonds, 393 residues, 6 models selected
> select subtract #14.4
3168 atoms, 3239 bonds, 386 residues, 5 models selected
> hide sel cartoons
> select add #14
6056 atoms, 6171 bonds, 758 residues, 4 models selected
> select subtract #14
5 models selected
> show #!1 models
> matchmaker #13/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 2gic VSV, chain A (#13), sequence alignment score = 150
RMSD between 24 pruned atom pairs is 1.239 angstroms; (across all 311 pairs:
18.159)
> show #!13 models
> hide #!1 models
> matchmaker #13/B to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 2gic VSV, chain B (#13), sequence alignment score = 148.2
RMSD between 12 pruned atom pairs is 1.463 angstroms; (across all 307 pairs:
17.801)
> matchmaker #13/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 2gic VSV, chain A (#13), sequence alignment score = 150
RMSD between 24 pruned atom pairs is 1.239 angstroms; (across all 311 pairs:
18.159)
> matchmaker #13/E to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 2gic VSV, chain E (#13), sequence alignment score = 141
RMSD between 15 pruned atom pairs is 1.276 angstroms; (across all 329 pairs:
23.821)
> select add #13
17432 atoms, 17883 bonds, 3 pseudobonds, 2146 residues, 2 models selected
> select subtract #13.6
14105 atoms, 14480 bonds, 3 pseudobonds, 1725 residues, 8 models selected
> select subtract #13.7
13205 atoms, 13491 bonds, 3 pseudobonds, 1680 residues, 7 models selected
> hide sel cartoons
> select add #13
17432 atoms, 17883 bonds, 3 pseudobonds, 2146 residues, 6 models selected
> select subtract #13
6 models selected
> show #!1 models
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> select subtract #1.8
1 model selected
> show #!10 models
> show #!9 models
> show #!8 models
> show #!3 models
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 2 models selected
> select subtract #1.8
41905 atoms, 42762 bonds, 14 pseudobonds, 5258 residues, 17 models selected
> select subtract #1.15
40222 atoms, 40911 bonds, 1 pseudobond, 5174 residues, 16 models selected
> hide sel cartoons
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 15 models selected
> select subtract #1
15 models selected
> select add #3
40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 2 models selected
> select subtract #3.9
37221 atoms, 37986 bonds, 2 pseudobonds, 4801 residues, 16 models selected
> select subtract #3.15
35665 atoms, 36275 bonds, 2 pseudobonds, 4723 residues, 15 models selected
> hide sel cartoons
> select clear
> select add #1.15
1683 atoms, 84 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 3 models selected
> select subtract #1
15 models selected
> select add #3.15
1556 atoms, 78 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> matchmaker #3/H to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 7nt5, chain H (#3), sequence alignment score = 1944.5
RMSD between 360 pruned atom pairs is 0.771 angstroms; (across all 395 pairs:
1.616)
> show #!19 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> select add #13
17432 atoms, 17883 bonds, 3 pseudobonds, 2146 residues, 2 models selected
> matchmaker #13/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 2gic VSV, chain A (#13), sequence alignment score = 150
RMSD between 24 pruned atom pairs is 1.239 angstroms; (across all 311 pairs:
18.159)
> matchmaker #13/R to #1/K pairing ss
Match chain (2gic VSV (#13) chain R) not compatible with BLOSUM-62 similarity
matrix
> matchmaker #13/E to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 2gic VSV, chain E (#13), sequence alignment score = 141
RMSD between 15 pruned atom pairs is 1.276 angstroms; (across all 329 pairs:
23.821)
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> select clear
> hide #!13 models
> show #!10 models
> hide #!10 models
> show #!9 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!9 models
> show #!19 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!13 models
> hide #!13 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!9 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison.cxs"
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 2 models selected
> hide #!19 models
> hide #!17 models
> hide #!18 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> hide #!10 models
> hide #!8 models
> hide #!3 models
> show sel cartoons
> select clear
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/dimer close
> aup.cxs"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.044, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
opened ChimeraX session
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> show sel surfaces
> select clear
> hide #!1 models
> show #!1 models
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 2 models selected
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison.cxs"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.044, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
opened ChimeraX session
> show #!9 models
> hide #!9 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!10 models
> hide #!8 models
> hide #!19 models
> hide #!3 models
> show #!9 models
> hide #!14 models
> select add #1.15
1683 atoms, 84 residues, 1 model selected
> show sel atoms
> select clear
> hide #!9 models
> show #!9 models
> hide #9.1 models
> show #9.1 models
> select add #9.2
2934 atoms, 373 residues, 1 model selected
> select subtract #9.2
1 model selected
> select add #9.1
2730 atoms, 347 residues, 1 model selected
> select subtract #9.1
1 model selected
> select add #9.2
2934 atoms, 373 residues, 1 model selected
> select add #9.1
5664 atoms, 720 residues, 2 models selected
> select subtract #9.2
2730 atoms, 347 residues, 3 models selected
> select add #9.2
5664 atoms, 720 residues, 2 models selected
> select subtract #9.1
2934 atoms, 373 residues, 3 models selected
> hide sel cartoons
> select add #9
5664 atoms, 5763 bonds, 720 residues, 2 models selected
> select subtract #9
2 models selected
> hide #!9 models
> show #!9 models
> hide #!1 models
Cell requested for row 10 is out of bounds for table with 36 rows! Resizing
table model.
> hide #!9 models
> show #!9 models
> select add #9
5664 atoms, 5763 bonds, 720 residues, 1 model selected
> select subtract #9
2 models selected
> select add #9.2
2934 atoms, 373 residues, 1 model selected
> show sel cartoons
> select subtract #9.2
1 model selected
> ui tool show Matchmaker
> show #!1 models
> hide #!9 models
> matchmaker #9/B to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 6c54 ebola, chain B (#9), sequence alignment score = 245.2
RMSD between 62 pruned atom pairs is 1.145 angstroms; (across all 317 pairs:
9.090)
> select add #9.2
2934 atoms, 373 residues, 1 model selected
> show #!9 models
> matchmaker #9/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 6c54 ebola, chain A (#9), sequence alignment score = 283.7
RMSD between 61 pruned atom pairs is 1.090 angstroms; (across all 329 pairs:
8.097)
> matchmaker #9/B to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 6c54 ebola, chain B (#9), sequence alignment score = 245.2
RMSD between 62 pruned atom pairs is 1.145 angstroms; (across all 317 pairs:
9.090)
> matchmaker #9/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 6c54 ebola, chain A (#9), sequence alignment score = 283.7
RMSD between 61 pruned atom pairs is 1.090 angstroms; (across all 329 pairs:
8.097)
> select subtract #9.2
1 model selected
> select add #9.2
2934 atoms, 373 residues, 1 model selected
> hide sel cartoons
> hide #!9 models
> select add #9
5664 atoms, 5763 bonds, 720 residues, 2 models selected
> show #!4 models
> select subtract #9
2 models selected
> show #!9 models
> hide #!9 models
> volume #4 level 0.03594
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> volume #4 level 0.02788
> volume #4 level 0.02
> hide #!4 models
> select clear
Cell requested for row 0 is out of bounds for table with 21 rows! Resizing
table model.
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison.cxs"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.044, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
opened ChimeraX session
> show #!9 models
> select add #9.2
2934 atoms, 373 residues, 1 model selected
> hide sel cartoons
> show #!13 models
> select add #9
5664 atoms, 5763 bonds, 720 residues, 2 models selected
> select subtract #9
2 models selected
> hide #!13 models
> show #!13 models
> hide #!13 models
> select add #3
40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 2 models selected
Drag select of 144 atoms, 142 bonds
> hide sel atoms
> select #1 /k :190-200
103 atoms, 105 bonds, 11 residues, 1 model selected
> select #1 /k :340-350
81 atoms, 80 bonds, 11 residues, 1 model selected
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 3 models selected
> select #1 /z :40-54
300 atoms, 329 bonds, 15 residues, 1 model selected
> show sel cartoons
> select #1 /z :42-51
200 atoms, 219 bonds, 10 residues, 1 model selected
> select #1 /z :40-54
300 atoms, 329 bonds, 15 residues, 1 model selected
> hide sel cartoons
> select up
1683 atoms, 1851 bonds, 84 residues, 2 models selected
> select #1 /z :42-51
200 atoms, 219 bonds, 10 residues, 1 model selected
> show sel cartoons
> select clear
> select #1 /k: 352
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 8 residues
> show sel atoms
> style sel stick
Changed 88 atom styles
> select clear
Cell requested for row 18 is out of bounds for table with 34 rows! Resizing
table model.
> hide #!19 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!3 models
> show #!19 models
> show #!18 models
> hide #!19 models
> show #!14 models
> hide #!18 models
> select #14/C:341
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #14/C:340
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #14/C:341@CB
1 atom, 1 residue, 1 model selected
Drag select of 1 residues
> show sel atoms
> select #14/C:339
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #14/C:338
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #14 /c: 341
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> select add #14.5
291 atoms, 10 bonds, 15 residues, 2 models selected
> select add #14
6056 atoms, 6171 bonds, 758 residues, 3 models selected
> select subtract #14
5 models selected
> select add #14.5
280 atoms, 14 residues, 1 model selected
> show sel cartoons
> select #14 /c: 332
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #14 /c: 263
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1 /k: 263
4 atoms, 3 bonds, 1 residue, 1 model selected
Cell requested for row 14 is out of bounds for table with 24 rows! Resizing
table model.
> open 8IUO fromDatabase pdb format mmcif
Summary of feedback from opening 8IUO fetched from pdb
---
note | Fetching compressed mmCIF 8iuo from http://files.rcsb.org/download/8iuo.cif
8iuo title:
respiratory syncytial virus nucleocapsid-like assembly [more info...]
Chain information for 8iuo #20
---
Chain | Description | UniProt
A B C D E | Nucleoprotein | A0A2H4WKL8_HRSV 1-362
F | RNA (35-MER) |
> select add #20
14789 atoms, 15092 bonds, 1846 residues, 3 models selected
> select add #1
59784 atoms, 60998 bonds, 26 pseudobonds, 7501 residues, 4 models selected
> select subtract #1
14785 atoms, 15089 bonds, 1845 residues, 16 models selected
> show sel cartoons
> show sel surfaces
> hide sel atoms
> hide sel surfaces
> select subtract #20
6 models selected
> ui tool show Matchmaker
> matchmaker #20/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8iuo, chain A (#20), sequence alignment score = 293.1
RMSD between 70 pruned atom pairs is 1.228 angstroms; (across all 336 pairs:
11.116)
> select add #20
14785 atoms, 15089 bonds, 1845 residues, 1 model selected
> select subtract #20.1
11968 atoms, 12225 bonds, 1483 residues, 7 models selected
> select subtract #20.6
11268 atoms, 11456 bonds, 1448 residues, 6 models selected
> hide sel cartoons
> select add #14
17324 atoms, 17627 bonds, 2206 residues, 6 models selected
> hide sel atoms
> select clear
> hide #!20 models
> hide #!14 models
> show #!20 models
> show #!14 models
> show #!9 models
> select #1 /k: 352
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1 /k: 263
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1 /k: 349
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> select #1 /k: 349
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 6 residues, 3 atoms, 2 bonds
Drag select of 5 residues
> show sel atoms
> style sel stick
Changed 54 atom styles
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!9 models
> hide #!20 models
> show #!20 models
> color (#!1,14,20 & sel) byhetero
> hide #!14 models
> select add #20.6
754 atoms, 40 residues, 6 models selected
> select add #20
14816 atoms, 15089 bonds, 1848 residues, 7 models selected
> select subtract #20
31 atoms, 3 residues, 10 models selected
> select add #14
6064 atoms, 6171 bonds, 759 residues, 4 models selected
> select subtract #14
8 atoms, 1 residue, 7 models selected
> select add #20.6
708 atoms, 36 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 708 atom styles
> select add #1
45699 atoms, 45909 bonds, 26 pseudobonds, 5691 residues, 5 models selected
> select subtract #1
700 atoms, 35 residues, 17 models selected
> select add #1.15
2383 atoms, 119 residues, 3 models selected
> show sel atoms
> select clear
> select #1/K:344
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #20/A:336
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
Cell requested for row 25 is out of bounds for table with 41 rows! Resizing
table model.
