![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 weeks ago
Last modified 3 weeks ago
#19548 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.7.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x000000020c7fe140 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, 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, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)
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"translated" : false,
"cpuType" : "ARM-64",
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"procLaunch" : "2025-12-30 22:59:07.2583 +1300",
"procStartAbsTime" : 688336080330,
"procExitAbsTime" : 964926797308,
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"crashReporterKey" : "B764343E-6690-75E4-BB9E-16AB9F8A0AF2",
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 18614,
"sleepWakeUUID" : "3178711B-6A28-4D40-B0FE-E8BE8C06A674",
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"exception" : {"codes":"0x0000000000000001, 0x000048900c8db5f0","rawCodes":[1,79783523104240],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000048900c8db5f0"},
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/New Folder/PCH45_Gp25_ModelChecking.cxs"
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc as #1, grid size 416,416,416, pixel
1.37, shown at level 0.496, step 1, values float32
Log from Tue Dec 30 21:54:50 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/PCH45 Gen 2Maps/PCH45
> Neck/PCH45_neck_RawData/PCH45_Neck_C6_3_40A_map_sharp.mrc"
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc as #1, grid size 416,416,416, pixel
1.37, shown at level 0.496, step 2, values float32
> surface dust #1 size 13.7
> volume #1 step 1
> open "/Users/croal939/Downloads/Output for PCH45_NonbulbRingoutput_output
> (3).cif"
Summary of feedback from opening /Users/croal939/Downloads/Output for
PCH45_NonbulbRingoutput_output (3).cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for Output for PCH45_NonbulbRingoutput_output (3).cif #2
---
Chain | Description
0 | No description available
1 | No description available
3 | No description available
5 8 | No description available
7 | No description available
A | No description available
A5 | No description available
A6 | No description available
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AA | No description available
AB | No description available
AD | No description available
AK | No description available
AL | No description available
Ad | No description available
B | No description available
BA | No description available
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BH | No description available
BI | No description available
BJ | No description available
BK | No description available
BL | No description available
BM | No description available
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BO | No description available
BP | No description available
BQ | No description available
BR | No description available
BS | No description available
BT | No description available
BU | No description available
BV | No description available
BW | No description available
BX | No description available
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BZ | No description available
Ba | No description available
Bb | No description available
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E | No description available
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I | No description available
J | No description available
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L | No description available
M | No description available
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O | No description available
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Q | No description available
R | No description available
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W | No description available
X | No description available
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Z | No description available
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b | No description available
c | No description available
d | No description available
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f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
m | No description available
n | No description available
o | No description available
p | No description available
r | No description available
s | No description available
u | No description available
z | No description available
> color #2 #929292ff
> hide atoms
> show cartoons
Computing secondary structure
> select add #2
11623 atoms, 12413 bonds, 1475 residues, 1 model selected
> show sel cartoons
> select add #1
11623 atoms, 12413 bonds, 1475 residues, 3 models selected
> transparency sel 50
> select clear
> open "/Users/croal939/Downloads/output_output (2).cif"
Summary of feedback from opening /Users/croal939/Downloads/output_output
(2).cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for output_output (2).cif #3
---
Chain | Description
0 K MU ps | No description available
02 | No description available
04 AJ4 zV | No description available
07 | No description available
08 | No description available
09 vf | No description available
