![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16973 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.9rc202411082121 (2024-11-08 21:21:14 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 0x0000000202dc7ac0 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, psutil._psutil_osx, psutil._psutil_posix, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 67)
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"procLaunch" : "2025-02-26 11:43:01.6806 -0600",
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"procExitAbsTime" : 1435578231762,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> mousemode middleMode center
> cofr centerOfView
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue
> alias cootmode_mesh set bgColor black; surface cap false; surface style
> mesh; lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball;
> style ions ball; size ballscale 0.2; size stickradius 0.07; cofr
> centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> #3d60ffff; transparency 50
> alias cootmode_off surface style solid; lighting soft; graphics silhouettes
> false; hide atoms; default_mol_display; transparency 0; symclip 40; color
> ##~num_residues grey; size stickradius 0.2;
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette Pastel1-5;
> lighting soft; color byhet
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1; style stick; size stickRadius 0.5; ~disp @H*; color byhet
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias rock_movie cofr showpivot false; movie record supersample 3; rock y
> 40; wait 136; movie encode ~/Desktop/rock_movie.mp4 quality high; stop
> alias publication_figure save Figure.png format png supersample 3
> transparentBackground true width 3000 height 3000
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add Hide_H command "~disp @H*"
> buttonpanel Shortcuts add Licorice command licorice
> buttonpanel Shortcuts add Ribbons command "preset ribbons"
> buttonpanel Shortcuts add RockMovie command rock_movie
> buttonpanel Shortcuts add SymClip10 command "symclip 10"
> buttonpanel Shortcuts add SymClip20 command "symclip 20"
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add PubFigure command publication_figure
> buttonpanel Shortcuts add coot_mode command cootmode
> buttonpanel Shortcuts add coot_mesh command cootmode_mesh
> buttonpanel Shortcuts add coot_off command cootmode_off
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> ui tool show "Model Panel"
UCSF ChimeraX version: 1.9rc202411082121 (2024-11-08)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/McLellan
> Lab/Manuscripts/In
> Progress/PIV3_HN_VHH/Structure/RV1_VHH60/Structure/RealSpaceRefine_11/RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb"
Chain information for RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #1
---
Chain | Description
A B | No description available
H I | No description available
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/RV3 HN
> VHH/Structures/RV3 HN
> VHH60/RV3_HN_086_kabat_seq_corrected_real_space_refined_001.pdb"
Chain information for
RV3_HN_086_kabat_seq_corrected_real_space_refined_001.pdb #2
---
Chain | Description
A B | No description available
H I | No description available
> mmaker #2 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb, chain A (#1)
with RV3_HN_086_kabat_seq_corrected_real_space_refined_001.pdb, chain B (#2),
sequence alignment score = 1381.7
RMSD between 378 pruned atom pairs is 0.961 angstroms; (across all 422 pairs:
1.450)
> color #2 bychain
> hide #!1 models
> color #!2 byhetero
> show #!2 atoms
> hide #!2 atoms
> interfaces select #2/H contacting #2/A bothSides true
44 contacting residues
> show #!1 models
> hide #!1 models
> select add #2
16994 atoms, 17210 bonds, 2 pseudobonds, 1102 residues, 2 models selected
> select subtract #2
Nothing selected
> interfaces select #2/I contacting #2/B bothSides true
44 contacting residues
> show (sel-residues & sidechain) target ab
> hide H
> select add #2
16994 atoms, 17210 bonds, 2 pseudobonds, 1102 residues, 2 models selected
> select subtract #2
Nothing selected
> interfaces select #2/I contacting #2/B bothSides true
44 contacting residues
> info residues sel saveFile
Missing "saveFile" keyword's argument
> info residues sel saveFile Lab/05 PIV HN/RV3 VHH60>
Expected a keyword
> info residues sel saveFile Lab/>
Expected a keyword
> info residues sel
residue id #2/I:32 name ASN index 31
residue id #2/I:37 name TYR index 36
residue id #2/I:44 name GLN index 43
residue id #2/I:45 name ARG index 44
residue id #2/I:47 name PHE index 46
residue id #2/I:50 name LEU index 49
residue id #2/I:52 name THR index 51
residue id #2/I:54 name GLY index 53
residue id #2/I:56 name VAL index 55
residue id #2/I:58 name ASN index 57
residue id #2/I:95 name VAL index 97
residue id #2/I:98 name PRO index 100
residue id #2/I:99 name SER index 101
residue id #2/I:100 name TRP index 102
residue id #2/I:100A name GLY index 103
residue id #2/I:100B name LEU index 104
residue id #2/I:100C name TYR index 105
residue id #2/I:100D name ASP index 106
residue id #2/I:101 name ASP index 107
residue id #2/I:103 name TRP index 109
residue id #2/B:192 name ARG index 49
residue id #2/B:214 name CYS index 71
residue id #2/B:215 name GLN index 72
residue id #2/B:254 name LYS index 111
residue id #2/B:255 name SER index 112
residue id #2/B:275 name ASP index 132
residue id #2/B:276 name GLU index 133
residue id #2/B:277 name ARG index 134
residue id #2/B:278 name SER index 135
residue id #2/B:281 name ALA index 138
residue id #2/B:358 name LYS index 215
residue id #2/B:362 name ASP index 219
residue id #2/B:370 name PRO index 227
residue id #2/B:371 name TRP index 228
residue id #2/B:373 name SER index 230
residue id #2/B:424 name ARG index 278
residue id #2/B:460 name ASN index 314
residue id #2/B:462 name GLU index 316
residue id #2/B:471 name ASP index 325
residue id #2/B:474 name ILE index 328
residue id #2/B:475 name THR index 329
residue id #2/B:502 name ARG index 356
residue id #2/B:530 name TYR index 384
residue id #2/B:558 name PHE index 412
> hide #!2 models
> show #!1 models
> select add #2
16994 atoms, 17210 bonds, 2 pseudobonds, 1102 residues, 2 models selected
> select subtract #2
Nothing selected
> interfaces select #1/H contacting #1/A bothSides true
45 contacting residues
> show (sel-residues & sidechain) target ab
> hide H
> info residues sel
residue id #1/A:194 name ARG index 49
residue id #1/A:195 name LEU index 50
residue id #1/A:216 name CYS index 71
residue id #1/A:217 name ALA index 72
residue id #1/A:256 name LYS index 111
residue id #1/A:257 name SER index 112
residue id #1/A:278 name GLU index 133
residue id #1/A:279 name THR index 134
residue id #1/A:280 name THR index 135
residue id #1/A:283 name SER index 138
residue id #1/A:339 name TYR index 194
residue id #1/A:372 name THR index 227
residue id #1/A:373 name TRP index 228
residue id #1/A:375 name LYS index 230
residue id #1/A:376 name LYS index 231
residue id #1/A:426 name ARG index 281
residue id #1/A:460 name ASN index 315
residue id #1/A:461 name PRO index 316
residue id #1/A:471 name ARG index 326
residue id #1/A:472 name GLU index 327
residue id #1/A:474 name ILE index 329
residue id #1/A:502 name ARG index 357
residue id #1/A:530 name TYR index 382
residue id #1/A:577 name NAG
residue id #1/A:581 name NAG
residue id #1/H:32 name ASN index 31
residue id #1/H:37 name TYR index 36
residue id #1/H:47 name PHE index 39
residue id #1/H:50 name LEU index 42
residue id #1/H:52 name THR index 44
residue id #1/H:53 name THR index 45
residue id #1/H:54 name GLY index 46
residue id #1/H:56 name VAL index 48
residue id #1/H:58 name ASN index 50
residue id #1/H:73 name ASN index 65
residue id #1/H:95 name VAL index 80
residue id #1/H:98 name PRO index 83
residue id #1/H:99 name SER index 84
residue id #1/H:100 name TRP index 85
residue id #1/H:100A name GLY index 86
residue id #1/H:100B name LEU index 87
residue id #1/H:100C name TYR index 88
residue id #1/H:100D name ASP index 89
residue id #1/H:101 name ASP index 90
residue id #1/H:103 name TRP index 92
> open /Users/zhouling95/Downloads/5l17.pdb
5l17.pdb title:
The crystal structure of neuraminidase In complex with zanamivir from
A/shanghai/2/2013 (H7N9) influenza virus [more info...]