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!20 models
> select #1 /k: 178
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!20 models
> select #1 /k: 192
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!20 models
> show #!20 models
> select #1 /k: 352
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!20 models
> show #!3 models
> select add #3
40211 atoms, 41026 bonds, 2 pseudobonds, 5197 residues, 4 models selected
> select add #1
85199 atoms, 86925 bonds, 28 pseudobonds, 10852 residues, 19 models selected
> show sel cartoons
> hide sel atoms
> hide #!3 models
> show #!4 models
> ui tool show "Volume Viewer"
> show #!10 models
> hide #!4 models
> select clear
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> select add #1.15
4777 atoms, 482 residues, 2 models selected
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 4 models selected
> select subtract #1.8
41905 atoms, 42762 bonds, 14 pseudobonds, 5258 residues, 17 models selected
> select subtract #1.15
40222 atoms, 40911 bonds, 1 pseudobond, 5174 residues, 16 models selected
> hide sel cartoons
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 15 models selected
> select subtract #1
15 models selected
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #!13 models
> hide #!13 models
> show #!9 models
> view
> hide #!9 models
> show #!13 models
> hide #!13 models
> open "/Users/kompa012/Desktop/NiP N protein
> article/cryosparc_P78_J400_008_volume_map_sharp.mrc"
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.0467, step 4, values float32
> volume #21 step 1
> ui tool show "Hide Dust"
> surface dust #21 size 5.31
> volume #21 level 0.04058
> volume #21 level 0.0329
> surface dust #21 size 8
> surface dust #21 size 1
> surface dust #21 size 10
> select add #1
44999 atoms, 45909 bonds, 26 pseudobonds, 5656 residues, 2 models selected
> show sel cartoons
> volume #21 style mesh
> select clear
> show #!11 models
> hide #!10 models
> select add #11
3094 atoms, 3147 bonds, 398 residues, 1 model selected
> select add #21
3094 atoms, 3147 bonds, 398 residues, 4 models selected
> transparency (#!11 & sel) 70
> volume #12 style surface
> volume #21 style surface
> transparency (#!11 & sel) 80
> select subtract #11
3 models selected
> select subtract #21
Nothing selected
> select add #21
2 models selected
> transparency #21.1 80
> select subtract #21
Nothing selected
> select add #11
3094 atoms, 3147 bonds, 398 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.97709,-0.21061,-0.030656,14.303,-0.19142,-0.93258,0.30603,387.27,-0.093043,-0.29315,-0.95153,704.51
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.80947,-0.56869,-0.14612,176.21,0.5863,0.76934,0.25373,-199.59,-0.031873,-0.29105,0.95618,123.99
> select add #21
3094 atoms, 3147 bonds, 398 residues, 4 models selected
> transparency (#!11 & sel) 50
> select subtract #11
3 models selected
> select subtract #21
Nothing selected
> select add #21
2 models selected
> transparency #21.1 40
> transparency #21.1 60
> view matrix models
> #21,0.98918,-0.14084,-0.04119,46.668,0.12092,0.94137,-0.31495,50.982,0.083133,0.30656,0.94821,-86.595
> undo
> select add #11
3094 atoms, 3147 bonds, 398 residues, 3 models selected
> select subtract #21
3094 atoms, 3147 bonds, 398 residues, 2 models selected
> view matrix models
> #11,0.65879,-0.75153,-0.034491,225.9,0.61025,0.56063,-0.55973,82.692,0.43999,0.3477,0.82796,-112.35
> volume #21 level 0.03751
> volume #21 level 0.045
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.65879,-0.75153,-0.034491,205.29,0.61025,0.56063,-0.55973,78.338,0.43999,0.3477,0.82796,-161.24
> view matrix models
> #11,0.65879,-0.75153,-0.034491,210.34,0.61025,0.56063,-0.55973,69.174,0.43999,0.3477,0.82796,-152.4
> view matrix models
> #11,0.65879,-0.75153,-0.034491,216.5,0.61025,0.56063,-0.55973,68.027,0.43999,0.3477,0.82796,-146.63
> ui tool show "Fit in Map"
> fitmap #11 inMap #21
Fit molecule 7nt5_J377_intactmodel-coot-Chain D.pdb (#11) to map
cryosparc_P78_J400_008_volume_map_sharp.mrc (#21) using 3094 atoms
average map value = 0.05214, steps = 148
shifted from previous position = 8.25
rotated from previous position = 11.7 degrees
atoms outside contour = 1211, contour level = 0.045
Position of 7nt5_J377_intactmodel-coot-Chain D.pdb (#11) relative to
cryosparc_P78_J400_008_volume_map_sharp.mrc (#21) coordinates:
Matrix rotation and translation
0.54311695 -0.83482788 -0.08992436 277.22021455
0.72539463 0.52044711 -0.45048577 14.51518958
0.42287895 0.17943581 0.88824331 -126.14497241
Axis 0.35811452 -0.29153202 0.88699666
Axis point 154.98966076 254.47231724 0.00000000
Rotation angle (degrees) 61.58179477
Shift along axis -16.84522838
> hide #!21 models
> show #!21 models
> view matrix models
> #11,0.54312,-0.83483,-0.089924,289.04,0.72539,0.52045,-0.45049,7.5805,0.42288,0.17944,0.88824,-121.18
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.67588,-0.70686,0.20865,135.66,0.65028,0.43869,-0.62023,96.772,0.34688,0.55488,0.75616,-148.78
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.67588,-0.70686,0.20865,129.93,0.65028,0.43869,-0.62023,100.09,0.34688,0.55488,0.75616,-149.13
> fitmap #11 inMap #21
Fit molecule 7nt5_J377_intactmodel-coot-Chain D.pdb (#11) to map
cryosparc_P78_J400_008_volume_map_sharp.mrc (#21) using 3094 atoms
average map value = 0.05292, steps = 164
shifted from previous position = 14.9
rotated from previous position = 18.7 degrees
atoms outside contour = 1177, contour level = 0.045
Position of 7nt5_J377_intactmodel-coot-Chain D.pdb (#11) relative to
cryosparc_P78_J400_008_volume_map_sharp.mrc (#21) coordinates:
Matrix rotation and translation
0.46060387 -0.88307112 0.08960724 254.61074277
0.78860320 0.36080492 -0.49792048 51.23137113
0.40736847 0.30000865 0.86258085 -146.79122358
Axis 0.42456506 -0.16907556 0.88947061
Axis point 125.43630444 226.67192948 0.00000000
Rotation angle (degrees) 70.00154402
Shift along axis -31.12962615
> volume #21 level 0.05
> view matrix models
> #11,0.4606,-0.88307,0.089607,266.27,0.7886,0.3608,-0.49792,41.609,0.40737,0.30001,0.86258,-141.97
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.97844,0.19718,-0.061461,-77.874,-0.18404,0.96743,0.17381,-37.099,0.093731,-0.15876,0.98286,12.68
> view matrix models
> #11,0.98727,0.15904,-0.0017248,-89.055,-0.15762,0.97977,0.12331,-32.104,0.021301,-0.12146,0.99237,20.615
> view matrix models
> #11,0.93631,0.30706,0.17038,-160.56,-0.33697,0.92217,0.18988,9.5611,-0.09881,-0.2352,0.96691,86.623
> view matrix models
> #11,0.98069,0.18349,0.067622,-113.45,-0.19215,0.96838,0.15911,-30.804,-0.036289,-0.16903,0.98494,49.238
> view matrix models
> #11,0.99442,0.10084,0.030876,-87.121,-0.10426,0.98409,0.14387,-53.46,-0.015877,-0.14629,0.98911,37.274
> view matrix models
> #11,0.99143,0.1242,0.040593,-94.602,-0.12887,0.98076,0.14662,-46.915,-0.021602,-0.15059,0.98836,40.026
> view matrix models
> #11,0.98433,0.086475,0.1537,-117.38,-0.10325,0.98913,0.10472,-43.329,-0.14298,-0.11895,0.98255,66.893
> view matrix models
> #11,0.9499,0.049627,0.3086,-145.4,-0.1102,0.97709,0.18209,-61.54,-0.29249,-0.20698,0.9336,141.76
> view matrix models
> #11,0.98946,0.066735,0.12852,-106.74,-0.086837,0.98365,0.15778,-62.13,-0.11589,-0.16728,0.97907,71.866
> view matrix models
> #11,0.99228,0.052798,0.11218,-99.445,-0.073191,0.97977,0.18627,-73.301,-0.10008,-0.19304,0.97607,74.489
> hide #!21 models
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.99228,0.052798,0.11218,-104.22,-0.073191,0.97977,0.18627,-64.515,-0.10008,-0.19304,0.97607,82.004
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.98984,-0.14202,0.0075545,-27.526,0.14175,0.9895,0.02823,-77.591,-0.011484,-0.026872,0.99957,12.864
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.98984,-0.14202,0.0075545,-24.655,0.14175,0.9895,0.02823,-78.858,-0.011484,-0.026872,0.99957,9.9628
> show #!21 models
> fitmap #11 inMap #21
Fit molecule 7nt5_J377_intactmodel-coot-Chain D.pdb (#11) to map
cryosparc_P78_J400_008_volume_map_sharp.mrc (#21) using 3094 atoms
average map value = 0.04927, steps = 152
shifted from previous position = 7.49
rotated from previous position = 27.1 degrees
atoms outside contour = 1563, contour level = 0.05
Position of 7nt5_J377_intactmodel-coot-Chain D.pdb (#11) relative to
cryosparc_P78_J400_008_volume_map_sharp.mrc (#21) coordinates:
Matrix rotation and translation
0.92853752 -0.36775218 -0.05075826 55.44894029
0.32349901 0.86860659 -0.37532782 23.73707880
0.18211659 0.33208572 0.92550128 -106.04641673
Axis 0.69619332 -0.22918124 0.68028731
Axis point 0.00000000 230.25064786 -41.16289940
Rotation angle (degrees) 30.53457877
Shift along axis -38.97894323
> hide #!21 models
> show #!21 models
> hide #!21 models
> undo
> view matrix models
> #11,0.92854,-0.36775,-0.050758,54.871,0.3235,0.86861,-0.37533,15.231,0.18212,0.33209,0.9255,-110.37
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.87573,-0.40689,0.2599,-13.724,0.4605,0.86567,-0.19639,-73.62,-0.14508,0.29166,0.94545,-19.347
> view matrix models
> #11,0.96613,-0.24471,0.081931,-22.894,0.16259,0.82377,0.54311,-202.7,-0.2004,-0.51139,0.83565,213.91
> view matrix models
> #11,0.98654,-0.16351,0.00026332,-23.033,0.16351,0.98651,-0.0084474,-77.666,0.0011215,0.0083768,0.99996,-8.961
> view matrix models
> #11,0.98627,-0.16497,0.007923,-24.885,0.16492,0.98629,0.0061985,-82.322,-0.0088369,-0.0048066,0.99995,-3.2382
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.98627,-0.16497,0.007923,-20.593,0.16492,0.98629,0.0061985,-76.589,-0.0088369,-0.0048066,0.99995,-0.33326
> show #!21 models
> view matrix models
> #11,0.98627,-0.16497,0.007923,-15.344,0.16492,0.98629,0.0061985,-80.079,-0.0088369,-0.0048066,0.99995,1.5124
> view matrix models
> #11,0.98627,-0.16497,0.007923,-18.916,0.16492,0.98629,0.0061985,-86.911,-0.0088369,-0.0048066,0.99995,-3.2798
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.97697,-0.21086,-0.032784,6.2295,0.20795,0.97522,-0.075453,-71.738,0.047882,0.066897,0.99661,-34.079
> view matrix models
> #11,0.95516,-0.22497,-0.19251,62.528,0.19851,0.96895,-0.14741,-46.495,0.21969,0.10259,0.97016,-80.508
> view matrix models
> #11,0.98709,-0.037861,-0.1556,-0.26389,-0.0019884,0.96868,-0.24832,37.036,0.16012,0.24542,0.9561,-93.497
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.98709,-0.037861,-0.1556,1.6198,-0.0019884,0.96868,-0.24832,39.161,0.16012,0.24542,0.9561,-93.079
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.99181,0.094491,-0.085878,-50.899,-0.10694,0.98221,-0.15436,36.349,0.069765,0.16228,0.98428,-57.965
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.99181,0.094491,-0.085878,-52.723,-0.10694,0.98221,-0.15436,37.57,0.069765,0.16228,0.98428,-55.652
> view matrix models
> #11,0.99181,0.094491,-0.085878,-44.875,-0.10694,0.98221,-0.15436,42.53,0.069765,0.16228,0.98428,-53.478
> ui mousemode right select
> select clear
> hide #!21 models
> ui mousemode right "rotate selected models"
> select add #11
3094 atoms, 3147 bonds, 398 residues, 1 model selected
> view matrix models
> #11,0.99287,0.067678,0.098085,-93.304,-0.040704,0.96618,-0.25463,58.144,-0.112,0.24882,0.96205,-18.316
> show #!13 models
> hide #!13 models
> show #!21 models
> view matrix models
> #11,0.98454,0.15106,0.088665,-107.6,-0.11302,0.93459,-0.33731,109.24,-0.13382,0.32207,0.93721,-22.103
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.98454,0.15106,0.088665,-108.1,-0.11302,0.93459,-0.33731,109.82,-0.13382,0.32207,0.93721,-22.469
> view matrix models
> #11,0.98454,0.15106,0.088665,-108.41,-0.11302,0.93459,-0.33731,114.11,-0.13382,0.32207,0.93721,-20.773
> view matrix models
> #11,0.98454,0.15106,0.088665,-111.19,-0.11302,0.93459,-0.33731,114.53,-0.13382,0.32207,0.93721,-18.059
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.98365,0.15899,0.08455,-111.57,-0.12067,0.9305,-0.34585,120.05,-0.13366,0.33,0.93447,-19.129
> view matrix models
> #11,0.99706,-0.076419,-0.005427,-34.051,0.064745,0.87837,-0.47357,120.24,0.040957,0.47183,0.88074,-82.831
> hide #!21 models
> show #!21 models
> hide #!21 models
> select #1 /e: 136-144
67 atoms, 67 bonds, 9 residues, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select #11 :114-121
65 atoms, 64 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 65 atom styles
> color (#!11 & sel) byhetero
> style sel ball
Changed 65 atom styles
> show #!21 models
> select add #11
3094 atoms, 3147 bonds, 398 residues, 2 models selected
> select subtract #11
1 model selected
> select add #11
3094 atoms, 3147 bonds, 398 residues, 1 model selected
> view matrix models
> #11,0.99724,-0.074143,-0.0047855,-34.815,0.063431,0.88316,-0.46477,116.89,0.038686,0.46318,0.88542,-81.604
> view matrix models
> #11,0.98176,-0.073119,0.17553,-84.186,0.1481,0.873,-0.46469,96.559,-0.11926,0.48221,0.8679,-38.569
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.98176,-0.073119,0.17553,-88.719,0.1481,0.873,-0.46469,95.639,-0.11926,0.48221,0.8679,-35.044
> ui mousemode right distance
> distance #1/E:142@NZ #11/D:119@OD2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/E
LYS 142 NZ and 7nt5_J377_intactmodel-coot-Chain D.pdb #11/D ASP 119 OD2:
14.339Å
> show #!6 models
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.97299,-0.056937,0.22371,-104.36,0.17913,0.79748,-0.57614,137.76,-0.1456,0.60065,0.78614,-31.27
> hide #!21 models
> view matrix models
> #11,0.99196,-0.12644,-0.005526,-25.603,0.10665,0.85858,-0.50147,120.94,0.068151,0.49685,0.86516,-87.774
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.99196,-0.12644,-0.005526,-23.947,0.10665,0.85858,-0.50147,119.76,0.068151,0.49685,0.86516,-96.324
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.99689,-0.061867,0.048814,-56.28,0.078404,0.84107,-0.53521,141.31,-0.0079441,0.53737,0.84331,-78.887
> view matrix models
> #11,0.99529,-0.091194,0.032811,-44.331,0.093179,0.80729,-0.58275,159.23,0.026656,0.58306,0.81199,-89.475
> view matrix models
> #11,0.98497,-0.027525,0.17052,-97.004,0.095404,0.90966,-0.40425,82.181,-0.14399,0.41444,0.89861,-30.341
> view matrix models
> #11,0.99558,-0.075196,-0.056277,-21.79,0.048989,0.92697,-0.37193,81.047,0.080135,0.36753,0.92655,-87.726
> view matrix models
> #11,0.98194,-0.18033,-0.057251,6.4998,0.11992,0.82726,-0.54887,137.44,0.14634,0.53209,0.83395,-116.19
> view matrix models
> #11,0.98687,-0.15679,0.038724,-28.632,0.15129,0.81359,-0.56141,135.92,0.056515,0.5599,0.82663,-96.438
> view matrix models
> #11,0.98418,-0.1364,0.11302,-54.587,0.17665,0.80325,-0.56885,133.72,-0.013193,0.57982,0.81464,-78.854
> view matrix models
> #11,0.98265,-0.13115,0.13112,-60.741,0.18298,0.80076,-0.57036,133.05,-0.030194,0.58445,0.81086,-74.263
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.98265,-0.13115,0.13112,-53.471,0.18298,0.80076,-0.57036,133.7,-0.030194,0.58445,0.81086,-75.588
> show #!21 models
> view matrix models
> #11,0.98265,-0.13115,0.13112,-61.738,0.18298,0.80076,-0.57036,131.77,-0.030194,0.58445,0.81086,-70.461
> view matrix models
> #11,0.98265,-0.13115,0.13112,-64.584,0.18298,0.80076,-0.57036,134.91,-0.030194,0.58445,0.81086,-70.08
> view matrix models
> #11,0.98265,-0.13115,0.13112,-63.468,0.18298,0.80076,-0.57036,135.39,-0.030194,0.58445,0.81086,-70.458
> hide #!21 models
> ui mousemode right select
> select #1/Q:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/D:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #1/D:140@NZ #1/Q:119@OD2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/D
LYS 140 NZ and /Q ASP 119 OD2: 13.464Å
> ui mousemode right select
> select #1/Q:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
Populating font family aliases took 160 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> swapaa interactive sel ASP rotLib Dunbrack
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Q ASP 119: phi
55.6, psi 44.1 trans
Changed 90 bond radii
> select #!1/D:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #!1/D LYS 140: phi
55.8, psi 50.9 trans
Changed 438 bond radii
> ui mousemode right distance
> distance #1.16.18/A:1@OD1 #1.17.11/A:1@NZ
Distance between rotamer 18 #1.16.18/A ASP 1 OD1 and rotamer 11 #1.17.11/A LYS
1 NZ: 7.790Å
> ui mousemode right select
> select #!1/Q:118
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #!1/Q:117
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #!1/Q:118
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #!1/Q:117
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select #1 /g: 269
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #!1/H:11