0C 36 CK La hU | No description available
0D 5T 67 AEu H5 ph u1 yZ | No description available
0F | No description available
0G 4u FH pu | No description available
0I yb | No description available
0M J5 | No description available
0O Be im | No description available
0Q | No description available
0W | No description available
0a Du iH iW jL | No description available
0d | No description available
0m 4K 4Y 6U Fs w2 | No description available
0u 61 7S HV Iv Q iS zZ | No description available
0x | No description available
0y A95 EY Mg NY sq tl | No description available
0z AJf MR wF yK | No description available
1 x | No description available
10 Di | No description available
11 8K D8 Hp NI | No description available
12 37 AE8 Kl cd xz | No description available
14 5i AEX AKG ha | No description available
15 3K Ct vF | No description available
17 AL NR uv | No description available
1B zu | No description available
1D | No description available
1E 7v hP | No description available
1F AE1 iF | No description available
1G | No description available
1L | No description available
1M 3i GZ ND | No description available
1Q 1a 3J 5O | No description available
1S EI GA | No description available
1U 8P sY yP | No description available
1W Kc tu zU | No description available
1Y 3V KF M9 Zj f5 rF uB uw | No description available
1b Vu ww | No description available
1c 2M 6G Bs hX iV ra v4 | No description available
1k | No description available
1m 6E | No description available
1n | No description available
1s AB9 xq | No description available
1u FU NF | No description available
1v Fl yI | No description available
1y | No description available
1z hT | No description available
2 v | No description available
20 AFy KH KL L9 tY x8 | No description available
27 | No description available
2A | No description available
2C | No description available
2E AR NO h9 wo | No description available
2F A9r AD NZ lO t | No description available
2I 5y A9 iN | No description available
2K iz s9 | No description available
2N | No description available
2P CD HC HE | No description available
2Q tI | No description available
2R | No description available
2S ACm AHF Bf sV zd | No description available
2U 80 Cq un y3 | No description available
2V 5X NV Xh vI | No description available
2W 4a 8I | No description available
2Z ACX yk | No description available
2e 4Z 7a DL | No description available
2h D6 | No description available
2i | No description available
2t | No description available
2u Lg x6 y9 yC | No description available
2y JK NQ V8 tQ | No description available
30 I4 M2 wZ | No description available
32 5N 8v B1 BJ c tg uC | No description available
35 | No description available
38 Cv F7 | No description available
3A CY | No description available
3E Gn | No description available
3F A9g AGr z6 | No description available
3I | No description available
3L 5f GU | No description available
3O IF | No description available
3S | No description available
3W NW uf | No description available
3Z | No description available
3h E1 | No description available
3m vg w7 | No description available
3n 5d AL0 AMM Kw wM xu | No description available
3o KM i4 z4 | No description available
3q Ef | No description available
3r | No description available
3z 4D 8T NM uZ | No description available
4 8p BU Ml rt | No description available
42 AAT AU EH s7 xy | No description available
44 Hv L sA | No description available
47 ABO MP | No description available
49 55 | No description available
4C Gc | No description available
4E | No description available
4F 5t Mo yM zL | No description available
4H Ho | No description available
4I Agx | No description available
4J | No description available
4L AML Hn yp | No description available
4N jr | No description available
4P A2 Hw he oZ sD uM xT | No description available
4T BI GM sE | No description available
4V | No description available
4b | No description available
4c B9 EX HZ | No description available
4d | No description available
4t | No description available
4x | No description available
4z AGK g8 vH | No description available
51 AF2 | No description available
54 G2 Gj Gl wD | No description available
5C 6n k3 yB zt | No description available
5L AAi ir xr | No description available
5U | No description available
5g AEl hc | No description available
5k Dl v9 yw | No description available
5l A7 FN MQ Mx | No description available
5p GJ L8 | No description available
5w 7 iA ye | No description available
6 ACM AIf AKI B6 Ek HG Lp Z3 hJ | No description available
6A 7U 8d IJ | No description available
6F ef fm | No description available
6K AHr i5 kc r1 wq xG | No description available
6M rk | No description available
6N yq | No description available
6S Gm | No description available
6Z AG4 wa | No description available
6f | No description available
6i Fw | No description available
6j A9H AGD Ft | No description available
6s Md i3 zv | No description available
6w AFC wz | No description available
70 CV Gz J0 J1 i9 | No description available
76 ln | No description available
77 Ap MO NL hE rq xR | No description available
7E AEZ MS xa | No description available
7K AB3 S hn xU | No description available
7L | No description available