Chain information for 5l17.pdb #3
---
Chain | Description | UniProt
A | neuraminidase | R4NFR6_9INFA 83-470
Non-standard residues in 5l17.pdb #3
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
CA — calcium ion
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
ZMR — zanamivir (4-guanidino-2-deoxy-2,3-dehydro-N-acetyl-neuraminicacid;
4-guanidino-NEU5AC2EN; modified sialic acid)
42 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 models
> show #!2 models
> select ~sel & ##selected
15567 atoms, 15785 bonds, 6 pseudobonds, 1011 residues, 2 models selected
> mmaker #3 to #2
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RV3_HN_086_kabat_seq_corrected_real_space_refined_001.pdb, chain B
(#2) with 5l17.pdb, chain A (#3), sequence alignment score = 127.2
RMSD between 37 pruned atom pairs is 1.429 angstroms; (across all 310 pairs:
16.473)
> color #3 bychain
> hide #!2 models
> select #3/A:ZMR
23 atoms, 23 bonds, 1 residue, 1 model selected
> color sel orange
> hide #!3 models
> show #!3 models
> select add #3
3374 atoms, 3298 bonds, 6 pseudobonds, 576 residues, 2 models selected
> color sel byhetero
> select subtract #3
Nothing selected
> show #!2 models
> open "/Users/zhouling95/Documents/Academic/McLellan Lab/05 PIV
> HN/VHH60_figure.cxs"
Opened cryosparc_P714_J220_map_sharp.mrc as #1, grid size 300,300,300, pixel
0.94, shown at level 0.07, step 1, values float32
Opened cryosparc_P714_J361_map_sharp.mrc as #4, grid size 300,300,300, pixel
0.933, shown at level 0.0658, step 1, values float32
opened ChimeraX session
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/McLellan
> Lab/Manuscripts/In
> Progress/PIV3_HN_VHH/Structure/RV3_VHH60/Phenix/RealSpaceRefine_1/RV3_HN_086_kabat_seq_corrected_real_space_refined_001.pdb"
Chain information for
RV3_HN_086_kabat_seq_corrected_real_space_refined_001.pdb #5
---
Chain | Description
A B | No description available
H I | No description available
> select #2/100
Nothing selected
> select #2/A:100
Nothing selected
> select #2/H:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/I:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #5
17000 atoms, 17215 bonds, 2 pseudobonds, 1103 residues, 3 models selected
> select subtract #5
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide #!2 models
> select #2/I:102
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!2 models
> select #2/I:103
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #!2 models
> select #2/I:104
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #3 models
> hide #3 models
> show #!2 models
> select #2/I:106
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #3 models
> hide #3 models
> show #!2 models
> select #2/I:107
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!2 models
> select #2/I:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> select #2/I:32
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> select #2/I:37
12 atoms, 12 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/H
Alignment identifier is 5/H
> select #5/H:2-8,18-26,31-39,46-52,57-59,67-72,77-82,88-97,100C-103,107-109
990 atoms, 993 bonds, 65 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:249-251,276-281,360-366,370-372,401-403
358 atoms, 358 bonds, 22 residues, 1 model selected
> close #3#1-2,4-5
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/McLellan
> Lab/Manuscripts/In Progress/PIV3_HN_VHH/Figure/RV3_VHH60_VHH59_colored.cxs"
Opened cryosparc_P714_J220_map_sharp.mrc as #1, grid size 300,300,300, pixel
0.94, shown at level 0.07, step 1, values float32
Opened cryosparc_P714_J361_map_sharp.mrc as #4, grid size 300,300,300, pixel
0.933, shown at level 0.0658, step 1, values float32
opened ChimeraX session
> open "/Users/zhouling95/Documents/Academic/McLellan Lab/05 PIV HN/RV1
> VHH60/Combined
> Phenix/RealSpaceRefine_11/RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb"
Chain information for RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5
---
Chain | Description
A B | No description available
H I | No description available
> open "/Users/zhouling95/Documents/Academic/McLellan Lab/05 PIV HN/RV1
> VHH60/cryosparc_P777_J313_map_sharp.mrc"
Opened cryosparc_P777_J313_map_sharp.mrc as #6, grid size 300,300,300, pixel
0.94, shown at level 0.000955, step 2, values float32
> surface dust #1 size 9.4
> surface dust #6 size 9.4
> volume #6 step 1
> volume #6 level 0.03987
> hide #!2 models
> hide #!1 models
> hide #!6 models
> show #!2 models
> select #5/H,I
2748 atoms, 2776 bonds, 4 pseudobonds, 188 residues, 2 models selected
> color (#!5 & sel) #ff9912ff
> color (#!5 & sel) #ff9914ff
> color (#!5 & sel) #fe9913ff
> color (#!5 & sel) #fd9813ff
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> color (#!5 & sel) #f39213ff
> color (#!5 & sel) #f29213ff
> color (#!5 & sel) #f29113ff
> color (#!5 & sel) #f19112ff
> select #5/A
6798 atoms, 6887 bonds, 1 pseudobond, 434 residues, 2 models selected
> color (#!5 & sel) #f1e9b1ff
> color (#!5 & sel) #f1e8b1ff
> color (#!5 & sel) #f1e7b0ff
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> color (#!5 & sel) #5f3df1ff
> color (#!5 & sel) #5937f1ff
> color (#!5 & sel) #5635f1ff
> color (#!5 & sel) #5534f1ff
> color (#!5 & sel) #5836f1ff
> color (#!5 & sel) #5937f1ff
> color (#!5 & sel) #5e39f1ff
> color (#!5 & sel) #603af1ff
> color (#!5 & sel) #663df1ff
> color (#!5 & sel) #6c3ff1ff
> color (#!5 & sel) #7040f1ff
> color (#!5 & sel) #7140f1ff
> color (#!5 & sel) #7341f1ff
> color (#!5 & sel) #7a45f1ff
> color (#!5 & sel) #814af1ff
> color (#!5 & sel) #854df1ff
> color (#!5 & sel) #8850f1ff
> color (#!5 & sel) #8a51f1ff
> color (#!5 & sel) #8a52f1ff
> color (#!5 & sel) #8b52f1ff
> color (#!5 & sel) #8d58f1ff
> color (#!5 & sel) #8e58f1ff
> color (#!5 & sel) #8e59f1ff
> color (#!5 & sel) #8f5af1ff
> color (#!5 & sel) #8f5bf1ff
> color (#!5 & sel) #8f5df1ff
> color (#!5 & sel) #8e5df1ff
> color (#!5 & sel) #8f5df1ff
> color (#!5 & sel) #8e5df1ff
> color (#!5 & sel) #8e5ef1ff
> color (#!5 & sel) #8e60f1ff
> color (#!5 & sel) #8d61f1ff
> color (#!5 & sel) #8d62f1ff
> color (#!5 & sel) #8c61f1ff
> color (#!5 & sel) #8b63f1ff
> color (#!5 & sel) #8964f1ff
> color (#!5 & sel) #8667f1ff
> color (#!5 & sel) #8568f1ff
> color (#!5 & sel) #8469f1ff
> color (#!5 & sel) #846af1ff
> color (#!5 & sel) #836bf1ff
> color (#!5 & sel) #826df1ff
> color (#!5 & sel) #836ef1ff
> color (#!5 & sel) #836ff1ff
> color (#!5 & sel) #8370f1ff
> color (#!5 & sel) #8371f1ff
> color (#!5 & sel) #8472f1ff
> color (#!5 & sel) #8474f1ff
> color (#!5 & sel) #8676f1ff
> color (#!5 & sel) #8978f1ff
> color (#!5 & sel) #8b7af1ff
> color (#!5 & sel) #8c7bf1ff
> color (#!5 & sel) #9682f1ff
> color (#!5 & sel) #9a85f1ff
> color (#!5 & sel) #9a84f1ff
> color (#!5 & sel) #9782f1ff
> color (#!5 & sel) #9681f1ff
> color (#!5 & sel) #947ff1ff
> color (#!5 & sel) #937ef1ff
> color (#!5 & sel) #927ef1ff
> color (#!5 & sel) #8f7df1ff
> color (#!5 & sel) #8d7cf1ff
> color (#!5 & sel) #887af1ff
> color (#!5 & sel) #8377f1ff
> color (#!5 & sel) #7e76f1ff
> color (#!5 & sel) #7b75f1ff
> color (#!5 & sel) #7a74f1ff
> color (#!5 & sel) #7873f1ff
> color (#!5 & sel) #7772f1ff
> color (#!5 & sel) #7571f1ff
> color (#!5 & sel) #716ef1ff
> color (#!5 & sel) #6e6cf1ff
> color (#!5 & sel) #6d6cf1ff
> color (#!5 & sel) #6c6cf1ff
> color (#!5 & sel) #6b6cf1ff
> color (#!5 & sel) #6c6df1ff