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #!1/G:267
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #!1/G:268
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #!1/G:301
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!21 models
> hide #!1 models
> show #!1 models
> hide #!21 models
> hide #!11 models
> show #!11 models
> show #!21 models
> volume #21 level 0.045
> hide #!21 models
> show #!21 models
> volume #21 level 0.035
> hide #!21 models
> hide #!20 models
> show #!5 models
> select #1 /g: 242
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide #!5 models
> show #!21 models
> hide #!21 models
> show #!21 models
> volume #21 level 0.04
> volume #21 level 0.03
> select #!1/Q:118
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide #!21 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!1 models
> show #!1 models
> show #!18 models
> hide #!1 models
> show #!7 models
> hide #!7 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!13 models
> hide #!13 models
> show #!15 models
> show #!16 models
> show #!17 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!8 models
> hide #!6 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #14/C to #!1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8pds HMPV, chain C (#14), sequence alignment score = 351.4
RMSD between 97 pruned atom pairs is 1.371 angstroms; (across all 335 pairs:
9.996)
> matchmaker #14/C to #!1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8pds HMPV, chain C (#14), sequence alignment score = 351.4
RMSD between 97 pruned atom pairs is 1.371 angstroms; (across all 335 pairs:
9.996)
> hide #!1 models
> show #!1 models
> select add #1
45107 atoms, 45999 bonds, 27 pseudobonds, 5674 residues, 22 models selected
> select subtract #1.8
42013 atoms, 42852 bonds, 15 pseudobonds, 5276 residues, 36 models selected
> select subtract #1.15
40330 atoms, 41001 bonds, 2 pseudobonds, 5192 residues, 35 models selected
> hide sel cartoons
> select add #1
45107 atoms, 45999 bonds, 27 pseudobonds, 5674 residues, 34 models selected
> select subtract #1
15 models selected
> select add #14
6056 atoms, 6171 bonds, 758 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.53649,0.6653,-0.5192,130.94,-0.6085,-0.12132,-0.78423,587.72,-0.58473,0.73666,0.33974,115.5
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.53649,0.6653,-0.5192,152.3,-0.6085,-0.12132,-0.78423,574.3,-0.58473,0.73666,0.33974,111.69
> view matrix models
> #14,0.53649,0.6653,-0.5192,151.89,-0.6085,-0.12132,-0.78423,575.69,-0.58473,0.73666,0.33974,106.98
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.60451,0.5049,-0.61615,183.83,-0.57474,-0.25913,-0.77623,589.16,-0.55158,0.82336,0.13354,129.28
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.60451,0.5049,-0.61615,179.53,-0.57474,-0.25913,-0.77623,587.07,-0.55158,0.82336,0.13354,127.05
> view matrix models
> #14,0.60451,0.5049,-0.61615,177.38,-0.57474,-0.25913,-0.77623,585.11,-0.55158,0.82336,0.13354,127.14
> hide #!14 models
> show #!21 models
> show #!14 models
> hide #!21 models
> ui tool show Matchmaker
> matchmaker #14/C to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 8pds HMPV, chain C (#14), sequence alignment score = 351.4
RMSD between 97 pruned atom pairs is 1.371 angstroms; (across all 335 pairs:
9.996)
> hide #!14 models
> ui mousemode right select
> select clear
> show #!21 models
> show #!5 models
> hide #!21 models
> select #1/K:136
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/prot comparison
> hel.cxs"
> hide #!1 models
> select add #1
44999 atoms, 45909 bonds, 27 pseudobonds, 5656 residues, 3 models selected
> select subtract #1
15 models selected
> hide #!5 models
> show #!20 models
> show #!11 models
> show #!1 models
> show #!5 models
> hide #!1 models
> show #!4 models
> hide #!5 models
> volume #4 level 0.03
> show #!21 models
> volume #21 level 0.04
> hide #!21 models
> hide #!4 models
> hide #!20 models
> hide #!11 models
> show #!1 models
> select add #1.4
3094 atoms, 398 residues, 1 model selected
> select add #1.5
6188 atoms, 796 residues, 2 models selected
> show sel cartoons
> select clear
> select #1 /g: 80,82,242,245,247,250,257,276,295,376,381,388,398,399
125 atoms, 113 bonds, 14 residues, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select #1 /h: 3,23,29,31,96,229,278,283,285,292,317,320,361,365,377
122 atoms, 107 bonds, 15 residues, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select clear
> measure buriedarea #1/G withAtoms2 #1/h
Buried area between #1/G and #1/h = 3271.6
area #1/G = 21820, area #1/h = 21773, area both = 37050
> select #1 /u: 3-18
Nothing selected
> select #1 /z: 3-18
320 atoms, 351 bonds, 16 residues, 1 model selected
> hide sel cartoons
> select #1 /z: 30-86
1143 atoms, 1257 bonds, 57 residues, 1 model selected
> hide sel cartoons
Drag select of 99 atoms, 97 bonds
> hide sel atoms
Drag select of 8 atoms, 398 residues, 7 bonds
> hide sel cartoons
> hide sel atoms
> select #1 /g: 80
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/H:31
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/G:80
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel cartoons
> ui mousemode right distance
> distance #1/G:80@O #1/H:31@N
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/G
TYR 80 O and /H LEU 31 N: 3.280Å
> show #!6 models
> ui mousemode right select
> select #1/G:80@CA
1 atom, 1 residue, 1 model selected
> select #1/G:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1 /g: 80
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1 /h: 31
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #1/H:29
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/G:82
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> ui mousemode right distance
> distance #1/G:82@N #1/H:29@O
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/G
GLU 82 N and /H ALA 29 O: 3.037Å
> select #1 /h: 29
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1 /g: 82
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1 /g: 242
4 atoms, 3 bonds, 1 residue, 1 model selected
> set bgColor black
> set bgColor transparent
> select #1 /g: 242
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1 /g: 245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /g: 242
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> distance #1/H:23@NE #1/G:242@O
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
ARG 23 NE and /G GLY 242 O: 3.321Å
> select #1 /g: 242
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1 /g: 245
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> distance #1/H:229@NZ #1/G:245@O
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
LYS 229 NZ and /G LYS 245 O: 3.308Å
> show sel cartoons
> select #1 /g: 247
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> distance #1/H:96@OD2 #1/G:247@N
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
ASP 96 OD2 and /G ARG 247 N: 3.290Å
> show sel cartoons
> select #1 /g: 250
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /h: 317
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> distance #1/H:317@N #1/G:250@OE1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
SER 317 N and /G GLU 250 OE1: 3.160Å
> show sel cartoons
> select #1 /g: 257
8 atoms, 7 bonds, 1 residue, 1 model selected
> distance #1/G:257@OD1 #1/H:320@OG1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/G
ASN 257 OD1 and /H THR 320 OG1: 2.782Å
> select #1 /g: 276
9 atoms, 8 bonds, 1 residue, 1 model selected
> distance #1/H:292@ND2 #1/G:276@OE1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
ASN 292 ND2 and /G GLU 276 OE1: 2.420Å
> select #1 /g: 295
9 atoms, 8 bonds, 1 residue, 1 model selected
> distance #1/H:3@OD2 #1/G:295@NZ
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
ASP 3 OD2 and /G LYS 295 NZ: 2.713Å
> select #1 /g: 376
9 atoms, 8 bonds, 1 residue, 1 model selected
> distance #1/H:285@OD1 #1/G:376@NE2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
ASN 285 OD1 and /G GLN 376 NE2: 2.506Å
> select #1 /h: 283
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1 /g: 376
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> distance #1/G:376@N #1/H:283@O
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/G
GLN 376 N and /H ALA 283 O: 3.195Å
> hide sel cartoons
> show sel cartoons
> select #1 /h: 283
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1 /g: 381
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> distance #1/H:278@NH2 #1/G:381@O
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
ARG 278 NH2 and /G ARG 381 O: 3.164Å
> show sel cartoons
> select #1 /g: 388
9 atoms, 8 bonds, 1 residue, 1 model selected
> distance #1/H:377@OD1 #1/G:388@NE2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
ASN 377 OD1 and /G GLN 388 NE2: 2.428Å
> select #1 /g: 398
9 atoms, 8 bonds, 1 residue, 1 model selected
> distance #1/H:365@NZ #1/G:398@OE1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
LYS 365 NZ and /G GLU 398 OE1: 2.946Å
> select #1 /g: 399
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> distance #1/H:361@NH1 #1/G:399@O
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
ARG 361 NH1 and /G THR 399 O: 2.919Å
> show sel cartoons
> select #1 /g: 272
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select #1 /h: 290
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> distance #1/H:290@OD1 #1/G:272@NH2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
ASP 290 OD1 and /G ARG 272 NH2: 3.522Å
> select #1 /h: 3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1 /h: 356
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select #1 /g: 343
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> distance #1/H:356@OE1 #1/G:343@NH1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
GLU 356 OE1 and /G ARG 343 NH1: 3.472Å
> select #1 /g: 398
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison.cxs"
> ui mousemode right select
> select clear
> select add #1.5
3094 atoms, 398 residues, 1 model selected
> show sel surfaces
> select clear
> select add #1.7
3094 atoms, 398 residues, 1 model selected
> select add #1.6
6188 atoms, 796 residues, 2 models selected
> select subtract #1.7
3094 atoms, 398 residues, 3 models selected
> select add #1.5
6188 atoms, 796 residues, 2 models selected
> select subtract #1.6
3094 atoms, 398 residues, 3 models selected
> transparency (#!1 & sel) 30
> select clear
> select add #1.5
3094 atoms, 398 residues, 1 model selected
> hide sel surfaces
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Intra dimer
> overall.png" width 3000 height 3078 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/hydrophobic
> core.png" width 3000 height 3078 supersample 3 transparentBackground true
> select add #1.5
3094 atoms, 398 residues, 1 model selected
> select clear
> select #1/G:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/G:247
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/G:82
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/H:31
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/Z:23
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/Z:23
20 atoms, 21 bonds, 1 residue, 1 model selected
Drag select of 1 atoms, 4 residues, 1 bonds
> select #1/G:80
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/G:80@CB
1 atom, 1 residue, 1 model selected
> select #1/G:80
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/NT core
> interactions.png" width 3000 height 3078 supersample 3 transparentBackground
> true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/CT core
> interactions.png" width 3000 height 3078 supersample 3 transparentBackground
> true
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot comparison
> hel.cxs"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.044, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.03, step 1, values float32
> set bgColor #ffffff00
opened ChimeraX session
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison.cxs"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.03, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.04, step 1, values float32
> set bgColor transparent
opened ChimeraX session
> show #!21 models
> hide #!21 models
> show #!20 models
> select clear
> show #!19 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> hide #!20 models
> select #1/G:247@CA
1 atom, 1 residue, 1 model selected
> select #1/G:247
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/G:82
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/H:31
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/H:29
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/G:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/G:80
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/G:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison.cxs"
> show #!11 models
> ui mousemode right "translate selected models"
> select add #1
44999 atoms, 45909 bonds, 44 pseudobonds, 5656 residues, 3 models selected
> select subtract #1
15 models selected
> select add #11
3094 atoms, 3147 bonds, 398 residues, 1 model selected
> view matrix models
> #11,0.98265,-0.13115,0.13112,-60.738,0.18298,0.80076,-0.57036,132.88,-0.030194,0.58445,0.81086,-68.345
> hide #!1 models
> show #!3 models
> volume #21 level 0.045
> volume #4 level 0.045
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.99172,-0.1153,0.056505,-44.789,0.12687,0.81203,-0.56966,145.08,0.019799,0.57212,0.81993,-81.545
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.99172,-0.1153,0.056505,-46.049,0.12687,0.81203,-0.56966,148.61,0.019799,0.57212,0.81993,-84.601
> hide #!3 models
> show #!1 models
> select add #1.4
6188 atoms, 3147 bonds, 796 residues, 3 models selected
> select subtract #1.4
3094 atoms, 3147 bonds, 398 residues, 3 models selected
> select add #1.3
6188 atoms, 3147 bonds, 796 residues, 3 models selected
> select subtract #1.3
3094 atoms, 3147 bonds, 398 residues, 3 models selected
> select add #1.2
6188 atoms, 3147 bonds, 796 residues, 3 models selected
> show sel cartoons
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99978,0.014188,0.015163,-6.6054,-0.014287,0.99988,0.0064856,1.6848,-0.015069,-0.0067008,0.99986,4.8476,#11,0.99361,-0.095081,0.060843,-51.819,0.11281,0.81729,-0.56508,150.38,0.0040026,0.56833,0.82279,-80.044
> undo
> select add #1
48093 atoms, 49056 bonds, 44 pseudobonds, 6054 residues, 5 models selected
> select subtract #1
3094 atoms, 3147 bonds, 398 residues, 17 models selected
> view matrix models
> #11,0.99586,0.022478,0.088132,-88.412,0.028739,0.84157,-0.53938,159.09,-0.086294,0.53968,0.83744,-53.855
> view matrix models
> #11,0.99548,-0.037805,0.08713,-74.053,0.068288,0.92249,-0.37994,82.64,-0.066013,0.38417,0.9209,-47.932
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.99548,-0.037805,0.08713,-73.915,0.068288,0.92249,-0.37994,82.046,-0.066013,0.38417,0.9209,-47.799
> hide #!4 models
> ui mousemode right select
> select #1/E:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!4 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> select add #1.8
3103 atoms, 8 bonds, 399 residues, 2 models selected
> select subtract #1.2
3094 atoms, 398 residues, 3 models selected
> select add #1.2
6188 atoms, 796 residues, 2 models selected
> style sel stick
Changed 6188 atom styles
> style sel ball
Changed 6188 atom styles
> show sel atoms
> select clear
> hide #!4 models
> ui mousemode right distance
> distance #1/K:133@CE #1/E:133@CE
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
LYS 133 CE and /E LYS 133 CE: 201.434Å
> show #!4 models
> hide #!4 models
> distance #1/K:109@O #1/E:129@SD
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
ASN 109 O and /E MET 129 SD: 196.817Å
> show #!4 models
> hide #!4 models
> distance #1/E:6@OE2 #1/K:6@OE1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/E
GLU 6 OE2 and /K GLU 6 OE1: 68.071Å
> show #!4 models
> hide #!4 models
> distance #1/E:386@OG #1/K:380@O
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/E
SER 386 OG and /K ASN 380 O: 57.837Å
> show #!4 models
> ~distance #1/E:6@OE2 #1/K:6@OE1
> hide #!4 models
> show #!5 models
> distance #1/E:119@OD2 #11/D:119@OD2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/E
ASP 119 OD2 and 7nt5_J377_intactmodel-coot-Chain D.pdb #11/D ASP 119 OD2:
47.182Å
> hide #!5 models
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> select subtract #1.8
1 model selected
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> ui mousemode right select
> select clear
Cell requested for row 3 is out of bounds for table with 36 rows! Resizing
table model.