7Q | No description available
7T 7e | No description available
7Z | No description available
7b | No description available
7d | No description available
7p | No description available
8 | No description available
85 AAC AAs AC AFd AKS FF Gb M4 Mj Na tz x0 yA | No description available
87 8B Ai Ao Hs qR vj w6 xX | No description available
8C | No description available
8H Dn Iy MB hm | No description available
8f A8 ADt s3 yu | No description available
8o AE4 rM tV | No description available
8w | No description available
9 | No description available
A | No description available
A1 | No description available
A4 | No description available
A93 | No description available
A94 Eo bN | No description available
A96 | No description available
A98 ADL n1 | No description available
A9v | No description available
AAa | No description available
AAb | No description available
AAr AFo An Dx JN | No description available
AB AEQ Ka Lc sr tE | No description available
ABF ik jD vq | No description available
ABH BT iY | No description available
ABR hl ud yY | No description available
ACJ | No description available
ACN | No description available
ACQ | No description available
ACU yo | No description available
ACc | No description available
ACg | No description available
ACi | No description available
ACj v7 | No description available
AD4 h8 | No description available
AD8 | No description available
ADJ DM | No description available
ADN | No description available
AE | No description available
AEN uu | No description available
AEY MM | No description available
AEs | No description available
AF AH3 Ie Lz iu | No description available
AFZ F0 qI | No description available
AFm AW Ex I Jf Jk | No description available
AFz D9 KU R h6 | No description available
AG | No description available
AGJ Db Gg Ll qN | No description available
AHy | No description available
AI | No description available
AIR | No description available
AJ | No description available
AJ1 Ma | No description available
AK | No description available
AKJ Ig | No description available
AL5 | No description available
ALE in | No description available
ALf h2 | No description available
AM | No description available
AM0 | No description available
AM1 | No description available
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AMd FS pp | No description available
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AN | No description available
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ANG | No description available
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ANI | No description available
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ANK | No description available
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ANT | No description available
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APE | No description available
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APH | No description available
API | No description available
APJ | No description available
APK | No description available
APL | No description available
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AY Cz Ir Is dg i6 tJ | No description available
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jS rY vm | No description available
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m0 o0 | No description available
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n | No description available
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og | No description available
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ot | No description available
ou | No description available
ov | No description available
ow | No description available
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oz | No description available
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pj qP | No description available
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pn | No description available
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pr | No description available
pt | No description available
pv | No description available
pw | No description available
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py | No description available
pz | No description available
q3 | No description available
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qM | No description available
qO | No description available
qQ t2 | No description available
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r3 | No description available
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rA | No description available
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rO | No description available
rP | No description available
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rW | No description available
rX | No description available
rc | No description available
re | No description available
rj | No description available
rm | No description available
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rp | No description available
rr | No description available
rs | No description available
ru | No description available
ry | No description available
s | No description available
s4 | No description available