> color (#!5 & sel) #6c6ef1ff
> color (#!5 & sel) #6c6ff1ff
> color (#!5 & sel) #6d70f1ff
> color (#!5 & sel) #6d72f1ff
> color (#!5 & sel) #6d73f1ff
> color (#!5 & sel) #6c73f1ff
> color (#!5 & sel) #6b73f1ff
> color (#!5 & sel) #6c74f1ff
> color (#!5 & sel) #6e78f1ff
> color (#!5 & sel) #6e77f1ff
> color (#!5 & sel) #6f78f1ff
> color (#!5 & sel) #7079f1ff
> color (#!5 & sel) #7179f1ff
> color (#!5 & sel) #7178f1ff
> color (#!5 & sel) #7279f1ff
> color (#!5 & sel) #737af1ff
> color (#!5 & sel) #7379f1ff
> color (#!5 & sel) #7479f1ff
> color (#!5 & sel) #747af1ff
> color (#!5 & sel) #757af1ff
> color (#!5 & sel) #777af1ff
> color (#!5 & sel) #787af1ff
> color (#!5 & sel) #7a7cf1ff
> color (#!5 & sel) #7a7df1ff
> color (#!5 & sel) #7b7df1ff
> color (#!5 & sel) #7c7ef1ff
> color (#!5 & sel) #7b7df1ff
> color (#!5 & sel) #787bf1ff
> color (#!5 & sel) #7679f1ff
> color (#!5 & sel) #7579f1ff
> color (#!5 & sel) #898df1ff
> color (#!5 & sel) #848af1ff
> color (#!5 & sel) #838af1ff
> color (#!5 & sel) #828bf1ff
> color (#!5 & sel) #818bf1ff
> color (#!5 & sel) #828cf1ff
> color (#!5 & sel) #818df1ff
> color (#!5 & sel) #818ef1ff
> color (#!5 & sel) #818ff1ff
> color (#!5 & sel) #8090f1ff
> color (#!5 & sel) #7f90f1ff
> color (#!5 & sel) #7e90f1ff
> color (#!5 & sel) #7d92f1ff
> color (#!5 & sel) #7c92f1ff
> color (#!5 & sel) #7b92f1ff
> color (#!5 & sel) #7a92f1ff
> color (#!5 & sel) #7a93f1ff
> color (#!5 & sel) #7792f1ff
> color (#!5 & sel) #7693f1ff
> color (#!5 & sel) #7593f1ff
> color (#!5 & sel) #7493f1ff
> color (#!5 & sel) #7193f1ff
> color (#!5 & sel) #7192f1ff
> color (#!5 & sel) #7091f1ff
> color (#!5 & sel) #7090f1ff
> color (#!5 & sel) #6f91f1ff
> color (#!5 & sel) #6f90f1ff
> color (#!5 & sel) #6f8ff1ff
> color (#!5 & sel) #718bf1ff
> color (#!5 & sel) #728bf1ff
> color (#!5 & sel) #738bf1ff
> color (#!5 & sel) #748bf1ff
> color (#!5 & sel) #758af1ff
> color (#!5 & sel) #788bf1ff
> color (#!5 & sel) #798bf1ff
> color (#!5 & sel) #7c8bf1ff
> color (#!5 & sel) #7d8bf1ff
> color (#!5 & sel) #7e8af1ff
> color (#!5 & sel) #7f8af1ff
> color (#!5 & sel) #8189f1ff
> color (#!5 & sel) #8289f1ff
> color (#!5 & sel) #8389f1ff
> color (#!5 & sel) #848af1ff
> color (#!5 & sel) #8589f1ff
> color (#!5 & sel) #8588f1ff
> color (#!5 & sel) #8688f1ff
> color (#!5 & sel) #8887f1ff
> color (#!5 & sel) #8987f1ff
> color (#!5 & sel) #8a87f1ff
> color (#!5 & sel) #8b88f1ff
> color (#!5 & sel) #8c89f1ff
> color (#!5 & sel) #8b88f1ff
> color (#!5 & sel) #8988f1ff
> color (#!5 & sel) #898af1ff
> color (#!5 & sel) #8a8ff1ff
> color (#!5 & sel) #8a90f1ff
> color (#!5 & sel) #8a91f1ff
> color (#!5 & sel) #8991f1ff
> color (#!5 & sel) #8993f1ff
> color (#!5 & sel) #8a95f1ff
> color (#!5 & sel) #8c98f1ff
> color (#!5 & sel) #8d99f1ff
> color (#!5 & sel) #8c99f1ff
> color (#!5 & sel) #8792f1ff
> color (#!5 & sel) #8591f1ff
> color (#!5 & sel) #8590f1ff
> color (#!5 & sel) #848ff1ff
> color (#!5 & sel) #818cf1ff
> color (#!5 & sel) #7f8af1ff
> color (#!5 & sel) #7c86f1ff
> color (#!5 & sel) #7c87f1ff
> color (#!5 & sel) #7c88f1ff
> color (#!5 & sel) #7e8af1ff
> color (#!5 & sel) #7f8cf1ff
> color (#!5 & sel) #808ef1ff
> color (#!5 & sel) #808ff1ff
> select #5/B
6798 atoms, 6887 bonds, 1 pseudobond, 434 residues, 2 models selected
> color (#!5 & sel) #879bf1ff
> color (#!5 & sel) #879cf1ff
> color (#!5 & sel) #889df1ff
> color (#!5 & sel) #899ef1ff
> color (#!5 & sel) #8a9ff1ff
> color (#!5 & sel) #8ca1f1ff
> color (#!5 & sel) #8ea3f1ff
> color (#!5 & sel) #91a5f1ff
> color (#!5 & sel) #92a5f1ff
> color (#!5 & sel) #93a6f1ff
> color (#!5 & sel) #95a8f1ff
> color (#!5 & sel) #96a9f1ff
> color (#!5 & sel) #97aaf1ff
> color (#!5 & sel) #98aaf1ff
> color (#!5 & sel) #98abf1ff
> color (#!5 & sel) #9aacf1ff
> color (#!5 & sel) #9badf1ff
> color (#!5 & sel) #9caef1ff
> color (#!5 & sel) #9daff1ff
> color (#!5 & sel) #9eaff1ff
> color (#!5 & sel) #9db0f1ff
> color (#!5 & sel) #9ab1f1ff
> color (#!5 & sel) #99b1f1ff
> color (#!5 & sel) #99b2f1ff
> color (#!5 & sel) #99b3f1ff
> color (#!5 & sel) #9ab4f1ff
> color (#!5 & sel) #99b4f1ff
> color (#!5 & sel) #9ab5f1ff
> color (#!5 & sel) #9ab6f1ff
> color (#!5 & sel) #9bb7f1ff
> color (#!5 & sel) #9bb8f1ff
> color (#!5 & sel) #9cbaf1ff
> color (#!5 & sel) #9dbbf1ff
> color (#!5 & sel) #9ebcf1ff
> color (#!5 & sel) #9fbdf1ff
> color (#!5 & sel) #9ebdf1ff
> color (#!5 & sel) #9dbdf1ff
> color (#!5 & sel) #9bbdf1ff
> color (#!5 & sel) #9abdf1ff
> color (#!5 & sel) #9abcf1ff
> color (#!5 & sel) #99bcf1ff
> color (#!5 & sel) #99bbf1ff
> color (#!5 & sel) #99baf1ff
> color (#!5 & sel) #98baf1ff
> color (#!5 & sel) #98b9f1ff
> color (#!5 & sel) #97b8f1ff
> color (#!5 & sel) #97b6f1ff
> color (#!5 & sel) #97b4f1ff
> color (#!5 & sel) #97b2f1ff
> color (#!5 & sel) #97b0f1ff
> color (#!5 & sel) #96aff1ff
> color (#!5 & sel) #97aff1ff
> color (#!5 & sel) #97aef1ff
> color (#!5 & sel) #97adf1ff
> color (#!5 & sel) #98adf1ff
> color (#!5 & sel) #99acf1ff
> color (#!5 & sel) #9aacf1ff
> color (#!5 & sel) #9bacf1ff
> color (#!5 & sel) #9cacf1ff
> color (#!5 & sel) #9daaf1ff
> color (#!5 & sel) #9eaaf1ff
> color (#!5 & sel) #9faaf1ff
> color (#!5 & sel) #a0a9f1ff
> color (#!5 & sel) #a1a9f1ff
> color (#!5 & sel) #a2a8f1ff
> color (#!5 & sel) #a3a8f1ff
> color (#!5 & sel) #a4a8f1ff
> color (#!5 & sel) #a4a7f1ff
> color (#!5 & sel) #a5a7f1ff
> color (#!5 & sel) #a6a6f1ff
> select #5
16344 atoms, 16550 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> color sel byhetero
> hide H
> show #!6 models
> color zone #6 near sel & #5 distance 5.64
> select subtract #5
Nothing selected
> hide #!5 models
> select #5/B
6798 atoms, 6887 bonds, 1 pseudobond, 434 residues, 2 models selected
> hide #!6 models
> show #!5 models
> color (#!5 & sel) #a6a4f1ff
> color (#!5 & sel) #a7a5f1ff
> color (#!5 & sel) #aaa7f1ff
> color (#!5 & sel) #aca9f1ff
> color (#!5 & sel) #adaaf1ff
> color (#!5 & sel) #aeaaf1ff
> color (#!5 & sel) #b2aef1ff
> color (#!5 & sel) #b4b0f1ff
> color (#!5 & sel) #b5b1f1ff
> color (#!5 & sel) #b6b3f1ff
> color (#!5 & sel) #b8b4f1ff
> color (#!5 & sel) #b9b6f1ff
> color (#!5 & sel) #bab7f1ff
> color (#!5 & sel) #bcb8f1ff
> color (#!5 & sel) #bcb9f1ff
> color (#!5 & sel) #bebaf1ff
> color (#!5 & sel) #c1bcf1ff
> color (#!5 & sel) #c3bff1ff
> color (#!5 & sel) #c3bef1ff
> color (#!5 & sel) #c3bff1ff
> color (#!5 & sel) #c2bff1ff
> color (#!5 & sel) #c1bff1ff
> show #!6 models
> select add #5
16344 atoms, 16550 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> select subtract #5
Nothing selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
> select add #5
16344 atoms, 16550 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> color zone #6 near sel & #5 distance 5.64
> select subtract #5
Nothing selected
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> volume #6 level 0.05284
> volume #6 level 0.04419
> show #!5 models
> show #!6 models
> select add #5
16344 atoms, 16550 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> hide #!2 models
> color zone #6 near sel & #5 distance 5.64
> color zone #6 near sel & #5 distance 6
> color zone #6 near sel & #5 distance 6.5
> color zone #6 near sel & #5 distance 6
> volume #6 color #dfdfdf
> color zone #6 near sel & #5 distance 6
> select subtract #5
Nothing selected
> hide #!5 models
> color zone #6 near sel & #5 distance 6.5
color zone: No atoms specified.