> open "/Users/kompa012/Desktop/NiP N protein article/NiV N
> protein/cryosparc_P78_J368_map_sharp_zflip.mrc"
Opened cryosparc_P78_J368_map_sharp_zflip.mrc as #22, grid size 360,360,360,
pixel 0.885, shown at level 0.0293, step 2, values float32
> open "/Users/kompa012/Desktop/NiP N protein article/NiV N
> protein/cryosparc_P78_J378_map_sharp.mrc"
Opened cryosparc_P78_J378_map_sharp.mrc as #23, grid size 540,540,540, pixel
1.18, shown at level 0.000682, step 4, values float32
> volume #22 step 1
> volume #23 step 1
> volume #23 level 0.02
> volume #23 level 0.01
> volume #23 level 0.005
> volume #22 level 0.005
> ui tool show "Hide Dust"
> surface dust #23 size 7.08
> surface dust #22 size 5.31
> hide #!22 models
> hide #!23 models
> open "/Users/kompa012/Desktop/NiP N protein article/NiV N
> protein/cryosparc_P78_J365_009_volume_map_zflip.mrc"
Opened cryosparc_P78_J365_009_volume_map_zflip.mrc as #24, grid size
360,360,360, pixel 0.885, shown at level 0.057, step 2, values float32
> open "/Users/kompa012/Desktop/NiP N protein article/NiV N
> protein/cryosparc_P78_J376_007_volume_map.mrc"
Opened cryosparc_P78_J376_007_volume_map.mrc as #25, grid size 540,540,540,
pixel 1.18, shown at level 0.0606, step 4, values float32
> volume #25 step 1
> volume #24 step 1
> surface dust #25 size 7.08
> surface dust #24 size 5.31
> show #!4 models
> select add #4
2 models selected
> transparency #4.1 0
> ui tool show "Fit in Map"
> fitmap #24 inMap #25
Fit map cryosparc_P78_J365_009_volume_map_zflip.mrc in map
cryosparc_P78_J376_007_volume_map.mrc using 465800 points
correlation = -0.2198, correlation about mean = -0.06575, overlap = -110.2
steps = 132, shift = 8.94, angle = 4.2 degrees
Position of cryosparc_P78_J365_009_volume_map_zflip.mrc (#24) relative to
cryosparc_P78_J376_007_volume_map.mrc (#25) coordinates:
Matrix rotation and translation
0.99780797 0.05858614 -0.03077219 -7.79281014
-0.05952998 0.99775410 -0.03070723 9.60438621
0.02890406 0.03247179 0.99905462 -15.91050879
Axis 0.43083465 -0.40694834 -0.80546543
Axis point 192.44365305 181.02496887 -0.00000000
Rotation angle (degrees) 4.20479490
Shift along axis 5.54946317
> fitmap #25 inMap #4
Fit map cryosparc_P78_J376_007_volume_map.mrc in map
cryosparc_P78_J377_009_volume_map.mrc using 1561081 points
correlation = 0.3364, correlation about mean = 0.09368, overlap = 2765
steps = 920, shift = 125, angle = 24.5 degrees
Position of cryosparc_P78_J376_007_volume_map.mrc (#25) relative to
cryosparc_P78_J377_009_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.91014926 0.11060382 -0.39924317 69.60776449
-0.10174970 0.99386392 0.04337639 -70.82033430
0.40159098 0.00114388 0.91581842 -168.30963211
Axis -0.05090794 -0.96534192 -0.25597529
Axis point 372.20045720 0.00000000 104.34372241
Rotation angle (degrees) 24.50628166
Shift along axis 107.90535703
> fitmap #24 inMap #4
Fit map cryosparc_P78_J365_009_volume_map_zflip.mrc in map
cryosparc_P78_J377_009_volume_map.mrc using 465800 points
correlation = 0.4348, correlation about mean = 0.247, overlap = 619.9
steps = 512, shift = 37.7, angle = 24.2 degrees
Position of cryosparc_P78_J365_009_volume_map_zflip.mrc (#24) relative to
cryosparc_P78_J377_009_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.93524401 -0.20583252 0.28801321 20.79887912
0.22087565 0.97508918 -0.02037254 -36.31543750
-0.27664524 0.08266840 0.95740971 58.96551002
Axis 0.14406933 0.78949163 0.59661293
Axis point 196.23870490 0.00000000 -23.33858479
Rotation angle (degrees) 20.95342213
Shift along axis 9.50533225
> select clear
> select add #24
2 models selected
> select add #25
4 models selected
> transparency #24.1#25.1 80
> select clear
> select add #24
2 models selected
> volume #25 level 0.045
> volume #24 level 0.045
> hide #!25 models
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.87152,0.0022541,0.49036,260.94,0.46176,-0.33278,0.82221,-13.963,0.16504,0.943,0.28898,-38.441
> view matrix models
> #24,-0.91842,0.30848,0.24769,261.33,0.12598,-0.36545,0.92227,31.472,0.37502,0.87823,0.29677,-65.22
> view matrix models
> #24,-0.90486,-0.11428,0.41008,296.85,0.12503,-0.99215,-0.00061553,272.69,0.40693,0.050716,0.91205,-43.892
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.90486,-0.11428,0.41008,289.39,0.12503,-0.99215,-0.00061553,191.57,0.40693,0.050716,0.91205,-62.118
> volume flip #24
Opened cryosparc_P78_J365_009_volume_map_zflip.mrc z flip as #26, grid size
360,360,360, pixel 0.885, shown at step 1, values float32
> select add #26
4 models selected
> select subtract #24
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.97406,-0.1093,-0.19812,396.48,0.11038,0.53482,-0.83773,98.258,0.19752,-0.83787,-0.50888,330.61
> view matrix models
> #26,-0.91642,-0.21718,0.33615,318.42,-0.39274,0.6496,-0.65099,133.16,-0.07698,-0.7286,-0.6806,386.12
> close #26
> show #!24 models
> select add #24
2 models selected
> view matrix models
> #24,-0.95518,0.2936,-0.037908,307.71,0.03623,0.24303,0.96934,-133.62,0.29381,0.92452,-0.24277,9.03
> view matrix models
> #24,-0.89474,-0.43232,0.11199,382.95,-0.129,0.01012,-0.99159,241.01,0.42755,-0.90167,-0.064822,233.07
> view matrix models
> #24,-0.98999,-0.037926,-0.13597,379.04,0.1374,-0.03785,-0.98979,203.17,0.032393,-0.99856,0.042682,296.97
> view matrix models
> #24,-0.99884,0.023904,-0.041689,356.23,0.040686,-0.040998,-0.99833,221.26,-0.025574,-0.99887,0.039978,307.19
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.99884,0.023904,-0.041689,409.23,0.040686,-0.040998,-0.99833,391.47,-0.025574,-0.99887,0.039978,410.16
> select subtract #24
Nothing selected
> select add #24
2 models selected
> view matrix models
> #24,-0.99884,0.023904,-0.041689,409.96,0.040686,-0.040998,-0.99833,390.94,-0.025574,-0.99887,0.039978,386.2
> view matrix models
> #24,-0.99884,0.023904,-0.041689,401.41,0.040686,-0.040998,-0.99833,390.33,-0.025574,-0.99887,0.039978,383.98
> ui tool show "Fit in Map"
> fitmap #24 inMap #4
Fit map cryosparc_P78_J365_009_volume_map_zflip.mrc in map
cryosparc_P78_J377_009_volume_map.mrc using 769185 points
correlation = 0.944, correlation about mean = 0.8246, overlap = 8419
steps = 748, shift = 8.88, angle = 11.4 degrees
Position of cryosparc_P78_J365_009_volume_map_zflip.mrc (#24) relative to
cryosparc_P78_J377_009_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.99940571 -0.03170933 0.01351903 404.69380565
-0.01785698 0.14078353 -0.98987935 380.21677427
0.02948515 -0.98953248 -0.14126608 403.68670400
Axis 0.01640811 -0.75523490 0.65524883
Axis point 205.02794506 0.00000000 368.20014476
Rotation angle (degrees) 179.39435513
Shift along axis -15.99747462
> ui mousemode right select
> select clear
> hide #!24 models
> show #!24 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!25 models
> select add #25
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.73962,0.48628,-0.46528,45.354,-0.45912,0.87005,0.17948,37.175,0.4921,0.080871,0.86677,-204.09
> view matrix models
> #25,-0.052947,-0.095059,-0.99406,631.26,-0.21696,0.97277,-0.081467,12.456,0.97474,0.21136,-0.07213,-100.42
> view matrix models
> #25,0.18704,0.054933,-0.98082,507.48,-0.24957,0.96834,0.0066418,-3.5612,0.95012,0.24354,0.19483,-185.7
> hide #!24 models
> hide #!11 models
> hide #!6 models
> hide #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.18704,0.054933,-0.98082,605.14,-0.24957,0.96834,0.0066418,-2.7222,0.95012,0.24354,0.19483,-239.26
> view matrix models
> #25,0.18704,0.054933,-0.98082,597.05,-0.24957,0.96834,0.0066418,-2.9553,0.95012,0.24354,0.19483,-235.92
> volume #25 level 0.03
> volume #25 level 0.06
> view matrix models
> #25,0.18704,0.054933,-0.98082,515.58,-0.24957,0.96834,0.0066418,4.9248,0.95012,0.24354,0.19483,-206.39
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.11397,0.075017,-0.99065,535.28,-0.099952,0.99295,0.063693,-68.338,0.98844,0.091758,0.12067,-145.94
> fitmap #25 inMap #4
Fit map cryosparc_P78_J376_007_volume_map.mrc in map
cryosparc_P78_J377_009_volume_map.mrc using 1586398 points
correlation = 0.6708, correlation about mean = 0.4941, overlap = 7485
steps = 272, shift = 7.06, angle = 3.8 degrees
Position of cryosparc_P78_J376_007_volume_map.mrc (#25) relative to
cryosparc_P78_J377_009_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.06438103 0.07805763 -0.99486787 556.33225021
-0.14405502 0.98722121 0.06813541 -49.59932709
0.98747315 0.13892909 0.07480291 -144.18456320
Axis 0.03546775 -0.99315611 -0.11127880
Axis point 349.53675070 0.00000000 227.45028939
Rotation angle (degrees) 86.37634386
Shift along axis 85.03641208
> hide #!4 models
> show #!1 models
> ui mousemode right select
> select clear
> show #!11 models
> show #!5 models
> show #!4 models
> hide #!25 models
> hide #!5 models
> hide #!4 models
> show #!20 models
> show #!19 models
> show #!18 models
> hide #!20 models
> show #!17 models
> show #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!14 models
> show #!13 models
> show #!10 models
> show #!9 models
> show #!8 models
> hide #!13 models
> hide #!15 models
Drag select of 2111 atoms, 1603 residues, 1761 bonds
> hide sel atoms
> hide sel cartoons
> select clear
> hide #!1 models
> show #!1 models
> show #!3 models
> select add #3
40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 2 models selected
> select subtract #3.9
37221 atoms, 37986 bonds, 2 pseudobonds, 4801 residues, 16 models selected
> hide sel cartoons
> select subtract #3.15
35665 atoms, 36275 bonds, 2 pseudobonds, 4723 residues, 15 models selected
> select add #3
40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 14 models selected
> select subtract #3
14 models selected
> select add #3.15
1556 atoms, 78 residues, 1 model selected
> show sel cartoons
> select #3 /n: 1-40
796 atoms, 875 bonds, 40 residues, 1 model selected
> hide sel cartoons
> select #3 /n: 51-78
560 atoms, 615 bonds, 28 residues, 1 model selected
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
> show #!7 models
> hide #!7 models
> hide #!9 models
> show #!9 models
> select add #14
6056 atoms, 6171 bonds, 758 residues, 2 models selected
> select subtract #14
5 models selected
> show #!15 models
> show #!20 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> select #20 /f: 1001-1020
400 atoms, 439 bonds, 20 residues, 1 model selected
> select #20 /f: 1001-1026
520 atoms, 571 bonds, 26 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select subtract #20.6
1 model selected
> select add #20.6
700 atoms, 35 residues, 1 model selected
> hide sel atoms
> select clear
> lighting flat
> lighting simple
> lighting flat
Drag select of 60 residues, 10 atoms, 8 bonds
> hide sel atoms
Drag select of 220 residues, 30 atoms, 31 bonds
> hide sel atoms
Drag select of 61 residues, 3 atoms, 3 bonds
> hide sel atoms
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein
> overlay.png" width 3000 height 2926 supersample 3 transparentBackground true
> lighting full
> select clear
Cell requested for row 13 is out of bounds for table with 31 rows! Resizing
table model.