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sB | No description available
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sI | No description available
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sN yR | No description available
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sa | No description available
se | No description available
sf | No description available
sj | No description available
so | No description available
sp u9 vV yd | No description available
ss | No description available
t5 | No description available
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tB | No description available
tF | No description available
tH | No description available
tM | No description available
tS | No description available
tb | No description available
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te | No description available
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to | No description available
tp | No description available
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ts | No description available
tw | No description available
u | No description available
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uP | No description available
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ub | No description available
uh | No description available
uj | No description available
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ut | No description available
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vB | No description available
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vy | No description available
w | No description available
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wC | No description available
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wN | No description available
wQ | No description available
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wb | No description available
wd | No description available
wl | No description available
wm | No description available
xD | No description available
xN | No description available
xP yU | No description available
xY | No description available
xc | No description available
xf | No description available
xm | No description available
xw | No description available
xx | No description available
y | No description available
y0 | No description available
yF | No description available
yJ | No description available
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ym | No description available
z | No description available
z0 zN | No description available
zP | No description available
zS | No description available
zc | No description available
zi | No description available
zq | No description available
zr | No description available
zs | No description available
zw | No description available
Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /AV3:13
Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /n9:8
Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /ANx:10
Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /ll:22
> hide #3 models
> show #3 models
> hide #3 models
> close #3
> open /Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45_CompletedModels/PCH45_Adaptor_G24_Refined.pdb
Chain information for PCH45_Adaptor_G24_Refined.pdb #3
---
Chain | Description
A | No description available
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/New Folder/PCH45_Gp25_BetaBulbFitted-coot-0.pdb"
Chain information for PCH45_Gp25_BetaBulbFitted-coot-0.pdb #4
---
Chain | Description
A | No description available
> save "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/New Folder/PCH45_Gp25_ModelChecking.cxs" includeMaps true
——— End of log from Tue Dec 30 21:54:50 2025 ———
> view name session-start
opened ChimeraX session
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/New Folder/PCH45_Gp25_BetaBulbFitted-coot-3.pdb"
Chain information for PCH45_Gp25_BetaBulbFitted-coot-3.pdb #5
---
Chain | Description
A | No description available
> hide #!1 models
> show #!1 models
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/New Folder/PCH45_Gp25Beta_NotBulb_Segmap5.mrc"
Opened PCH45_Gp25Beta_NotBulb_Segmap5.mrc as #6, grid size 416,416,416, pixel
1.37, shown at level 5.31e-05, step 2, values float32
> hide #!6 models
> show #!6 models
> select add #6
2 models selected
> volume #6 step 1
> volume #6 level 0.496
> surface dust #6 size 13.7
> hide #!6 models
> show #!6 models
> hide #!6 models
> volume #1 level 0.444
> volume #!1 showOutlineBox true
> ui mousemode right "crop volume"
> volume #1 region 0,0,0,415,372,415
> volume #1 region 0,0,0,125,372,415
> volume #1 region 0,0,0,415,372,415
> volume #1 region 0,0,0,415,372,202
> volume #1 region 0,0,204,415,372,204
> volume #1 region 0,0,95,415,372,204
> volume #1 region 0,0,95,415,372,210
> volume #!1 showOutlineBox false
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #5 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #5 models
> ui mousemode right "mark surface"
> set bgColor white
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> volume #!1 showOutlineBox true
> ui mousemode right "crop volume"
> volume #1 region 197,0,95,415,372,210
> volume #1 region 197,0,95,262,372,210