> show #!5 models
> select add #5
16344 atoms, 16550 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> color zone #6 near sel & #5 distance 6.5
> color zone #6 near sel & #5 distance 6
> color zone #6 near sel & #5 distance 7
> volume #6 level 0.06581
> volume #6 level 0.07013
> color zone #6 near sel & #5 distance 7.5
> select subtract #5
Nothing selected
> hide #!5 models
> color zone #6 near sel & #5 distance 7
color zone: No atoms specified.
> show #!5 models
> select add #5
16344 atoms, 16550 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> color zone #6 near sel & #5 distance 7
> color zone #6 near sel & #5 distance 6
> color zone #6 near sel & #5 distance 6.6
> color zone #6 near sel & #5 distance 4
> color zone #6 near sel & #5 distance 3
> color zone #6 near sel & #5 distance 5
> color zone #6 near sel & #5 distance 10
> color zone #6 near sel & #5 distance 8
> volume #6 level 0.07013
> color zone #6 near sel & #5 distance 7
> color zone #6 near sel & #5 distance 6.3
> color zone #6 near sel & #5 distance 6.5
> select subtract #5
Nothing selected
> hide #!5 models
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> show #!5 models
> select add #5
16344 atoms, 16550 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> color zone #6 near sel & #5 distance 7
> select subtract #5
Nothing selected
> hide #!5 models
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> hide #!6 models
> show #!5 models
> select #5
16344 atoms, 16550 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> color sel byhetero
> hide H
> select #5:NAG
336 atoms, 336 bonds, 12 residues, 1 model selected
> color sel #a5dfa5ff
> color sel #a4dfa4ff
> color sel #a3dfa4ff
> color sel #a1dfa2ff
> color sel #a0dfa0ff
> color sel #8edf90ff
> color sel #82df85ff
> color sel #7bdf7fff
> color sel #7adf7dff
> color sel #79df7dff
> color sel #78df7cff
> color sel #77df7bff
> color sel #73df77ff
> color sel #72df77ff
> color sel #71df76ff
> color sel #71df77ff
> color sel #72df78ff
> color sel #72df79ff
> color sel #74df7cff
> color sel #75df7eff
> color sel #78df84ff
> color sel #7ddf8cff
> color sel #82df93ff
> color sel #86df98ff
> color sel #96dfacff
> color sel #a8dfc5ff
> color sel #acdfceff
> color sel #b7dadfff
> color sel #b6cbdfff
> color sel #b3c4dfff
> color sel #afbadfff
> color sel #acb4dfff
> color sel #abb3dfff
> color sel #a8aedfff
> color sel #a6abdfff
> color sel #a5a7dfff
> color sel #a3a4dfff
> color sel #a39edfff
> color sel #a192dfff
> color sel #a18cdfff
> color sel #a18bdfff
> color sel #a08ddfff
> color sel #a191dfff
> color sel #a194dfff
> color sel #9e9ddfff
> color sel #a6b0dfff
> color sel #afd5dfff
> color sel #abdfd9ff
> color sel #a7dfd3ff
> color sel #a6dfd2ff
> color sel #a5dfd2ff
> color sel #a4dfd2ff
> color sel #a3dfd2ff
> color sel #a2dfd2ff
> color sel #a1dfd2ff
> color sel #a0dfd1ff
> color sel #9fdfd1ff
> color sel #9edfd1ff
> color sel #99dfd1ff
> color sel #93dfd2ff
> color sel #92dfd2ff
> color sel #92dfd0ff
> color sel #92dfcfff
> color sel #91dfcbff
> color sel #90dfbdff
> color sel #8edfb3ff
> color sel #8edfb1ff
> color sel #8ddfb0ff
> color sel #8ddfafff
> color sel #8cdfabff
> color sel #8cdfa8ff
> color sel #8cdfa7ff
> color sel #8ddfa7ff
> color sel #8ddfa6ff
> color sel #8edfa5ff
> color sel #8fdfa4ff
> color sel #90dfa2ff
> color sel #91dfa2ff
> color sel #93dfa0ff
> color sel #93df9fff
> color sel #95df9fff
> color sel #96df9fff
> color sel #99dfa4ff
> color sel #9cdfa7ff
> color sel #9ddfa8ff
> color sel #9edfabff
> color sel #a0dfafff
> color sel #a0dfb0ff
> color sel #a1dfb3ff
> color sel #a4dfc7ff
> color sel #a5dfd1ff
> color sel #a5dfd7ff
> color sel #a6dfdcff
> color sel #a1cadfff
> color sel #9fc6dfff
> color sel #99b6dfff
> color sel #98b3dfff
> color sel #98b2dfff
> color sel #96b0dfff
> color sel #96afdfff
> color sel #95b0dfff
> color sel #96b2dfff
> color sel #94bedfff
> color sel #93c1dfff
> color sel #92cbdfff
> color sel #93cddfff
> color sel #93cedfff
> color sel #93cfdfff
> color sel #93d1dfff
> color sel #92d3dfff
> color sel #92d4dfff
> color sel #92d5dfff
> color sel #93d5dfff
> color sel #94d5dfff
> color sel #96d5dfff
> color sel #97d5dfff
> color sel #99d5dfff
> color sel #9cd6dfff
> color sel #9ed5dfff
> color sel #a1d3dfff
> color sel #a1cfdfff
> color sel #a2ccdfff
> color sel #a1cadfff
> color sel #a0c7dfff
> color sel #a0c6dfff
> color sel #9fc5dfff
> color sel #9ec4dfff
> color sel #9dc2dfff
> color sel #9dc1dfff
> color sel #9cc1dfff
> color sel #9cc0dfff
> color sel #9abcdfff
> color sel #9abadfff
> color sel #99b8dfff
> color sel #97b1dfff
> color sel #95abdfff
> color sel #94a8dfff
> color sel #93a6dfff
> color sel #93a5dfff
> color sel #92a4dfff
> color sel #91a3dfff
> color sel #8fa2dfff
> color sel #8da0dfff
> color sel #8c9fdfff
> color sel #8b9fdfff
> color sel #8aa0dfff
> color sel #88a1dfff
> color sel #86a4dfff
> color sel #84a7dfff
> color sel #84a8dfff
> color sel #83aadfff
> color sel #82aedfff
> color sel #80b0dfff
> color sel #7fb1dfff
> color sel #7eb2dfff
> color sel #7cb4dfff
> color sel #7cbedfff
> color sel #7dc8dfff
> color sel #7dd1dfff
> color sel #7ddddfff
> color sel #7cdfd4ff
> color sel #7bdfceff
> color sel #78dfbeff
> color sel #77dfbcff
> color sel #74dfafff
> color sel #72dfa9ff
> color sel #71dfa8ff
> color sel #71dfa7ff
> color sel #71dfa6ff
> color sel #6fdfa3ff
> color sel #6fdfa1ff
> color sel #6cdf9bff
> color sel #69df96ff
> color sel #69df95ff
> color sel #65df8fff
> color sel #62df8bff
> color sel #62df8aff
> color sel #61df8aff
> color sel #60df8aff
> color sel #5fdf8aff
> color sel #5edf8aff
> color sel #5ddf8bff
> color sel #5adf8bff
> color sel #56df8aff
> color sel #53df89ff
> color sel #50df88ff
> color sel #4fdf88ff
> color sel #4ddf87ff
> color sel #4cdf87ff
> color sel #48df87ff
> color sel #46df87ff
> color sel #42df87ff
> color sel #41df87ff
> color sel #41df85ff
> color sel #40df85ff
> color sel #3cdf7eff
> color sel #38df76ff
> color sel #35df6eff
> color sel #35df6cff
> color sel #35df64ff
> color sel #35df60ff
> color sel #35df5fff
> color sel #35df5dff
> color sel #34df57ff
> color sel #34df52ff
> color sel #33df50ff
> color sel #34df50ff
> color sel #34df4dff
> color sel #35df4cff
> color sel #35df4bff
> color sel #35df4aff
> color sel #36df49ff
> color sel #36df48ff
> color sel #37df46ff
> color sel #38df46ff
> color sel #39df43ff
> color sel #3adf41ff
> color sel #3bdf41ff
> color sel #3bdf40ff
> color sel #3bdf3eff
> color sel #3ddf3cff
> color sel #43df3eff
> color sel #4adf40ff
> color sel #51df42ff
> color sel #53df42ff
> color sel #54df42ff
> color sel #55df42ff
> color sel #56df42ff
> color sel #57df42ff
> color sel #58df42ff
> color sel #5adf42ff
> color sel #5bdf41ff
> color sel #5ddf41ff
> color sel #5cdf40ff
> color sel #5ddf40ff
> color sel #5ddf41ff
> color sel #5edf41ff
> color sel #5edf47ff
> color sel #5ddf4cff
> color sel #5ddf4dff
> color sel #5cdf4eff
> color sel #5adf50ff
> color sel #59df50ff
> color sel #55df58ff
> color sel #55df5bff
> color sel #55df5cff
> color sel #55df5dff
> color sel #55df5eff
> color sel #54df5eff
> color sel #52df5fff
> color sel #4fdf60ff
> color sel #4ddf62ff
> color sel #4ddf65ff
> color sel #4edf69ff
> color sel #4edf6cff
> color sel #4edf6dff
> color sel #4edf70ff
> color sel #4edf75ff
> color sel #4edf76ff
> color sel #4fdf7aff
> color sel #4fdf7cff
> color sel #50df7dff
> color sel #50df7eff
> color sel #50df7fff
> color sel #51df80ff
> color sel #51df82ff
> color sel #51df83ff
> color sel #52df84ff
> color sel #52df85ff
> color sel #54df8aff
> color sel #54df8cff
> color sel #54df8eff
> color sel #52df8eff
> color sel #47df8cff
> color sel #45df8cff
> color sel #42df8aff
> color sel #3fdf89ff
> color sel #3edf89ff
> color sel #3bdf87ff
> color sel #38df86ff
> color sel #37df86ff
> color sel #35df86ff
> color sel #34df87ff
> color sel #34df8aff
> color sel #34df8cff
> color sel #35df91ff
> color sel #37df94ff
> color sel #38df9aff
> color sel #39df9bff
> color sel #39df9cff
> color sel #3adf9dff
> color sel #3adf9eff
> color sel #3adf9fff
> color sel #39dfa0ff
> color sel #39dfa2ff
> color sel #38dfa2ff
> color sel #38dfa3ff
> color sel #38dfa4ff
> color sel #38dfa5ff
> color sel #39dfa7ff
> color sel #39dfa8ff
> color sel #3adfa9ff
> color sel #3bdfaaff