> hide #!14 models
> hide #!16 models
> hide #!17 models
> hide #!15 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!3 models
> select #1 /k: 104-121
131 atoms, 131 bonds, 18 residues, 1 model selected
> select #1 /k: 148-153
46 atoms, 46 bonds, 6 residues, 1 model selected
> select #1 /k: 157-176
154 atoms, 155 bonds, 20 residues, 1 model selected
> select #1 /k: 186-200
132 atoms, 134 bonds, 15 residues, 1 model selected
> select #1 /k: 210-224
127 atoms, 128 bonds, 15 residues, 1 model selected
> select #1 /k: 225-240
134 atoms, 134 bonds, 16 residues, 1 model selected
> select #1 /k: 246-260
114 atoms, 114 bonds, 15 residues, 1 model selected
> select #1 /k: 264-275
93 atoms, 95 bonds, 12 residues, 1 model selected
> select #1 /k: 279-284
45 atoms, 46 bonds, 6 residues, 1 model selected
> select #1 /k: 285-287
28 atoms, 28 bonds, 3 residues, 1 model selected
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison1.cxs"
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/dimer close
> 44-49.cxs" format session
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.044, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
> set bgColor #ffffff00
opened ChimeraX session
> select #1/K:349@CA
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> ui mousemode right distance
> distance #1/Z:45@O2' #1/K:349@N
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z
U 45 O2' and /K ASN 349 N: 3.275Å
> distance #1/K:349@ND2 #1/Z:45@O2
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
ASN 349 ND2 and /Z U 45 O2: 4.187Å
> ui mousemode right select
> select #1/K:263
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1 /k: 263
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1 /k: 178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 192
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!4 models
> select #1 /k: 193
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1 /k: 258
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1 /k: 196
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 200
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 199
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> select subtract #1.8
1 model selected
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> select subtract #1.9
1 model selected
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> transparency (#!1 & sel) 70
> transparency (#!1 & sel) 50
> transparency (#!1 & sel) 80
> select clear
> show #!4 models
> hide #!4 models
> select clear
> set bgColor black
> set bgColor transparent
> hide #!5 models
> select #1 /k: 352
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1 /k: 265
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> select add #1.9
3099 atoms, 4 bonds, 399 residues, 4 models selected
> select subtract #1.8
3094 atoms, 398 residues, 5 models selected
> transparency (#!1 & sel) 80
> transparency (#!1 & sel) 70
> select clear
> select #1 /k: 349
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1 /k: 344
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1 /k: 178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 192
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1 /k: 193
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1 /k: 258
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1 /k: 196
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Monomer_44-49
> zoom.png" width 3000 height 2926 supersample 3 transparentBackground true
> select #1 /k: 196
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 199
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 200
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /l: 352
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1 /l: 265
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #1 /l: 349
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1 /l: 178
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1 /l: 344
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select add #1
44999 atoms, 45909 bonds, 28 pseudobonds, 5656 residues, 5 models selected
> select subtract #1
15 models selected
> ui mousemode right distance
> distance #1/L:344@O #1/Z:52@O2'
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L
SER 344 O and /Z U 52 O2': 2.742Å
> show #!1 cartoons
> undo
> select #1 /l: 344
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1 /l: 178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /l: 192
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1 /l: 193
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1 /l: 258
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1 /l: 196
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1 /l: 199
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1 /l: 200
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> ui mousemode right select
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Monomer_49-53
> zoom.png" width 3000 height 2926 supersample 3 transparentBackground true
> select #1 /l: 196
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /l: 192
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1 /l: 193
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1 /l: 192
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select add #1.9
3094 atoms, 398 residues, 3 models selected
> hide sel surfaces
> select clear
> select #1 /l: 178
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right distance
> distance #1/L:178@NZ #1/Z:52@OP1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L
LYS 178 NZ and /Z U 52 OP1: 2.932Å
> ui mousemode right select
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Monomer_49-53
> zoom.png" width 3000 height 2926 supersample 3 transparentBackground true
> show #!1 surfaces
> undo
> redo
> undo
> select add #1.9
3094 atoms, 8 bonds, 398 residues, 4 models selected
> select add #1
44999 atoms, 45909 bonds, 30 pseudobonds, 5656 residues, 9 models selected
> hide sel surfaces
> select subtract #1
15 models selected
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> select add #1.9
6188 atoms, 796 residues, 4 models selected
> select subtract #1.8
3094 atoms, 398 residues, 5 models selected
> show sel surfaces
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Monomer_49-53
> zoom.png" width 3000 height 2926 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/dimer close
> 44-49.cxs"
> select #1 /k: 196
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 178
9 atoms, 8 bonds, 1 residue, 1 model selected
Cell requested for row 0 is out of bounds for table with 28 rows! Resizing
table model.
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/dimer close
> 44-49.cxs"
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison.cxs" format session
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.03, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.04, step 1, values float32
opened ChimeraX session
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/NT core
> interactions.png" width 3000 height 3044 supersample 3 transparentBackground
> true
> hide #!4 models
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison1.cxs" format session
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J368_map_sharp_zflip.mrc as #22, grid size 360,360,360,
pixel 0.885, shown at level 0.005, step 1, values float32
Opened cryosparc_P78_J378_map_sharp.mrc as #23, grid size 540,540,540, pixel
1.18, shown at level 0.005, step 1, values float32
Opened cryosparc_P78_J365_009_volume_map_zflip.mrc as #24, grid size
360,360,360, pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J376_007_volume_map.mrc as #25, grid size 540,540,540,
pixel 1.18, shown at level 0.06, step 1, values float32
opened ChimeraX session
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #!13 models
> hide #!13 models
> show #!10 models
> show #!9 models
> show #!8 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Helix 16.png"
> width 3000 height 3044 supersample 3 transparentBackground true
> hide #!9 models
> hide #!20 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!9 models
> hide #!14 models
> hide #!9 models
> show #!9 models
> show #!14 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Helix 5.png"
> width 3000 height 3044 supersample 3 transparentBackground true
> select add #1.4
3122 atoms, 28 bonds, 401 residues, 1 model selected
> select subtract #1.4
28 atoms, 28 bonds, 3 residues, 3 models selected
> select add #1.3
3122 atoms, 28 bonds, 401 residues, 2 models selected
> select subtract #1.3
28 atoms, 28 bonds, 3 residues, 3 models selected
> select add #1.2
3122 atoms, 28 bonds, 401 residues, 2 models selected
> select subtract #1.2
28 atoms, 28 bonds, 3 residues, 3 models selected
> select add #1.1
3122 atoms, 28 bonds, 401 residues, 2 models selected
> select subtract #1.1
28 atoms, 28 bonds, 3 residues, 3 models selected
> select subtract #1.8
1 model selected
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> select subtract #1.8
1 model selected
> select #1 /k: 352
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 9 residues
> select clear
Drag select of 15 residues
> show sel atoms
> hide sel atoms
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> select clear
> hide #!15 models
> select #1 /k: 352
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #9 /k: 309
Nothing selected
> select #9 /a: 309
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!10 models
> hide #!8 models
> hide #!14 models
> hide #!16 models
> hide #!17 models
> show #!20 models
> hide #!19 models
> hide #!18 models
> hide #!1 models
> show #!1 models
> hide #!9 models
> show #!9 models
> select add #9
5664 atoms, 5763 bonds, 720 residues, 2 models selected
> select subtract #9
2 models selected
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!20 models
> hide #!9 models
> hide #!1 models
> select #13 /r: 1-38
760 atoms, 835 bonds, 38 residues, 1 model selected
> hide sel cartoons
> show #!1 models
> hide #!13 models
> select add #13
17432 atoms, 17883 bonds, 3 pseudobonds, 2146 residues, 3 models selected
> select subtract #13
6 models selected
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> select #1 /u: 44-49
Nothing selected
> show #!1 cartoons
> undo
> select #1 /z: 44-49
120 atoms, 131 bonds, 6 residues, 1 model selected
> show sel cartoons
Cell requested for row 12 is out of bounds for table with 40 rows! Resizing
table model.
> select add #1
44999 atoms, 45909 bonds, 47 pseudobonds, 5656 residues, 3 models selected
> show #!13 models
> select clear
> hide #!13 models
> hide #!1 models
> show #!25 models
> show #!24 models
> show #!4 models
> hide #!25 models
> hide #!24 models
> volume #25 level 0.045
> show #!25 models
> show #!24 models
> hide #!25 models
> hide #!24 models
> show #!24 models
> hide #!4 models
> select add #24
2 models selected
> select add #25
4 models selected
> show #!25 models
> transparency #24.1#25.1 0
> hide #!25 models
> select subtract #25
2 models selected
> show #!4 models
> hide #!24 models
> select subtract #24
Nothing selected
> select add #4
2 models selected
> transparency #4.1 0
> hide #!4 models
> select subtract #4
Nothing selected
> show #!24 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/540 box.png"
> width 3000 height 3044 supersample 3 transparentBackground true
> hide #!24 models
> show #!25 models
> volume #25 level 0.06
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/960 box.png"
> width 3000 height 3044 supersample 3 transparentBackground true
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!1 models
> hide #!1 models
> show #!4 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> select add #25
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.064381,0.078058,-0.99487,497.35,-0.14406,0.98722,0.068135,-46.639,0.98747,0.13893,0.074803,-140.82
> ui mousemode right select
> select clear
> hide #!25 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/720 box.png"
> width 3000 height 3044 supersample 3 transparentBackground true
> show #!25 models
> hide #!4 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/960 box.png"
> width 3000 height 2926 supersample 3 transparentBackground true
> show #!4 models
> hide #!25 models
> show #!1 models
> select add #4
2 models selected
> transparency #4.1 80
> show #!11 models
> select add #11
3094 atoms, 3147 bonds, 398 residues, 3 models selected
> select subtract #4
3094 atoms, 3147 bonds, 398 residues, 2 models selected
> show sel cartoons
> select add #1
48093 atoms, 49056 bonds, 47 pseudobonds, 6054 residues, 4 models selected
> select subtract #11
44999 atoms, 45909 bonds, 47 pseudobonds, 5656 residues, 18 models selected
> show sel cartoons
> select clear
> volume #4 level 0.03
> hide #!4 models
> select #1 /f-p
34034 atoms, 34617 bonds, 18 pseudobonds, 4378 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1 /z :15-75
1223 atoms, 1345 bonds, 61 residues, 1 model selected
> hide sel cartoons
> show #!5 models
> hide #!5 models
> show #!4 models
> volume #4 level 0.035
> volume #4 level 0.038
> hide #!1 models
> hide #!11 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/layers
> interaction map 720.png" width 3000 height 2926 supersample 3
> transparentBackground true
> show #!1 models
> show #!11 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/layers
> interaction map 720 prot.png" width 3000 height 2926 supersample 3
> transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/layers
> interaction map 720 prot zoom.png" width 3000 height 2926 supersample 3
> transparentBackground true
> hide #!4 models
> open 4co6 fromDatabase pdb format mmcif
Summary of feedback from opening 4co6 fetched from pdb
---
notes | Fetching compressed mmCIF 4co6 from http://files.rcsb.org/download/4co6.cif
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif
Fetching CCD BR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/BR/BR.cif
4co6 title:
Crystal structure of the Nipah virus RNA free nucleoprotein- phosphoprotein
complex [more info...]