> volume #1 region 197,0,95,278,372,210
> volume #1 region 197,197,95,278,372,210
> hide #2 models
> ui mousemode right select
> volume #!1 showOutlineBox false
> volume #1 level 0.4766
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> ui mousemode right "mark surface"
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> hide #3 models
> marker #7 position 350.4,340,259.7 color yellow radius 1
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> ui tool show "Side View"
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> ui mousemode right "delete markers"
> marker delete #7:23
> ui mousemode right "mark surface"
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> ui mousemode right "delete markers"
> marker delete #7:50
> marker delete #7:51
> marker delete #7:49
> volume #1 level 0.5303
> ui mousemode right "mark surface"
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> volume #1 level 0.4564
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> marker #7 position 319.9,340.4,236 color yellow radius 1
> marker #7 position 317.4,340.2,237 color yellow radius 1
> marker #7 position 316.7,341.6,238.2 color yellow radius 1
> marker #7 position 315.8,342,238.2 color yellow radius 1
> marker #7 position 316.6,344.4,236.6 color yellow radius 1
> marker #7 position 315.7,344.7,236.8 color yellow radius 1
> marker #7 position 315,346.1,237.9 color yellow radius 1
> marker #7 position 315.7,346.6,239.9 color yellow radius 1
> marker #7 position 316.6,345.7,241 color yellow radius 1
> marker #7 position 316.4,345.1,242.1 color yellow radius 1
> marker #7 position 316.7,347.4,242.2 color yellow radius 1
> marker #7 position 318.6,349.9,243.2 color yellow radius 1
> marker #7 position 316.2,349.3,245.4 color yellow radius 1
> marker #7 position 320.5,348.7,246.4 color yellow radius 1
> marker #7 position 320.1,348.2,247.2 color yellow radius 1
> marker #7 position 322.8,348.8,248.6 color yellow radius 1
> marker #7 position 323.3,349,250.7 color yellow radius 1
> marker #7 position 324.7,350.4,249.3 color yellow radius 1
> marker #7 position 326.1,351.2,248.6 color yellow radius 1
> marker #7 position 327.5,351.7,249.1 color yellow radius 1
> marker #7 position 328.7,351.7,250.5 color yellow radius 1
> marker #7 position 329.4,349.5,253.4 color yellow radius 1
> marker #7 position 330,348.9,254.8 color yellow radius 1
> marker #7 position 329.8,349.6,256.3 color yellow radius 1
> marker #7 position 331.4,351.3,256.6 color yellow radius 1
> marker #7 position 333,350,258.1 color yellow radius 1
> marker #7 position 333.9,348.3,259.3 color yellow radius 1
> marker #7 position 333.9,348.7,262.7 color yellow radius 1
> marker #7 position 335,347.7,265.5 color yellow radius 1
> marker #7 position 334.8,346.3,266.8 color yellow radius 1
> marker #7 position 332.4,344.7,270.6 color yellow radius 1
> marker #7 position 329.7,347,268.8 color yellow radius 1
> marker #7 position 328.9,346.2,269.3 color yellow radius 1
> marker #7 position 325.8,343.6,269.6 color yellow radius 1
> marker #7 position 324.9,343.2,271 color yellow radius 1
> marker #7 position 324.1,342.3,273 color yellow radius 1
> marker #7 position 323.6,341.3,274.2 color yellow radius 1
> marker #7 position 322.7,339.4,274.2 color yellow radius 1
> marker #7 position 322.7,336.6,274.6 color yellow radius 1
> marker #7 position 321.2,333.7,273.8 color yellow radius 1
> marker #7 position 319.6,334.6,270.1 color yellow radius 1
> marker #7 position 318.9,336.2,270.2 color yellow radius 1
> volume zone #2 nearAtoms #7 newMap true range 4
> volume zone #1 nearAtoms #7 newMap true range 4
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #8, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32
> surface dust #8 size 13.7
> volume #8 level 0.5476
> transparency #8.1 50
> volume #8 level 0.3824
> volume #8 level 0.473
> show #!1 models
> hide #7 models
> show #4 models
> hide #4 models
> show #4 models
> show #7 models
> marker #7 position 354.7,337.2,256.9 color yellow radius 1
> marker #7 position 335.9,339.6,258.8 color yellow radius 1
> volume #8 level 0.5263
> volume #*level .55
Expected a density maps specifier or a keyword
> volume #* level .55
> volume subtract #1 #8
Opened volume difference as #9, grid size 416,416,416, pixel 1.37, shown at
step 1, values float32
> surface dust #9 size 13.7
> volume #!9 showOutlineBox true
> ui mousemode right "crop volume"
> volume #9 region 0,0,0,415,415,203
> volume #9 region 0,0,0,415,266,203
> volume #9 region 158,0,0,415,266,203
> volume #9 region 158,0,138,415,266,203
> volume #9 region 158,0,138,415,266,210
> volume #!9 showOutlineBox false
> transparency #9.1 50
> hide #7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #9
1 atom, 1 residue, 4 models selected
> volume #8 region 197,197,95,278,372,218
> ui mousemode right select
> select clear
> show #2 models
> hide #2 models
> show #!1 models
> volume #1 level 0.4963
> volume #* level .475
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> hide #!9 models
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp025/fold_pch45_gp025_model_0.cif"
Chain information for fold_pch45_gp025_model_0.cif #10
---
Chain | Description
A | .