> color sel #3cdfacff
> color sel #3cdfaeff
> color sel #3ddfafff
> color sel #3ddfb0ff
> color sel #3cdfb0ff
> color sel #3bdfb0ff
> color sel #3adfb0ff
> color sel #3adfb1ff
> color sel #39dfb1ff
> color sel #38dfb1ff
> color sel #37dfb1ff
> color sel #35dfb1ff
> color sel #34dfb2ff
> color sel #33dfb2ff
> color sel #32dfb2ff
> color sel #32dfb1ff
> color sel #32dfb0ff
> color sel #32dfafff
> color sel #31dfaeff
> color sel #32dfaeff
> color sel #34dfaeff
> color sel #36dfaeff
> color sel #3ddfb0ff
> color sel #48dfb1ff
> color sel #50dfb3ff
> color sel #58dfb3ff
> color sel #5ddfb4ff
> color sel #5edfb4ff
> color sel #62dfb4ff
> color sel #68dfb5ff
> color sel #6bdfb5ff
> color sel #70dfb5ff
> color sel #71dfb6ff
> color sel #72dfb6ff
> color sel #74dfb6ff
> color sel #76dfb6ff
> color sel #77dfb6ff
> color sel #7edfb7ff
> color sel #84dfb7ff
> color sel #85dfb7ff
> color sel #87dfb6ff
> color sel #8adfb6ff
> color sel #8bdfb5ff
> color sel #8bdfb4ff
> color sel #8ddfaeff
> color sel #8ddfabff
> color sel #8ddfaaff
> color sel #8ddfa8ff
> color sel #8ddfa5ff
> color sel #8ddfa2ff
> color sel #8ddfa1ff
> color sel #8fdfa0ff
> color sel #8fdf9fff
> color sel #8fdf9eff
> color sel #8edf9dff
> color sel #8edf9cff
> color sel #8ddf9bff
> color sel #8ddf9aff
> color sel #8cdf99ff
> color sel #8ddf99ff
> color sel #8cdf98ff
> color sel #8cdf97ff
> color sel #8adf96ff
> color sel #89df95ff
> color sel #86df94ff
> color sel #85df92ff
> color sel #84df92ff
> color sel #82df90ff
> color sel #81df90ff
> color sel #80df8fff
> color sel #80df8eff
> color sel #7fdf8fff
> color sel #7ddf8dff
> color sel #7bdf8bff
> color sel #7adf8bff
> color sel #78df8aff
> color sel #77df8aff
> color sel #76df89ff
> color sel #75df89ff
> color sel #74df88ff
> color sel #73df88ff
> color sel #74df88ff
> color sel #74df89ff
> color sel #76df89ff
> color sel #76df8aff
> color sel #77df8aff
> color sel #79df8bff
> color sel #7adf8cff
> color sel #7ddf8eff
> color sel #7fdf8fff
> color sel #82df92ff
> color sel #86df95ff
> color sel #86df96ff
> color sel #89df99ff
> color sel #8adf99ff
> color sel #8bdf9bff
> color sel #8cdf9bff
> color sel #8edf9cff
> color sel #90df9eff
> color sel #93df9fff
> color sel #94dfa0ff
> color sel #9adfa2ff
> color sel #9ddfa0ff
> color sel #9fdf9fff
> color sel #a5dfa0ff
> color sel #a9df9fff
> color sel #aadf9fff
> color sel #aedf9eff
> color sel #b1df9eff
> color sel #b3df9eff
> color sel #b4df9eff
> color sel #b3df9dff
> color sel #b3df9cff
> color sel #b2df9bff
> color sel #b1df99ff
> color sel #b1df98ff
> color sel #b0df97ff
> color sel #afdf96ff
> color sel #aedf94ff
> color sel #addf93ff
> color sel #abdf92ff
> color sel #abdf91ff
> color sel #aadf91ff
> color sel #aadf90ff
> color sel #a9df90ff
> color sel #a7df8fff
> color sel #a6df8fff
> color sel #a5df8eff
> color sel #a4df8eff
> color sel #a3df8eff
> color sel #a3df8dff
> color sel #a3df8cff
> color sel #a2df8cff
> color sel #a1df8bff
> color sel #9fdf89ff
> color sel #9fdf88ff
> color sel #9edf88ff
> color sel #9edf87ff
> color sel #9cdf86ff
> color sel #9adf85ff
> color sel #99df85ff
> color sel #98df84ff
> color sel #99df85ff
> color sel #99df86ff
> color sel #9adf86ff
> color sel #9adf87ff
> color sel #9bdf88ff
> color sel #9ddf8bff
> color sel #9edf8cff
> color sel #a0df8fff
> color sel #a2df92ff
> color sel #a3df93ff
> color sel #a4df94ff
> color sel #a5df95ff
> color sel #a5df96ff
> color sel #a5df97ff
> color sel #a4df98ff
> color sel #a3df98ff
> color sel #a2df98ff
> color sel #a1df99ff
> color sel #a0df99ff
> color sel #9fdf99ff
> color sel #9edf99ff
> color sel #9ddf99ff
> color sel #9adf98ff
> color sel #97df98ff
> color sel #97df99ff
> color sel #90d693ff
> color sel #90d592ff
> color sel #8fd492ff
> color sel #8acd8cff
> color sel #87c889ff
> color sel #86c789ff
> color sel #86c788ff
> color sel #86c688ff
> color sel #85c687ff
> color sel #85c587ff
> color sel #84c487ff
> color sel #84c486ff
> color sel #84c386ff
> color sel #80c37eff
> color sel #7fc37dff
> color sel #80c37eff
> color sel #7fc37eff
> color sel #7ec37eff
> color sel #7fc37eff
> color sel #7ec380ff
> color sel #7fc380ff
> color sel #7ec381ff
> color sel #7fc382ff
> color sel #80c383ff
> color sel #81c385ff
> color sel #81c386ff
> color sel #80c386ff
> color sel #80c387ff
> color sel #7fc386ff
> color sel #7fc385ff
> color sel #7dc37dff
> color sel #7dc37bff
> color sel #7dc37aff
> color sel #7dc379ff
> color sel #7ec37aff
> color sel #7fc37aff
> color sel #80c37bff
> color sel #81c37cff
> color sel #82c37cff
> color sel #84c37dff
> color sel #87c37eff
> color sel #88c37eff
> color sel #87c37cff
> color sel #86c37cff
> color sel #85c37cff
> color sel #82c37aff
> color sel #80c379ff
> color sel #7dc377ff
> color sel #7cc377ff
> color sel #7bc377ff
> color sel #79c376ff
> color sel #76c376ff
> color sel #75c376ff
> color sel #74c376ff
> color sel #71c376ff
> color sel #6fc376ff
> color sel #6ec376ff
> color sel #6ec375ff
> color sel #6ec376ff
> color sel #6dc375ff
> color sel #6dc376ff
> color sel #6ec377ff
> color sel #6fc378ff
> color sel #70c379ff
> color sel #70c37aff
> color sel #70c37bff
> color sel #71c37dff
> color sel #71c37eff
> color sel #71c37fff
> color sel #70c37fff
> color sel #70c380ff
> color sel #6fc380ff
> color sel #6ec381ff
> color sel #6dc381ff
> color sel #6cc381ff
> color sel #6bc381ff
> color sel #68c382ff
> color sel #67c382ff
> color sel #65c382ff
> color sel #65c383ff
> color sel #66c383ff
> color sel #67c383ff
> color sel #67c384ff
> color sel #68c385ff
> color sel #68c386ff
> color sel #69c387ff
> color sel #69c388ff
> color sel #6ac389ff
> color sel #6bc38aff
> color sel #6cc38aff
> color sel #6cc38bff
> color sel #6dc38bff
> color sel #6dc38aff
> color sel #6dc389ff
> color sel #6ec389ff
> color sel #6fc389ff
> color sel #70c388ff
> color sel byhetero
> select add #5
16344 atoms, 16550 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> select subtract #5
Nothing selected
> graphics silhouettes true
> select #5/A,B
13596 atoms, 13774 bonds, 2 pseudobonds, 868 residues, 2 models selected
> select #5/A,B ~NAG
Expected a keyword
> select #5/A:~NAG,B:~NAG
Expected an objects specifier or a keyword
> select #5/A:~NAG, sel #5/B:~NAG
Expected an objects specifier or a keyword
> select #5:NAG
336 atoms, 336 bonds, 12 residues, 1 model selected
> select ~sel
33056 atoms, 33678 bonds, 6 pseudobonds, 3238 residues, 10 models selected
> hide sel & #!5 atoms
> undo
> select #5:NAG, sel #5:173,551, 511,460, 363,464
488 atoms, 486 bonds, 24 residues, 1 model selected
> select #5:NAG, sel #5:173,551, 511,460, 363,464,277
514 atoms, 512 bonds, 26 residues, 1 model selected
> select ~sel
32878 atoms, 33486 bonds, 6 pseudobonds, 3224 residues, 10 models selected
> hide sel & #!5 atoms
> select add #5
33392 atoms, 34026 bonds, 6 pseudobonds, 3250 residues, 10 models selected
> select subtract #5
17048 atoms, 17476 bonds, 2194 residues, 8 models selected
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> volume #6 level 0.04851
> undo
> hide #!5 models
> show #!5 models
> select add #5
33392 atoms, 34026 bonds, 6 pseudobonds, 3250 residues, 10 models selected
> select subtract #5
17048 atoms, 17476 bonds, 2194 residues, 8 models selected
> ui tool show "Side View"
> show #!2 models
> select subtract #2
8470 atoms, 8682 bonds, 1092 residues, 7 models selected
> select subtract #6
8470 atoms, 8682 bonds, 1092 residues, 5 models selected
> select subtract #1
8470 atoms, 8682 bonds, 1092 residues, 3 models selected
> select subtract #4
8470 atoms, 8682 bonds, 1092 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #!5 models
> select #2:NAG
84 atoms, 84 bonds, 6 residues, 1 model selected
> color sel #70c388ff
> color sel #70c488ff
> color sel byhetero
> select add #2
8578 atoms, 8794 bonds, 1102 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
8578 atoms, 8794 bonds, 1102 residues, 1 model selected
> color sel byhetero
> select subtract #2
Nothing selected
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> save "/Users/zhouling95/Documents/Academic/McLellan Lab/05 PIV
> HN/colored_all.cxs" includeMaps true
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!2 models
> interfaces select #5/H contacting #5/A bothSides true
45 contacting residues
> show (sel-residues & sidechain) target ab