Chain information for 4co6 #26
---
Chain | Description | UniProt
A B C | NUCLEOPROTEIN | NCAP_NIPAV 32-383
D E F | PHOSPHOPROTEIN | PHOSP_NIPAV 1-50
Non-standard residues in 4co6 #26
---
BR — bromide ion
CL — chloride ion
4co6 mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 models
> hide #!26 models
> show #!26 models
> hide #!11 models
> ui tool show Matchmaker
> matchmaker #26/A to #11/D pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-Chain D.pdb, chain D (#11) with 4co6,
chain A (#26), sequence alignment score = 1661.4
RMSD between 202 pruned atom pairs is 0.799 angstroms; (across all 330 pairs:
4.701)
> show #!11 models
> select add #26
8863 atoms, 8996 bonds, 10 pseudobonds, 1139 residues, 4 models selected
> select add #1
52639 atoms, 53560 bonds, 57 pseudobonds, 6734 residues, 5 models selected
> select subtract #1
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 17 models selected
> style sel stick
Changed 7640 atom styles
> show sel cartoons
> hide sel atoms
> select clear
> select add #26
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #26.2
5046 atoms, 5009 bonds, 8 pseudobonds, 748 residues, 8 models selected
> hide sel cartoons
> select add #26
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 7 models selected
> select subtract #26
6 models selected
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!26 models
> select add #26.2
2594 atoms, 330 residues, 1 model selected
> select subtract #26.2
1 model selected
> show #!26 models
> select add #26.2
2594 atoms, 330 residues, 1 model selected
> color (#!26 & sel) forest green
> select clear
> matchmaker #26/A to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 4co6, chain A (#26), sequence alignment score = 1669.8
RMSD between 202 pruned atom pairs is 0.769 angstroms; (across all 330 pairs:
4.712)
> hide #!11 models
> show #!1 models
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> show sel cartoons
> select clear
> select #1 /z :44-49
120 atoms, 131 bonds, 6 residues, 1 model selected
> show sel cartoons
> select clear
> show #!20 models
> hide #!20 models
> show #!19 models
> show #!18 models
> hide #!26 models
> show #!4 models
> hide #!4 models
> hide #!19 models
> hide #!18 models
> show #!26 models
> lighting flat
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/RNA bound and
> unbound.png" width 3000 height 2926 supersample 3 transparentBackground true
> lighting full
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!11 models
> hide #!11 models
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> coulombic sel
Coulombic values for 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb_K
SES surface #1.8: minimum, -15.77, mean -0.30, maximum 13.72
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!26 models
> select add #1.9
6188 atoms, 796 residues, 2 models selected
> show sel surfaces
> coulombic sel
Coulombic values for 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb_K
SES surface #1.8: minimum, -15.77, mean -0.30, maximum 13.72
Coulombic values for 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb_L
SES surface #1.9: minimum, -16.04, mean -0.34, maximum 14.15
To also show corresponding color key, enter the above coulombic command and
add key true
> select #1 /z :44-55
240 atoms, 263 bonds, 12 residues, 1 model selected
> show sel cartoons
> show sel surfaces
> select clear
> select #1 /z :44-55
240 atoms, 263 bonds, 12 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
Drag select of 1217 residues
> hide sel cartoons
> ui mousemode right "color key"
> key blue-white-red :min : :m
> key blue-white-red :min : :mi
> key blue-white-red :min : :min
> key blue-white-red :min : :minu
> key blue-white-red :min : :minus
> key blue-white-red :min : :-
> key blue-white-red :min : :-1
> key blue-white-red :min : :-15
> key blue-white-red :min : :-15,
> key blue-white-red :min : :-15,7
> key blue-white-red :min : :-15,
> key blue-white-red :min : :-15
> key blue-white-red :min : :-1
> key blue-white-red :min : :-16
> key blue-white-red :mi : :-16
> key blue-white-red :m : :-16
> key blue-white-red : : :-16
> key blue-white-red : : :n
> key blue-white-red : : :ne
> key blue-white-red : : :neg
> key blue-white-red : : :nega
> key blue-white-red : : :negat
> key blue-white-red : : :negati
> key blue-white-red : : :negativ
> key blue-white-red : : :negative
> key blue-white-red : : :-
> key blue-white-red : : :-1
> key blue-white-red : : :-16
> key blue-white-red :1 : :-16
> key blue-white-red :15 : :-16
> key blue-white-red :15 : ":-16 "
> key blue-white-red :15 : ":-16 kcal/(mol·e)"
> key blue-white-red :15kcal/(mol·e) : ":-16 kcal/(mol·e)"
> key blue-white-red :15kcal/(mol·e) : ":-16 "
> key blue-white-red ":15 kcal/(mol·e)" : ":-16 "
> key blue-white-red ":15 kcal/(mol·e) " : ":-16 "
> key blue-white-red ":15 kcal/(mol·e) " : ":-16 "
> key blue-white-red ":15 kcal/(mol·e) " : ":-16 kcal/(mol·e)"
> key blue-white-red ":15 kcal/(mol·e) " : ": -16 kcal/(mol·e)"
> key blue-white-red ":15 kcal/(mol·e) " : ": -16 kcal/(mol·e) "
> key blue-white-red ":15 kcal/(mol·e) " : ": -16 kcal/(mol·e) "
> key blue-white-red ":15 kcal/(mol·e) " : ": -16 kcal/(mol·e) "
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key size 0.25000,0.04000
> key pos 0.383786,0.0828935
> save "/Users/kompa012/Desktop/NiP N protein
> article/Figures/electrostatic.png" width 3000 height 2926 supersample 3
> transparentBackground true
> ui mousemode right select
> select clear
> ui mousemode right "color key"
> key delete
> ui mousemode right select
> select #1 /z :44-55
240 atoms, 263 bonds, 12 residues, 1 model selected
> hide sel atoms
> hide sel surfaces
> select add #1.9
3334 atoms, 263 bonds, 410 residues, 2 models selected
> hide sel surfaces
> show sel surfaces
> select #1 /z :44-55
240 atoms, 263 bonds, 12 residues, 1 model selected
> hide sel surfaces
> show sel atoms
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/electrostatic
> zoom.png" width 3000 height 2926 supersample 3 transparentBackground true
> hide #1.9 models
> select #1 /z :44-55
240 atoms, 263 bonds, 12 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> ui mousemode right distance
> distance #1/K:178@NZ #1/K:348@CD1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
LYS 178 NZ and LEU 348 CD1: 9.165Å
> show #!6 models
> show #6.1 models
> hide #6.1 models
> select add #1.8
3334 atoms, 263 bonds, 410 residues, 2 models selected
> show sel atoms
> select #1 /z :44-55
240 atoms, 263 bonds, 12 residues, 1 model selected
> hide sel atoms
> distance #1/K:348@CD1 #1/K:182@CB
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
LEU 348 CD1 and ALA 182 CB: 9.238Å
> hide #!6 models
> distance #1/K:192@NH1 #1/K:261@CD
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
ARG 192 NH1 and GLU 261 CD: 17.913Å
> show #!6 models
> distance #1/K:192@NH1 #1/K:262@CA
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
ARG 192 NH1 and THR 262 CA: 15.039Å
> distance #1/K:261@O #1/K:192@NH1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
GLU 261 O and ARG 192 NH1: 15.714Å
> hide #!6 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/electrostatic
> zoomside chanel.png" width 3000 height 2926 supersample 3
> transparentBackground true
> show #!6 models
> select add #1.8
3334 atoms, 263 bonds, 410 residues, 2 models selected
> hide sel surfaces
> hide sel atoms
> ui mousemode right select
> select clear
> show #!26 models
> select #1 /z :44-49
120 atoms, 131 bonds, 6 residues, 1 model selected
> show sel atoms
> select clear
> lighting flat
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/RNA bound and
> unbound.png" width 3000 height 2926 supersample 3 transparentBackground true
> turn y -90
> turn y 90
> turn y -120
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/RNA bound and
> unbound 120 turn.png" width 3000 height 2926 supersample 3
> transparentBackground true
> hide #!26 models
> show #!25 models
> hide #!25 models
> show #!20 models
> show #!19 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #!13 models
> hide #!13 models
> show #!10 models
> show #!9 models
> show #!8 models
> hide #!9 models
> show #!9 models
> select #1 /z :44-49
120 atoms, 131 bonds, 6 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein
> overlay.png" width 3000 height 2926 supersample 3 transparentBackground true
> hide #!20 models
> show #!20 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!14 models
> hide #!20 models
> hide #!9 models
> hide #!10 models
> show #!10 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein overlay
> h5 one family.png" width 3000 height 2926 supersample 3
> transparentBackground true
> show #!14 models
> show #!20 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!10 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!1 models
> show #!1 models
> select add #20
14785 atoms, 15089 bonds, 1845 residues, 1 model selected
> color (#!20 & sel) orange
> select clear
> color #14,20#1.1-8,10-15#!1,6 cornflower blue
> undo
> select add #20
14785 atoms, 15089 bonds, 1845 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cyan
> color sel light sea green
> color sel light sky blue
> color sel sky blue
> color sel light blue
> color sel pale turquoise
> color sel light blue
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein overlay
> h5 pneumo family.png" width 3000 height 2926 supersample 3
> transparentBackground true
> show #!9 models
> hide #!14 models
> hide #!20 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!8 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein overlay
> h5 ebola family.png" width 3000 height 2926 supersample 3
> transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein overlay
> h16 ebola family.png" width 3000 height 2926 supersample 3
> transparentBackground true
> hide #!9 models
> show #!14 models
> show #!20 models
> hide #!1 models
> show #!1 models
> show #!9 models
> hide #!9 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein overlay
> h16 pneumo family.png" width 3000 height 2926 supersample 3
> transparentBackground true
> hide #!14 models
> show #!15 models
> show #!16 models
> show #!17 models
> show #!18 models
> show #!19 models
> hide #!20 models
> show #!8 models
> show #!10 models
> show #!20 models
> hide #!20 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein overlay
> h16 one family.png" width 3000 height 2926 supersample 3
> transparentBackground true
> select #1 /k: 352
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 11 atom styles
> hide sel atoms
> select #1 /k: 258
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 12 atom styles
> hide sel atoms
> show #!9 models
> show #!20 models
> show #!14 models
> show sel atoms
> style sel stick
Changed 12 atom styles
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> style sel sphere
Changed 12 atom styles
> show sel atoms
> select clear
> select #1 /k: 258
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!10 models
> hide #!19 models
> hide #!8 models
> hide #!1 models
Drag select of 14 residues
Drag select of 6 residues
> show sel atoms
> color (#!9,14,20 & sel) byhetero
> select add #12
41 atoms, 6 residues, 8 models selected
> hide #!14 models
> select subtract #12
41 atoms, 6 residues, 6 models selected
> hide #!20 models
> style sel & #!9 sphere
Changed 14 atom styles
> show #!14 models
> show #!20 models
> show #!1 models
> style sel sphere
Changed 41 atom styles
> style sel stick
Changed 41 atom styles
> select clear
> select #1 /k: 178
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 4 residues
> show sel atoms
> style sel stick
Changed 36 atom styles
> select #1 /k: 193
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 8 residues
Drag select of 7 residues
> show sel atoms
> style sel stick
Changed 78 atom styles
> ui mousemode right distance
> ~distance #1/K:192@NH1 #1/K:262@CA
> ~distance #1/K:261@O #1/K:192@NH1
> ui mousemode right select
> select clear
> select #1 /k: 199
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 120
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 200
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 196
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/K:193
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1 /k: 194
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!14 models
> hide #!20 models
> select #1 /z :44-51
160 atoms, 175 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #1 /k: 199
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 2 atoms, 4 residues, 2 bonds
> show sel atoms
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein overlay
> DNA ebola family.png" width 3000 height 2926 supersample 3
> transparentBackground true
> hide #!9 models
> show #!20 models
> show #!14 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein overlay
> DAN pneumo family.png" width 3000 height 2926 supersample 3
> transparentBackground true
> hide #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!12 models
> hide #!12 models
> hide #!14 models
> show #!8 models
> show #!10 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein overlay
> dna one family.png" width 3000 height 2926 supersample 3
> transparentBackground true
> show #!9 models
> show #!20 models
> show #!14 models
Drag select of 7 atoms, 20 residues, 6 bonds
> hide sel atoms
Drag select of 23 atoms, 71 residues, 20 bonds
> hide sel atoms
Drag select of 4 atoms, 39 residues
> hide sel atoms
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein overlay
> dna y 258 all.png" width 3000 height 2926 supersample 3
> transparentBackground true
> hide #!10 models
> hide #!8 models
> hide #!14 models
> hide #!15 models
> show #!14 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!14 models
> hide #!20 models
> hide #!9 models
> show #!14 models
> show #!20 models
> show #!26 models
> hide #!20 models
> hide #!14 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/angle
> measurement.png" width 609 height 594 supersample 3 transparentBackground
> true
> show #!14 models
> show #!20 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/angle
> measurement ncore.png" width 609 height 594 supersample 3
> show #!9 models
> hide #!20 models
> hide #!14 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/angle
> measurement ncore eb.png" width 609 height 594 supersample 3
> hide #!26 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #!8 models
> show #!10 models
> select #1 /k: 349
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 8 atom styles
> hide sel atoms
> select #1 /k: 344
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1 /k: 354
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1 /k: 348
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1.9
3102 atoms, 7 bonds, 399 residues, 2 models selected
> show #1.9 models
> show sel surfaces
> select clear
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> select add #1.8
6188 atoms, 796 residues, 2 models selected
> show sel surfaces
> select #1 /k: 258
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 12 atom styles
> hide sel surfaces
> select subtract #1.8
1 model selected
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> hide sel surfaces
> select subtract #1.8
1 model selected
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> show sel surfaces
> select #1 /l: 258
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 12 atom styles
> select subtract #1.9
1 model selected
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> select add #1.8
6188 atoms, 796 residues, 2 models selected
> select subtract #1.9
3094 atoms, 398 residues, 3 models selected
> hide sel surfaces
> select #1 /k: 258
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #1.9
3106 atoms, 12 bonds, 399 residues, 2 models selected
> select subtract #1.9
12 atoms, 12 bonds, 1 residue, 3 models selected
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> show #!26 models
> select #1 /k: 324
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1 /z: 43-55
260 atoms, 285 bonds, 13 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> select #1 /k: 345
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!5 models
> select #1 /k: 258
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #1 /k: 354
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1 /z: 41-55
300 atoms, 329 bonds, 15 residues, 1 model selected
> show sel atoms
> select #1 /k: 181
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> style sel sphere
Changed 7 atom styles
> style sel sphere
Changed 7 atom styles
> select #1 /k: 185
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1 /k: 181
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 7 atom styles
> color (#!1 & sel) byhetero
> select #1 /k: 189
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select #1 /k: 319
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select #1/K:319@NE2
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> distance #1/K:319@NE2 #1/Z:43@O2'
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
GLN 319 NE2 and /Z U 43 O2': 3.667Å
> hide #!26 models
> select #1 /k: 181
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel THR rotLib Dunbrack
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K THR 181: phi
-106.7, psi 115.7 trans
Changed 12 bond radii
> select add #1.16
22 atoms, 18 bonds, 4 residues, 6 models selected
> style sel ball
Changed 22 atom styles
> color (#1.16.1-3#!1 & sel) byhetero
> hide #1.16.3 models
> show #1.16.3 models
> hide #1.16.2 models
> show #1.16.2 models
> hide #1.16.1 models
> hide #1.16.2 models
> hide #1.16.3 models
> show #1.16.3 models
> select #1 /k: 324
7 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1 /k: 348
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1 /k: 345
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!5 models
> select #1 /k: 320
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1 /k: 312
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
40207 atoms, 41022 bonds, 2 pseudobonds, 5197 residues, 4 models selected
> show sel atoms
> style sel stick
Changed 40207 atom styles
> select subtract #3
7 atoms, 6 bonds, 1 residue, 16 models selected
> select #1 /k: 312
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #!3 models
> show #!3 models
> select add #3
40207 atoms, 41022 bonds, 2 pseudobonds, 5197 residues, 4 models selected
> hide sel cartoons
> color (#!1,3 & sel) byhetero
> select subtract #3
7 atoms, 6 bonds, 1 residue, 16 models selected
> hide #!3 models
> show sel cartoons
> hide sel atoms
> select #1 /k: 319
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 /k: 181
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> ui mousemode right distance
> distance #1/K:319@NE2 #1/Z:44@OP1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
GLN 319 NE2 and /Z U 44 OP1: 3.770Å
> show #!26 models
> hide #!1 models
> select add #26.1
7 atoms, 6 bonds, 10 pseudobonds, 1 residue, 3 models selected
> select subtract #26.1
7 atoms, 6 bonds, 1 residue, 2 models selected
> select add #26.2
2601 atoms, 6 bonds, 331 residues, 3 models selected
> select subtract #26.2
7 atoms, 6 bonds, 1 residue, 3 models selected
> select add #26.3
2581 atoms, 6 bonds, 325 residues, 3 models selected
> select add #26.4
4020 atoms, 6 bonds, 525 residues, 4 models selected
> select add #26.5
4337 atoms, 6 bonds, 565 residues, 5 models selected
> select add #26.7
4636 atoms, 6 bonds, 602 residues, 6 models selected
> select add #26.6
4945 atoms, 6 bonds, 641 residues, 7 models selected
> show sel & #!26 cartoons
> select subtract #26.3
2371 atoms, 6 bonds, 317 residues, 8 models selected
> select subtract #26.5
2054 atoms, 6 bonds, 277 residues, 7 models selected
> hide sel & #!26 cartoons
> select add #26.3
4628 atoms, 6 bonds, 601 residues, 6 models selected
> hide sel & #!26 cartoons
> show #!1 models
> select add #1.9
7722 atoms, 6 bonds, 999 residues, 7 models selected
> hide sel surfaces
> show sel cartoons
> select subtract #1.8
7715 atoms, 998 residues, 8 models selected
> hide sel cartoons
> select #1 /k: 181
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1 /k: 319
9 atoms, 8 bonds, 1 residue, 1 model selected
Cell requested for row 29 is out of bounds for table with 49 rows! Resizing
table model.
> show #!5 models
Cell requested for row 23 is out of bounds for table with 34 rows! Resizing
table model.
> hide #!5 models
> select #1 /k: 267
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1 /k: 268
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1 /k: 301
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!26 models
> select add #1.9
3106 atoms, 12 bonds, 399 residues, 2 models selected
> show sel cartoons
> ui mousemode right select
> select clear
Cell requested for row 23 is out of bounds for table with 42 rows! Resizing
table model.
> hide #!6 models
> show #!6 models
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> select add #1.9
6188 atoms, 796 residues, 2 models selected
> show sel atoms
> select clear
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #!10 models
> show #!19 models
> hide #!10 models
> select add #19.2
4774 atoms, 482 residues, 3 models selected
> show sel cartoons
> hide sel cartoons
> select clear
> select add #19.1
1680 atoms, 84 residues, 1 model selected
> show sel cartoons
> hide #!19 models
> select clear
Cell requested for row 10 is out of bounds for table with 57 rows! Resizing
table model.
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> select add #1.8
6188 atoms, 796 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> show #!13 models
> hide #!1 models
> select add #13.7
900 atoms, 45 residues, 1 model selected
> show sel cartoons
> select add #13.3
4190 atoms, 460 residues, 2 models selected
> show sel cartoons
> select add #13.4
7465 atoms, 873 residues, 3 models selected
> show sel cartoons
> select add #13.2
10792 atoms, 1294 residues, 4 models selected
> select subtract #13.3
7502 atoms, 879 residues, 5 models selected
> select subtract #13.4
4227 atoms, 466 residues, 4 models selected
> select subtract #13.7
3327 atoms, 421 residues, 3 models selected
> hide sel cartoons
> select subtract #13.2
1 model selected
> select add #13.6
3327 atoms, 421 residues, 1 model selected
> select subtract #13.6
1 model selected
> select add #13.2
3327 atoms, 421 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select subtract #13.2
1 model selected
> select add #13.7
900 atoms, 45 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 900 atom styles
> style sel ball
Changed 900 atom styles
> select clear
> select add #13.7
900 atoms, 45 residues, 1 model selected
> color (#!13 & sel) byhetero
> select clear
> select #13/B:230
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #13/B:290
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #13/B:223
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #13/B:317
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #13.4
3286 atoms, 10 bonds, 414 residues, 2 models selected
> select add #13.2
6613 atoms, 10 bonds, 835 residues, 3 models selected
> select add #13.5
9911 atoms, 10 bonds, 1251 residues, 4 models selected
> select add #13.6
13238 atoms, 10 bonds, 1672 residues, 5 models selected
> select subtract #13.6
9911 atoms, 10 bonds, 1251 residues, 6 models selected
> show #!1 models
> hide #!1 models
> hide sel cartoons
> hide sel atoms
> select add #13.6
13238 atoms, 10 bonds, 1672 residues, 5 models selected
> select subtract #13.6
9911 atoms, 10 bonds, 1251 residues, 6 models selected
> select subtract #13.5
6613 atoms, 10 bonds, 835 residues, 5 models selected
> select add #13.5
9911 atoms, 10 bonds, 1251 residues, 4 models selected
> select subtract #13.4
6636 atoms, 10 bonds, 838 residues, 5 models selected
> select add #13.4
9911 atoms, 10 bonds, 1251 residues, 4 models selected
> select subtract #13.3
9900 atoms, 1250 residues, 5 models selected
> select add #13.3
13190 atoms, 1665 residues, 4 models selected
> select subtract #13.2
9863 atoms, 1244 residues, 5 models selected
> hide sel cartoons
> hide sel atoms
> select add #13
17432 atoms, 17883 bonds, 3 pseudobonds, 2146 residues, 5 models selected
> select subtract #13
6 models selected
> show #!1 models
> select #1 /k: 258
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide #!13 models
> show #!11 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> select add #1
44999 atoms, 45909 bonds, 52 pseudobonds, 5656 residues, 3 models selected
> select subtract #1
15 models selected
> show #!26 models
> show #!1 models
> hide #!26 models
> show #!26 models
> hide #!11 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!9 models
> show #!1 models
> hide #1.9 models
> show #1.9 models
> hide #1.8 models
> show #1.8 models
> select add #1.8
3094 atoms, 398 residues, 1 model selected
> select subtract #1.8
1 model selected
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> hide sel cartoons
> hide #!1 models
> show #!1 models
> hide #!26 models
> select add #9.2
6028 atoms, 771 residues, 3 models selected
> show sel cartoons
> hide sel cartoons
> select clear
> select add #9.2
2934 atoms, 373 residues, 1 model selected
> show sel cartoons
> hide #!9 models
> open 9CGI fromDatabase pdb format mmcif
Summary of feedback from opening 9CGI fetched from pdb
---
note | Fetching compressed mmCIF 9cgi from http://files.rcsb.org/download/9cgi.cif
9cgi title:
Cryo-EM structure of the Nipah Virus polymerase (L) protein in complex with
the tetrameric phosphoprotein (P) [more info...]
Chain information for 9cgi #28
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase L | L_NIPAV 1-2244
B C D E | Phosphoprotein | PHOSP_NIPAV 1-709
> show #!9 models
> select clear
> select add #9.2
2934 atoms, 373 residues, 1 model selected
> hide sel cartoons
> select add #9
5664 atoms, 5763 bonds, 720 residues, 2 models selected
> select subtract #9
2 models selected
> select #9 /a: 26-44
52 atoms, 53 bonds, 6 residues, 1 model selected
> hide #!1 models
> select #9 /a: 22-37
Nothing selected
Cell requested for row 11 is out of bounds for table with 45 rows! Resizing
table model.
> select #9 /a: 281-296
119 atoms, 122 bonds, 16 residues, 1 model selected
> select #9 /a: 247-258
97 atoms, 97 bonds, 12 residues, 1 model selected
> select #9 /a: 20-37
Nothing selected
> select #9 /a: 40-50
90 atoms, 91 bonds, 11 residues, 1 model selected
> select #9 /a: 274-291
133 atoms, 134 bonds, 18 residues, 1 model selected
> show #!1 models
> select #9 /a: 245-254
80 atoms, 80 bonds, 10 residues, 1 model selected
> select add #1.9
3174 atoms, 80 bonds, 408 residues, 3 models selected
> select subtract #1.9
80 atoms, 80 bonds, 10 residues, 3 models selected
> show sel atoms
> style sel sphere
Changed 80 atom styles
> select clear
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> show sel cartoons
> hide #!1 models
> show #!1 models
Cell requested for row 11 is out of bounds for table with 45 rows! Resizing
table model.
> show #!5 models
> select add #28
17845 atoms, 15029 bonds, 5 pseudobonds, 2237 residues, 4 models selected
> select clear
> select add #28
14751 atoms, 15029 bonds, 5 pseudobonds, 1839 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #28,1,0,0,-41.17,0,1,0,0.46162,0,0,1,84.798
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.50879,0.86017,0.03518,-106.87,-0.83394,0.5026,-0.22788,277.28,-0.2137,0.086605,0.97305,113.27
> view matrix models
> #28,0.25295,0.9019,0.35013,-133.73,-0.13286,0.39085,-0.91081,313.42,-0.95831,0.18387,0.21869,382.61
> view matrix models
> #28,0.011561,0.92863,0.37081,-100.13,-0.087222,0.37036,-0.92478,311.73,-0.99612,-0.021652,0.085279,451.23
> view matrix models
> #28,0.050207,0.97697,-0.20738,3.802,-0.036572,-0.20571,-0.97793,410.65,-0.99807,0.056683,0.025401,450.7
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.050207,0.97697,-0.20738,-11.49,-0.036572,-0.20571,-0.97793,376.53,-0.99807,0.056683,0.025401,453.25
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.02663,0.63594,0.77128,-141.8,-0.18547,0.75501,-0.62894,169.36,-0.98229,-0.1598,0.097844,472
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.02663,0.63594,0.77128,-85.774,-0.18547,0.75501,-0.62894,178.82,-0.98229,-0.1598,0.097844,478.13
> view matrix models
> #28,-0.02663,0.63594,0.77128,-172.72,-0.18547,0.75501,-0.62894,269.98,-0.98229,-0.1598,0.097844,449.91
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.1234,0.68335,0.71959,-153.09,-0.027847,0.72246,-0.69085,260.52,-0.99197,-0.10529,-0.07012,476.97
> view matrix models
> #28,0.27404,0.95496,-0.11377,-97.229,-0.49052,0.037038,-0.87064,493.93,-0.82722,0.2944,0.47858,268.06
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.27404,0.95496,-0.11377,-52.118,-0.49052,0.037038,-0.87064,522.45,-0.82722,0.2944,0.47858,245.78
> hide #!9 models
> view matrix models
> #28,0.27404,0.95496,-0.11377,-52.241,-0.49052,0.037038,-0.87064,522.61,-0.82722,0.2944,0.47858,246.07
> hide #!1 models
> show #!1 models
> select add #1
59750 atoms, 60938 bonds, 57 pseudobonds, 7495 residues, 4 models selected
> show sel cartoons
> view matrix models
> #1,1,0,0,-0.22063,0,1,0,0.028153,0,0,1,-0.041152,#6,1,0,0,0,0,1,0,0,0,0,1,0,#28,0.27404,0.95496,-0.11377,-52.462,-0.49052,0.037038,-0.87064,522.64,-0.82722,0.2944,0.47858,246.03
> ui mousemode right select
> select clear
> select add #28
14751 atoms, 15029 bonds, 5 pseudobonds, 1839 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.27404,0.95496,-0.11377,-32.27,-0.49052,0.037038,-0.87064,385.25,-0.82722,0.2944,0.47858,366.58
> show sel cartoons
> hide sel atoms
> open 7pno fromDatabase pdb format mmcif
Summary of feedback from opening 7pno fetched from pdb
---
note | Fetching compressed mmCIF 7pno from http://files.rcsb.org/download/7pno.cif
7pno title:
C terminal domain of Nipah Virus Phosphoprotein fused to the Ntail α more of
the Nucleoprotein. [more info...]
Chain information for 7pno #29
---
Chain | Description | UniProt
A C E G I K M | Phosphoprotein | PHOSP_NIPAV 655-709
B D F H J L N | alpha MoRE of Nipah virus Nucleoprotein tail |
> select add #29
18549 atoms, 18813 bonds, 5 pseudobonds, 2339 residues, 3 models selected
> select subtract #28
3798 atoms, 3784 bonds, 500 residues, 1 model selected
> select add #28
18549 atoms, 18813 bonds, 5 pseudobonds, 2339 residues, 3 models selected
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> select subtract #28
3798 atoms, 3784 bonds, 500 residues, 20 models selected
> select subtract #29
14 models selected
> select add #29.1
395 atoms, 49 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #29/A to #28/C pairing ss
Parameters
---
Chain pairing | ss
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 9cgi, chain C (#28) with 7pno, chain A (#29), sequence alignment
score = 264.9
RMSD between 47 pruned atom pairs is 0.588 angstroms; (across all 49 pairs:
0.738)
> select add #29
3798 atoms, 3784 bonds, 500 residues, 2 models selected
> select subtract #29.1
3403 atoms, 3388 bonds, 451 residues, 15 models selected
> select subtract #29.2
3242 atoms, 3228 bonds, 428 residues, 14 models selected
> hide sel cartoons
> hide sel atoms
> select add #29
3798 atoms, 3784 bonds, 500 residues, 13 models selected
> select subtract #29
14 models selected
> select add #28
14751 atoms, 15029 bonds, 5 pseudobonds, 1839 residues, 2 models selected
> view matrix models
> #28,0.27404,0.95496,-0.11377,-53.773,-0.49052,0.037038,-0.87064,422.49,-0.82722,0.2944,0.47858,318.72
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.2125,-0.14522,-0.96631,320.47,0.79068,0.60661,0.082711,-97.443,0.57417,-0.78162,0.24373,303.14
> view matrix models
> #28,0.89726,0.010391,-0.44138,64.565,0.1398,0.94159,0.30637,-86.139,0.41878,-0.3366,0.8434,130.5
> view matrix models
> #28,0.9683,0.052719,-0.24415,3.9083,0.0088929,0.96958,0.24462,-55.014,0.24962,-0.23904,0.93838,124
> view matrix models
> #28,0.94417,0.20293,-0.25956,-14.065,-0.14867,0.96545,0.21401,-20.237,0.29402,-0.16347,0.94172,102.71
> view matrix models
> #28,0.94388,0.21093,-0.25417,-16.49,-0.15263,0.96098,0.23071,-22.255,0.29291,-0.17897,0.93924,106.04
> view matrix models
> #28,0.93788,0.25617,-0.234,-27.282,-0.20746,0.95465,0.21357,-7.9746,0.2781,-0.15175,0.94849,102.12
> view matrix models
> #28,0.88687,0.45301,0.090819,-119.15,-0.46056,0.88246,0.095642,73.275,-0.036817,-0.12665,0.99126,144.37
> select #1 /k: 157-176
154 atoms, 155 bonds, 20 residues, 1 model selected
> hide #!6 models
> hide #!5 models
Cell requested for row 0 is out of bounds for table with 29 rows! Resizing
table model.