> hide H
> size stickRadius 0.3
Changed 34026 bond radii
> select add #5
16344 atoms, 16550 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> show #!6 models
> volume #6 color #dfdfdf3e
> volume #6 color #dfdfdf3d
> hide #!6 models
> select subtract #5
Nothing selected
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.02257
> hide #!6 models
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> interfaces select #15/H contacting #5/A bothSides true
No atoms specified
> interfaces select #5/H contacting #5/A bothSides true
45 contacting residues
> hbonds sel
79 hydrogen bonds found
> hbonds sel intraMol false
40 hydrogen bonds found
> select add #5
16344 atoms, 16550 bonds, 14 pseudobonds, 1056 residues, 3 models selected
> select subtract #5
Nothing selected
> select #5/H:97-101
131 atoms, 134 bonds, 9 residues, 1 model selected
> interfaces select #5/H:97-101 contacting #5/A bothSides true
21 contacting residues
> show (sel-residues & sidechain) target ab
> hide H
> hbonds sel
38 hydrogen bonds found
> hbonds sel intrMol False
Expected a keyword
> hbonds sel intrMol false
Expected a keyword
> hbonds intrMol false
Expected a keyword
> hbonds sel
38 hydrogen bonds found
> addh
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for real_space_refined_085-coot-0_real_space_refined_086.pdb (#2) chain A; guessing termini instead
No usable SEQRES records for
real_space_refined_085-coot-0_real_space_refined_086.pdb (#2) chain B;
guessing termini instead
No usable SEQRES records for
real_space_refined_085-coot-0_real_space_refined_086.pdb (#2) chain H;
guessing termini instead
No usable SEQRES records for
real_space_refined_085-coot-0_real_space_refined_086.pdb (#2) chain I;
guessing termini instead
Chain-initial residues that are actual N termini:
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/A THR 143,
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/B THR 143,
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/H GLN 1,
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/I GLN 1
Chain-initial residues that are not actual N termini:
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/A SER 390,
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/B SER 390
Chain-final residues that are actual C termini:
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/A SER 572,
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/B SER 572,
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/H GLY 121,
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/I GLY 121
Chain-final residues that are not actual C termini:
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/A LYS 386,
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/B LYS 386
862 hydrogen bonds
Adding 'H' to real_space_refined_085-coot-0_real_space_refined_086.pdb #2/A
SER 390
Adding 'H' to real_space_refined_085-coot-0_real_space_refined_086.pdb #2/B
SER 390
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/A LYS 386 is not
terminus, removing H atom from 'C'
real_space_refined_085-coot-0_real_space_refined_086.pdb #2/B LYS 386 is not
terminus, removing H atom from 'C'
No usable SEQRES records for RV3_HN_VHH59_dimer_real_space_refined_019.pdb
(#3) chain A; guessing termini instead
No usable SEQRES records for RV3_HN_VHH59_dimer_real_space_refined_019.pdb
(#3) chain B; guessing termini instead
No usable SEQRES records for RV3_HN_VHH59_dimer_real_space_refined_019.pdb
(#3) chain C; guessing termini instead
No usable SEQRES records for RV3_HN_VHH59_dimer_real_space_refined_019.pdb
(#3) chain D; guessing termini instead
Chain-initial residues that are actual N termini:
RV3_HN_VHH59_dimer_real_space_refined_019.pdb #3/A VAL 2,
RV3_HN_VHH59_dimer_real_space_refined_019.pdb #3/B VAL 2,
RV3_HN_VHH59_dimer_real_space_refined_019.pdb #3/C THR 143,
RV3_HN_VHH59_dimer_real_space_refined_019.pdb #3/D THR 143
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
RV3_HN_VHH59_dimer_real_space_refined_019.pdb #3/A SER 120,
RV3_HN_VHH59_dimer_real_space_refined_019.pdb #3/B SER 120,
RV3_HN_VHH59_dimer_real_space_refined_019.pdb #3/C SER 569,
RV3_HN_VHH59_dimer_real_space_refined_019.pdb #3/D SER 569
Chain-final residues that are not actual C termini:
878 hydrogen bonds
No usable SEQRES records for
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb (#5) chain A; guessing
termini instead
No usable SEQRES records for
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb (#5) chain B; guessing
termini instead
No usable SEQRES records for
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb (#5) chain H; guessing
termini instead
No usable SEQRES records for
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb (#5) chain I; guessing
termini instead
Chain-initial residues that are actual N termini:
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/A HIS 145,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/B HIS 145,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/H GLN 1,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/I GLN 1
Chain-initial residues that are not actual N termini:
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/A ILE 516,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/B ILE 516,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/H GLU 46,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/H VAL 89,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/I GLU 46,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/I VAL 89
Chain-final residues that are actual C termini:
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/A SER 575,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/B SER 575
Chain-final residues that are not actual C termini:
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/A THR 512,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/B THR 512,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/H GLY 104,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/H ARG 38,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/H GLN 81,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/I GLY 104,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/I ARG 38,
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/I GLN 81
779 hydrogen bonds
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/H GLY 104 is not
terminus, removing H atom from 'C'
RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/I GLY 104 is not
terminus, removing H atom from 'C'
16731 hydrogens added
> interfaces select #5/H:97-101 contacting #5/A bothSides true
21 contacting residues
> hbonds showDist
Missing "showDist" keyword's argument
> hbonds
2931 hydrogen bonds found
> hbonds hide
Expected a keyword
> interfaces select #5/H:97-101 contacting #5/A bothSides true
21 contacting residues
> hbonds
2931 hydrogen bonds found
> hbonds sel
33 hydrogen bonds found
> hbonds sel intraMol false
15 hydrogen bonds found
> show sel target ab
> select #5/A:426@HH22
1 atom, 1 residue, 1 model selected
> select add #5/A:426@HH12
2 atoms, 1 residue, 1 model selected
> select add #5/H:99@HG
3 atoms, 2 residues, 1 model selected
> select add #5/A:502@HH22
4 atoms, 3 residues, 1 model selected
> select add #5/A:502@HH12
5 atoms, 3 residues, 1 model selected
> select ~sel
50118 atoms, 50752 bonds, 15 pseudobonds, 3250 residues, 11 models selected
> hide H
> select ~sel
5 atoms, 3 residues, 1 model selected
> hbonds sel intraMol false
0 hydrogen bonds found
> show sel target ab
> hbonds sel intraMol false
0 hydrogen bonds found
> hbonds sel intraMol false
0 hydrogen bonds found
> interfaces select #5/H:97-101 contacting #5/A bothSides true
21 contacting residues
> hbonds sel intraMol false
15 hydrogen bonds found
> select add #5
16345 atoms, 16551 bonds, 12 pseudobonds, 1056 residues, 3 models selected
> select subtract #5
Nothing selected
> select #5/H:103
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> select clear
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> select #5/278
Nothing selected
> select #5/A:278
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> select #5/A:426@HH22
1 atom, 1 residue, 1 model selected
> select add #5/A:426@HH12
2 atoms, 1 residue, 1 model selected
> select add #5/A:502@HH22
3 atoms, 2 residues, 1 model selected
> select add #5/H:99@HG
4 atoms, 3 residues, 1 model selected
> hide sel
> ui tool show Distances
> select #5/A:426@NH1
1 atom, 1 residue, 1 model selected
> select #5/H:100A
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #5/A:426@NH1
8 atoms, 6 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select #5/H:100A
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #5/A:426@NH1
8 atoms, 6 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select #5/H:100A
7 atoms, 6 bonds, 1 residue, 1 model selected
> cartoon hide sel
> cartoon sel
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> cartoon sel
> show (sel-residues & sidechain) target ab
> select #5/A:502@HH12
1 atom, 1 residue, 1 model selected
> select #5/A:502@HH12
1 atom, 1 residue, 1 model selected
> hide sel
> select #5/H:100D@OD1
1 atom, 1 residue, 1 model selected
> select add #5/A:502@NH1
2 atoms, 2 residues, 1 model selected
> distance #5/H:100D@OD1 #5/A:502@NH1
Distance between RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/H ASP
100D OD1 and /A ARG 502 NH1: 2.913Å
> select #5/H:100A
7 atoms, 6 bonds, 1 residue, 1 model selected
> cartoon hide sel
> select #5/H:100A@O
1 atom, 1 residue, 1 model selected
> select add #5/A:426@NH1
2 atoms, 2 residues, 1 model selected
> select add #5/A:426@NH2
3 atoms, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select #5/A:426@NH2
1 atom, 1 residue, 1 model selected
> select add #5/H:100A@O
2 atoms, 2 residues, 1 model selected
> distance #5/A:426@NH2 #5/H:100A@O
Distance between RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/A ARG
426 NH2 and /H GLY 100A O: 3.252Å
> select #5/A:426@NH1
1 atom, 1 residue, 1 model selected
> select add #5/H:100A@O
2 atoms, 2 residues, 1 model selected
> distance #5/A:426@NH1 #5/H:100A@O
Distance between RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/A ARG
426 NH1 and /H GLY 100A O: 2.884Å
> select #5/H:100A@C
1 atom, 1 residue, 1 model selected
> select #5/H:100A
7 atoms, 6 bonds, 1 residue, 1 model selected
> cartoon sel
> select #5/A:216
10 atoms, 9 bonds, 1 residue, 1 model selected
> cartoon hide sel
> select #5/H:99@OG
1 atom, 1 residue, 1 model selected
> select #5/A:216@O
1 atom, 1 residue, 1 model selected
> select add #5/H:99@OG
2 atoms, 2 residues, 1 model selected
> distance #5/A:216@O #5/H:99@OG
Distance between RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/A CYS
216 O and /H SER 99 OG: 2.729Å
> select #5/A:216
10 atoms, 9 bonds, 1 residue, 1 model selected
> cartoon hide sel
> cartoon sel
> distance style symbol false
> distance style symbol true
> distance style symbol false
> distance style symbol true
> hide #8.1 models
> select #5/A:502@NH2
1 atom, 1 residue, 1 model selected
> select add #5/H:100D@OD1
2 atoms, 2 residues, 1 model selected
> distance #5/A:502@NH2 #5/H:100D@OD1
Distance between RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/A ARG
502 NH2 and /H ASP 100D OD1: 2.732Å
> select #5/H:100D@OD1
1 atom, 1 residue, 1 model selected
> delete pseudobonds sel
> select #5/A:530
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel
> color #8 #faf076ff models
> color #8 #faef68ff models
> color #8 #faf878ff models
> color #8 #faf676ff models
> color #8 #faf475ff models
> select add #5
16345 atoms, 16551 bonds, 16 pseudobonds, 1056 residues, 4 models selected
> select subtract #5
Nothing selected
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> select #5/A:278
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hbonds sel
2 hydrogen bonds found
> interfaces select #5/H:97-101 contacting #5/A bothSides true
21 contacting residues
> hbonds sel
33 hydrogen bonds found
> select #5/A:279
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide #7 models
> hide H
> select #5/A:460
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show Distances
> select #5/H:101@OD2
1 atom, 1 residue, 1 model selected
> select add #5/A:460@ND2
2 atoms, 2 residues, 1 model selected
> distance #5/H:101@OD2 #5/A:460@ND2
Distance between RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/H ASP
101 OD2 and /A ASN 460 ND2: 2.754Å
> distance style color #fae47b
> distance style color #fae47c
> distance style color #fae483
> distance style color #fae484
> distance style color #fae485
> distance style color #fae486
> distance style color #fae388
> distance style color #fae48b
> distance style color #fae48c
> distance style color #fae38d
> distance style color #fae38e
> distance style color #fae48e
> distance style color #fae38c
> distance style color #fae38b
> distance style color #fae28a
> distance style color #fae289
> distance style color #fae288
> distance style color #fae287
> distance style color #fae083
> distance style color #fae082
> distance style color #fadf81
> distance style color #fadf80
> distance style color #fae07d
> distance style color #fadf7b
> distance style color #fadf7a
> select #5/A:472
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #5/H:37@OH
16 atoms, 14 bonds, 2 residues, 1 model selected
> select subtract #5/A:472@OE1
15 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/A:472@OE1
1 atom, 1 residue, 1 model selected
> select add #5/H:37@OH
2 atoms, 2 residues, 1 model selected
> distance #5/A:472@OE1 #5/H:37@OH
Distance between RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/A GLU
472 OE1 and /H TYR 37 OH: 3.188Å
> select #5/A:278
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #5/A:278@OE2
1 atom, 1 residue, 1 model selected
> select add #5/H:100C@OH
2 atoms, 2 residues, 1 model selected
> distance #5/A:278@OE2 #5/H:100C@OH
Distance between RV1_HN_60_dimer_07-isolde_real_space_refined_011.pdb #5/A GLU
278 OE2 and /H TYR 100C OH: 2.795Å
> select #5/A:321
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide H
> select #5/A:322
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #5/A:339
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/A:372
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5/A:472
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #5
16345 atoms, 16551 bonds, 37 pseudobonds, 1056 residues, 4 models selected
> select subtract #5
Nothing selected
> save "/Users/zhouling95/Documents/Academic/McLellan Lab/05 PIV
> HN/colored_all_hbonds.cxs"
> select #5/H:95
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel
> select add #5
16345 atoms, 16551 bonds, 37 pseudobonds, 1056 residues, 4 models selected
> select subtract #5
Nothing selected
> select #5/H:32
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel
> select add #5
16345 atoms, 16551 bonds, 37 pseudobonds, 1056 residues, 4 models selected
> select subtract #5
Nothing selected
> select #5/A:373
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel
> select #5/A:474
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel
> select add #5
16345 atoms, 16551 bonds, 37 pseudobonds, 1056 residues, 4 models selected
> select subtract #5
Nothing selected
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> select #5/A:339
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:575
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/A:145-575
6630 atoms, 6713 bonds, 14 pseudobonds, 428 residues, 3 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/C
Alignment identifier is 3/C
> select #3/C:143
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/C
6657 atoms, 6745 bonds, 427 residues, 1 model selected
> select add #3
16774 atoms, 16986 bonds, 1092 residues, 1 model selected
> select subtract #3
Nothing selected
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/RV3 HN
> VHH/Structures/RV3 HN
> VHH59/RV3_HN_VHH59_024_kabat_combine_real_space_refined_025.pdb"
Chain information for
RV3_HN_VHH59_024_kabat_combine_real_space_refined_025.pdb #9
---
Chain | Description
A B | No description available
H I | No description available
Computing secondary structure
> hide #!8 models
> hide #!5 models
> show #3 models
> hide #3 models
> show #3 models
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/RV3 HN
> VHH/Structures/RV3 HN
> VHH59/RV3_HN_VHH59_024_kabat_combine_real_space_refined_025.pdb"
Chain information for
RV3_HN_VHH59_024_kabat_combine_real_space_refined_025.pdb #10
---
Chain | Description
A B | No description available
H I | No description available
Computing secondary structure
> close #10
> open "/Users/zhouling95/Documents/Academic/McLellan Lab/05 PIV
> HN/VHH59/RV3_59.pdb"