> select add #1
44999 atoms, 45909 bonds, 52 pseudobonds, 5656 residues, 3 models selected
> select subtract #1
15 models selected
> select add #28
14751 atoms, 15029 bonds, 5 pseudobonds, 1839 residues, 2 models selected
> view matrix models
> #28,0.7809,0.36309,0.5083,-172.07,0.30198,0.49288,-0.81601,194.59,-0.54682,0.79072,0.27524,227.67
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.7809,0.36309,0.5083,-117.17,0.30198,0.49288,-0.81601,197.1,-0.54682,0.79072,0.27524,245.3
> view matrix models
> #28,0.7809,0.36309,0.5083,-130.18,0.30198,0.49288,-0.81601,200.7,-0.54682,0.79072,0.27524,239.25
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.0034456,-0.99652,-0.08334,360.87,0.93504,0.026335,-0.35356,72.171,0.35452,-0.079145,0.93169,91.463
> view matrix models
> #28,-0.29858,-0.60166,-0.74085,482.64,0.87828,-0.47699,0.033408,86.9,-0.37348,-0.6407,0.67084,368.78
> view matrix models
> #28,0.054663,0.21722,-0.97459,330.51,0.57556,-0.80443,-0.14701,233.07,-0.81593,-0.5529,-0.169,606.33
> view matrix models
> #28,-0.5166,0.42373,-0.74403,348.11,0.32206,-0.70899,-0.62738,361.36,-0.79335,-0.56373,0.2298,521.29
> view matrix models
> #28,0.25205,0.84529,-0.47112,84.831,-0.047668,-0.4754,-0.87848,439.06,-0.96654,0.24388,-0.079533,479.37
> view matrix models
> #28,0.27117,0.77852,-0.56602,112.5,-0.55416,-0.35454,-0.75313,481.64,-0.787,0.51789,0.33529,315.19
> hide #!1 models
> ui mousemode right select
> select clear
> show #!1 models
> select clear
> select add #28
14751 atoms, 15029 bonds, 5 pseudobonds, 1839 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.27117,0.77852,-0.56602,47.995,-0.55416,-0.35454,-0.75313,481.77,-0.787,0.51789,0.33529,275.69
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 9cgi_A SES surface #28.2: minimum, -21.89, mean -1.27,
maximum 23.84
Coulombic values for 9cgi_B SES surface #28.3: minimum, -17.78, mean -3.16,
maximum 11.29
Coulombic values for 9cgi_C SES surface #28.4: minimum, -16.72, mean -3.70,
maximum 11.33
Coulombic values for 9cgi_D SES surface #28.5: minimum, -17.18, mean -2.14,
maximum 10.58
Coulombic values for 9cgi_E SES surface #28.6: minimum, -17.72, mean -2.81,
maximum 11.54
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!1 models
> hide sel surfaces
> show sel surfaces
> show #!13 models
> hide #!13 models
> show #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.50814,0.46503,-0.72495,267.64,-0.19359,-0.88184,-0.42998,443.12,-0.83924,-0.07815,0.53812,344.23
> view matrix models
> #28,-0.40827,0.57337,-0.71033,229.29,-0.27784,-0.81926,-0.50161,461.65,-0.86955,-0.0074301,0.49379,346.57
> view matrix models
> #28,-0.49181,0.55114,-0.67407,240.21,-0.076432,-0.79851,-0.59711,442.65,-0.86734,-0.24214,0.43484,397.57
> view matrix models
> #28,-0.51585,0.52657,-0.67574,248.85,-0.053493,-0.80705,-0.58806,438.28,-0.85501,-0.2672,0.44448,397.71
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.51585,0.52657,-0.67574,278.59,-0.053493,-0.80705,-0.58806,447.08,-0.85501,-0.2672,0.44448,411.48
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.33525,0.65102,-0.68101,227.42,-0.22591,-0.75731,-0.61274,473.56,-0.91464,-0.051576,0.40096,394.3
> view matrix models
> #28,-0.59633,-0.065336,-0.80008,416.94,-0.43388,-0.81232,0.38972,314.79,-0.67538,0.57954,0.45607,235.49
> view matrix models
> #28,-0.61463,0.10273,-0.78209,388.07,-0.63113,-0.65881,0.40945,319.25,-0.47319,0.74526,0.46976,169.42
> view matrix models
> #28,-0.60293,0.10794,-0.79046,386.85,-0.6635,-0.61801,0.4217,315.54,-0.44299,0.77873,0.44424,163.71
> view matrix models
> #28,-0.49039,0.15799,-0.85706,372.33,-0.71781,-0.63094,0.2944,353.03,-0.49424,0.75958,0.42281,180.22
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.49039,0.15799,-0.85706,374.96,-0.71781,-0.63094,0.2944,356.59,-0.49424,0.75958,0.42281,180.58
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.49039,0.15799,-0.85706,382.39,-0.71781,-0.63094,0.2944,356.68,-0.49424,0.75958,0.42281,194.3
> hide sel surfaces
> ui tool show Rotamers
> ui tool show Matchmaker
> matchmaker #29/A to #28/C pairing ss
Parameters
---
Chain pairing | ss
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 9cgi, chain C (#28) with 7pno, chain A (#29), sequence alignment
score = 264.9
RMSD between 47 pruned atom pairs is 0.588 angstroms; (across all 49 pairs:
0.738)
> ui mousemode right select
> select clear
> select add #28
14751 atoms, 15029 bonds, 5 pseudobonds, 1839 residues, 2 models selected
> show sel surfaces
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.51958,0.16893,-0.83756,381.69,-0.68744,-0.66478,0.29237,357.5,-0.5074,0.72768,0.46154,194.11
> view matrix models
> #28,-0.44545,0.13011,-0.8858,385.07,-0.79483,-0.51286,0.32437,344.18,-0.41208,0.84856,0.33187,183.44
> view matrix models
> #28,-0.30768,0.13771,-0.94147,371.01,-0.72445,-0.67537,0.13797,397.11,-0.61685,0.7245,0.30756,245.08
> view matrix models
> #28,-0.32846,-0.15263,-0.9321,421.75,-0.63145,-0.69841,0.33688,344.24,-0.70241,0.69923,0.13302,299.85
> view matrix models
> #28,-0.46134,-0.12567,-0.87828,429.33,-0.70191,-0.55378,0.44793,309.4,-0.54266,0.82313,0.16727,244.04
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.46134,-0.12567,-0.87828,425.89,-0.70191,-0.55378,0.44793,321.01,-0.54266,0.82313,0.16727,233.22
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.56653,-0.31995,-0.75939,452.62,-0.65627,-0.38213,0.6506,243.04,-0.49835,0.86695,0.0065105,250.85
> view matrix models
> #28,-0.66699,0.019599,-0.74481,410.33,-0.7426,-0.098809,0.66241,208.4,-0.060612,0.99491,0.080458,138.46
> view matrix models
> #28,-0.94041,0.25693,-0.22274,312.04,-0.33191,-0.55116,0.76555,191.66,0.073928,0.79386,0.60359,42.307
> view matrix models
> #28,-0.96311,0.13262,-0.23417,339.17,-0.26152,-0.66648,0.69815,212.45,-0.063483,0.73364,0.67657,61.501
> view matrix models
> #28,-0.84054,0.33004,-0.42962,324.15,-0.52267,-0.70264,0.48281,307.5,-0.14252,0.63037,0.7631,75.129
> view matrix models
> #28,-0.71855,0.33607,-0.60889,338.26,-0.63812,-0.66672,0.38507,341.23,-0.27655,0.66524,0.69353,106.56
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.71855,0.33607,-0.60889,352.89,-0.63812,-0.66672,0.38507,327.2,-0.27655,0.66524,0.69353,126.42
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.48055,0.29142,-0.82713,363.2,-0.8296,-0.45685,0.32102,338.11,-0.28432,0.84045,0.4613,145.26
> view matrix models
> #28,-0.39073,0.2794,-0.87708,359.65,-0.7948,-0.58305,0.16835,384.22,-0.46435,0.76288,0.44988,192.12
> view matrix models
> #28,-0.38159,0.32149,-0.86662,348.82,-0.80538,-0.57573,0.14105,390.36,-0.45359,0.75179,0.47862,186.25
> view matrix models
> #28,-0.38113,0.32334,-0.86614,348.33,-0.79981,-0.58523,0.13347,392.52,-0.46373,0.74361,0.48166,188.79
> view matrix models
> #28,-0.4231,0.29345,-0.85725,358.93,-0.77633,-0.60526,0.17598,383.18,-0.46722,0.73997,0.4839,189.56
> view matrix models
> #28,-0.42606,0.299,-0.85386,357.82,-0.77533,-0.60703,0.1743,383.64,-0.4662,0.73629,0.49045,188.68
> view matrix models
> #28,-0.41274,0.28301,-0.86577,360.61,-0.76133,-0.62898,0.15735,388.34,-0.50002,0.72408,0.47507,199.78
> view matrix models
> #28,-0.44734,0.31685,-0.83636,354.98,-0.8137,-0.53231,0.23355,365.73,-0.3712,0.78502,0.49594,162.72
> view matrix models
> #28,-0.70247,0.11736,-0.70197,405.85,-0.59537,-0.63733,0.48923,293.55,-0.38997,0.7616,0.51758,165.56
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.70247,0.11736,-0.70197,398.64,-0.59537,-0.63733,0.48923,306.45,-0.38997,0.7616,0.51758,164.7
> view matrix models
> #28,-0.70247,0.11736,-0.70197,398.04,-0.59537,-0.63733,0.48923,314.26,-0.38997,0.7616,0.51758,161.02
> view matrix models
> #28,-0.70247,0.11736,-0.70197,395.06,-0.59537,-0.63733,0.48923,310.18,-0.38997,0.7616,0.51758,162.57
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.61405,0.24654,-0.74978,367.62,-0.709,-0.5897,0.38675,342.72,-0.34679,0.76907,0.5369,149.88
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.61405,0.24654,-0.74978,367.76,-0.709,-0.5897,0.38675,337,-0.34679,0.76907,0.5369,151.39
> view matrix models
> #28,-0.61405,0.24654,-0.74978,371.07,-0.709,-0.5897,0.38675,332.82,-0.34679,0.76907,0.5369,155.51
> ui tool show Matchmaker
> matchmaker #29/A to #28/C pairing ss
Parameters
---
Chain pairing | ss
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 9cgi, chain C (#28) with 7pno, chain A (#29), sequence alignment
score = 264.9
RMSD between 47 pruned atom pairs is 0.588 angstroms; (across all 49 pairs:
0.738)
> select add #29
18549 atoms, 18813 bonds, 5 pseudobonds, 2339 residues, 8 models selected
> ui mousemode right select
Drag select of 5 residues
> show sel atoms
Drag select of 6 residues
> show sel atoms
> style sel sphere
Changed 41 atom styles
> select clear
> ui mousemode right distance
> distance #1/Q:398@OE2 #29/B:491@CA
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Q
GLU 398 OE2 and 7pno #29/B ALA 491 CA: 81.075Å
> ui tool show "Show Sequence Viewer"
> sequence chain #1/Q
Alignment identifier is 1/Q
> ui tool show "Model Loops"
> ui tool show "Show Sequence Viewer"
> sequence chain #29/B
Alignment identifier is 29/B
> ui tool show "Model Loops"
> modeller refine 1/Q:1:all-missing 29/B:1:all-missing numModels 1 fast false
> adjacentFlexible 1 protocol standard
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> open "/Users/kompa012/Desktop/NiP N protein article/Archive/model1.pdb"
> "/Users/kompa012/Desktop/NiP N protein article/Archive/model1p.pdb"
> "/Users/kompa012/Desktop/NiP N protein article/Archive/model2.pdb"
> "/Users/kompa012/Desktop/NiP N protein article/Archive/model2p.pdb"
> "/Users/kompa012/Desktop/NiP N protein article/Archive/model3.pdb"
> "/Users/kompa012/Desktop/NiP N protein article/Archive/model3p.pdb"
> "/Users/kompa012/Desktop/NiP N protein article/Archive/model4.pdb"
> "/Users/kompa012/Desktop/NiP N protein article/Archive/model4p.pdb"
> "/Users/kompa012/Desktop/NiP N protein article/Archive/model5.pdb"
> "/Users/kompa012/Desktop/NiP N protein article/Archive/model5p.pdb"
Chain information for model1.pdb #30
---
Chain | Description
A | No description available
Chain information for model1p.pdb #31
---
Chain | Description
A | No description available
Chain information for model2.pdb #32
---
Chain | Description
A | No description available
Chain information for model2p.pdb #33
---
Chain | Description
A | No description available
Chain information for model3.pdb #34
---
Chain | Description
A | No description available
Chain information for model3p.pdb #35
---
Chain | Description
A | No description available
Chain information for model4.pdb #36
---
Chain | Description
A | No description available
Chain information for model4p.pdb #37
---
Chain | Description
A | No description available
Chain information for model5.pdb #38
---
Chain | Description
A | No description available
Chain information for model5p.pdb #39
---
Chain | Description
A | No description available
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
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: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16S0005DLL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 20 days, 21 hours, 20 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: 2.15.0
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-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-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 , 7 months ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in Modeller tool _update_sequence_menus in Qt call meth_QFormLayout_removeRow() |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate of #15753