Chain information for RV3_59.pdb #10
---
Chain | Description
A B | No description available
H I | No description available
Computing secondary structure
> close #9
> show #!2 models
> hide #!2 models
> color #10 by #3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #10/A
6733 atoms, 6816 bonds, 1 pseudobond, 430 residues, 2 models selected
> ui tool show "Color Actions"
> color sel royal blue
> select #10/B
6733 atoms, 6816 bonds, 1 pseudobond, 430 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> color sel light steel blue
> color sel sky blue
> color sel light blue
> select #10/H,I
1774 atoms, 1808 bonds, 238 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale violet red
> hide #3 models
> select #10:NAG
168 atoms, 168 bonds, 6 residues, 1 model selected
> color sel #70c388ff
> color sel byhetero
> select down
168 atoms, 168 bonds, 6 residues, 1 model selected
> select #10/A,B:308,323
40 atoms, 36 bonds, 4 residues, 1 model selected
> select #10/A,B:308,323,575
96 atoms, 92 bonds, 6 residues, 1 model selected
> select #10/A,B:308,323,523
66 atoms, 60 bonds, 6 residues, 1 model selected
> select #10/A,B:308,323,523,351
92 atoms, 84 bonds, 8 residues, 1 model selected
> select #10/A,B:308,523,351
78 atoms, 72 bonds, 6 residues, 1 model selected
> color sel byhetero
> select ~sel
65285 atoms, 66107 bonds, 48 pseudobonds, 4342 residues, 15 models selected
> hide sel & #!10 atoms
> undo
> select #10/A,B:308,523,351, NAG
246 atoms, 246 bonds, 12 residues, 1 model selected
> select ~sel
65117 atoms, 65939 bonds, 48 pseudobonds, 4336 residues, 15 models selected
> hide sel & #!10 atoms
> select subtract #1
65117 atoms, 65939 bonds, 48 pseudobonds, 4336 residues, 13 models selected
> select subtract #2
48113 atoms, 48719 bonds, 44 pseudobonds, 3234 residues, 12 models selected
> select subtract #3
31339 atoms, 31733 bonds, 39 pseudobonds, 2142 residues, 11 models selected
> select subtract #8.1
31339 atoms, 31733 bonds, 39 pseudobonds, 2142 residues, 10 models selected
> select add #8
31339 atoms, 31733 bonds, 39 pseudobonds, 2142 residues, 11 models selected
> select subtract #8.1
31339 atoms, 31733 bonds, 39 pseudobonds, 2142 residues, 10 models selected
> select add #8
31339 atoms, 31733 bonds, 39 pseudobonds, 2142 residues, 11 models selected
> select subtract #8.1
31339 atoms, 31733 bonds, 39 pseudobonds, 2142 residues, 10 models selected
> select subtract #4
31339 atoms, 31733 bonds, 39 pseudobonds, 2142 residues, 8 models selected
> select subtract #6
31339 atoms, 31733 bonds, 39 pseudobonds, 2142 residues, 6 models selected
> select subtract #5
14994 atoms, 15182 bonds, 2 pseudobonds, 1086 residues, 2 models selected
> select add #10
15240 atoms, 15440 bonds, 2 pseudobonds, 1098 residues, 2 models selected
> select subtract #10
Nothing selected
> show #!4 models
> select add #10
15240 atoms, 15440 bonds, 2 pseudobonds, 1098 residues, 2 models selected
> color zone #4 near sel & #10 distance 5.6
> select #10:NAG
168 atoms, 168 bonds, 6 residues, 1 model selected
> select #10/A:NAG
84 atoms, 84 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select #10/B:NAG
84 atoms, 84 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light blue
> color zone #4 near sel & #10 distance 5.6
> select add #10
15240 atoms, 15440 bonds, 2 pseudobonds, 1098 residues, 2 models selected
> color zone #4 near sel & #10 distance 5.6
> select #10/A
6733 atoms, 6816 bonds, 1 pseudobond, 430 residues, 2 models selected
> ui tool show "Color Actions"
> color sel royal blue
> select #10/B
6733 atoms, 6816 bonds, 1 pseudobond, 430 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light blue
> select add #10
15240 atoms, 15440 bonds, 2 pseudobonds, 1098 residues, 2 models selected
> color zone #4 near sel & #10 distance 5.6
> select subtract #10
Nothing selected
> select #10/A
6733 atoms, 6816 bonds, 1 pseudobond, 430 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dodger blue
> select #10/B
6733 atoms, 6816 bonds, 1 pseudobond, 430 residues, 2 models selected
> color sel light steel blue
> color zone #4 near sel & #10 distance 5.6
> select add #10
15240 atoms, 15440 bonds, 2 pseudobonds, 1098 residues, 2 models selected
> select subtract #10
Nothing selected
> select add #10
15240 atoms, 15440 bonds, 2 pseudobonds, 1098 residues, 2 models selected
> color zone #4 near sel & #10 distance 5.6
> hide #!10 models
> select subtract #10
Nothing selected
> select add #10
15240 atoms, 15440 bonds, 2 pseudobonds, 1098 residues, 2 models selected
> show #!10 models
> select subtract #10
Nothing selected
> select #10/B:NAG
84 atoms, 84 bonds, 3 residues, 1 model selected
> color sel #71c388ff
> color sel byhetero
> select add #10
15240 atoms, 15440 bonds, 2 pseudobonds, 1098 residues, 2 models selected
> select subtract #10
Nothing selected
> select #10/NAG
Nothing selected
> select #10:NAG
168 atoms, 168 bonds, 6 residues, 1 model selected
> color sel #70c388ff
> color sel byhetero
> select add #10
15240 atoms, 15440 bonds, 2 pseudobonds, 1098 residues, 2 models selected
> select subtract #10
Nothing selected
> save "/Users/zhouling95/Documents/Academic/McLellan Lab/05 PIV
> HN/colored_all_hbonds_59.cxs" includeMaps true
> hide #!10 models
> graphics silhouettes false
> volume #4 level 0.08057
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> mousemode middleMode center
> cofr centerOfView
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue
> alias cootmode_mesh set bgColor black; surface cap false; surface style
> mesh; lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball;
> style ions ball; size ballscale 0.2; size stickradius 0.07; cofr
> centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> #3d60ffff; transparency 50
> alias cootmode_off surface style solid; lighting soft; graphics silhouettes
> false; hide atoms; default_mol_display; transparency 0; symclip 40; color
> ##~num_residues grey; size stickradius 0.2;
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette Pastel1-5;
> lighting soft; color byhet
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1; style stick; size stickRadius 0.5; ~disp @H*; color byhet
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias rock_movie cofr showpivot false; movie record supersample 3; rock y
> 40; wait 136; movie encode ~/Desktop/rock_movie.mp4 quality high; stop
> alias publication_figure save Figure.png format png supersample 3
> transparentBackground true width 3000 height 3000
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add Hide_H command "~disp @H*"
> buttonpanel Shortcuts add Licorice command licorice
> buttonpanel Shortcuts add Ribbons command "preset ribbons"
> buttonpanel Shortcuts add RockMovie command rock_movie
> buttonpanel Shortcuts add SymClip10 command "symclip 10"
> buttonpanel Shortcuts add SymClip20 command "symclip 20"
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add PubFigure command publication_figure
> buttonpanel Shortcuts add coot_mode command cootmode
> buttonpanel Shortcuts add coot_mesh command cootmode_mesh
> buttonpanel Shortcuts add coot_off command cootmode_off
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> ui tool show "Model Panel"
UCSF ChimeraX version: 1.9rc202411082121 (2024-11-08)
© 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 M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,8
Model Number: MX2J3LL/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B2091)
Kernel Version: Darwin 24.1.0
Time since boot: 1 day, 43 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
U32J59x:
Resolution: 4096 x 2304
UI Looks like: 2048 x 1152 @ 30.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
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: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-Clipper: 0.23.0
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: 1.9rc202411082121
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.5
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.11
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.2.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.8
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.54.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.1
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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