Computing secondary structure
> select add #10
3715 atoms, 3815 bonds, 462 residues, 1 model selected
> color bfactor sel
3715 atoms, 462 residues, atom bfactor range 25.6 to 96.9
> select clear
> ui tool show Matchmaker
> matchmaker #10 to #3
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 PCH45_Adaptor_G24_Refined.pdb, chain A (#3) with
fold_pch45_gp025_model_0.cif, chain A (#10), sequence alignment score = 52.4
RMSD between 5 pruned atom pairs is 1.228 angstroms; (across all 195 pairs:
29.877)
> view
> show #2 models
> ui tool show Matchmaker
> matchmaker #10 to #5
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 PCH45_Gp25_BetaBulbFitted-coot-3.pdb, chain A (#5) with
fold_pch45_gp025_model_0.cif, chain A (#10), sequence alignment score = 2133.8
RMSD between 370 pruned atom pairs is 0.883 angstroms; (across all 462 pairs:
2.453)
> hide #5 models
> hide #4 models
> show #5 models
> show #!6 models
> show #!1 models
> transparency #1.1#6.1#8.1 0
> transparency #1.1#6.1#8.1 50
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #7 models
> ui mousemode right "mark surface"
> marker #7 position 321.5,334.3,268.7 color yellow radius 1
> marker #7 position 322.6,334.4,267.9 color yellow radius 1
> marker #7 position 324.2,334,266.7 color yellow radius 1
> marker #7 position 325,335.9,266.2 color yellow radius 1
> marker #7 position 326.1,337.4,265.6 color yellow radius 1
> marker #7 position 326.9,338.2,265 color yellow radius 1
> marker #7 position 326.9,344.1,264 color yellow radius 1
> marker #7 position 330.3,347.6,261.5 color yellow radius 1
> marker #7 position 328,338.8,265.8 color yellow radius 1
> marker #7 position 328,340.7,269.5 color yellow radius 1
> marker #7 position 329,342.3,272.2 color yellow radius 1
> marker #7 position 330.9,340.8,271.4 color yellow radius 1
> marker #7 position 330.2,338.9,269.5 color yellow radius 1
> marker #7 position 331.2,339,269.7 color yellow radius 1
> marker #7 position 330.6,338.4,266.6 color yellow radius 1
> marker #7 position 331.3,337.1,268.4 color yellow radius 1
> marker #7 position 331.1,335.5,269.4 color yellow radius 1
> marker #7 position 330,335.7,270.5 color yellow radius 1
> marker #7 position 329.1,336.5,271.6 color yellow radius 1
> marker #7 position 332.2,333.4,268.5 color yellow radius 1
> marker #7 position 336.2,334.4,267.3 color yellow radius 1
> marker #7 position 333.3,333.9,267.4 color yellow radius 1
> marker #7 position 336.5,336.2,265.9 color yellow radius 1
> marker #7 position 339.3,339,266.8 color yellow radius 1
> marker #7 position 339.8,345.6,265 color yellow radius 1
> marker #7 position 338.2,341,265.9 color yellow radius 1
> marker #7 position 338.6,346.3,263.2 color yellow radius 1
> marker #7 position 338.5,346.4,264.8 color yellow radius 1
> marker #7 position 336.9,344.9,263.6 color yellow radius 1
> marker #7 position 337.9,342.9,264.2 color yellow radius 1
> marker #7 position 336.8,342.1,265 color yellow radius 1
> marker #7 position 336.7,340.9,265.8 color yellow radius 1
> marker #7 position 336.9,339.4,266.4 color yellow radius 1
> marker #7 position 335.5,337.6,265.3 color yellow radius 1
> marker #7 position 334.3,341.4,263 color yellow radius 1
> marker #7 position 333.3,341.2,261.9 color yellow radius 1
> marker #7 position 331.9,340.1,260.8 color yellow radius 1
> marker #7 position 332,341.6,257.2 color yellow radius 1
> marker #7 position 330.6,342.3,257 color yellow radius 1
> marker #7 position 328.5,343.1,257.3 color yellow radius 1
> marker #7 position 327.2,342.8,258.5 color yellow radius 1
> marker #7 position 326.1,342.4,258.5 color yellow radius 1
> marker #7 position 325.2,342.8,259.2 color yellow radius 1
> marker #7 position 328.4,343.7,258.5 color yellow radius 1
> marker #7 position 329.1,345.3,258.9 color yellow radius 1
> marker #7 position 328.7,347.1,258.9 color yellow radius 1
> marker #7 position 327.7,349.9,262 color yellow radius 1
> marker #7 position 326.8,350.6,262.8 color yellow radius 1
> marker #7 position 325.6,350.5,263 color yellow radius 1
> marker #7 position 327,346.3,259.2 color yellow radius 1
> marker #7 position 326.4,344.6,260 color yellow radius 1
> marker #7 position 324.1,349.8,263.8 color yellow radius 1
> marker #7 position 323.3,350.4,264.3 color yellow radius 1
> marker #7 position 322,351.2,264 color yellow radius 1
> marker #7 position 320.9,351.7,262.7 color yellow radius 1
> marker #7 position 319.8,352.6,263.1 color yellow radius 1
> marker #7 position 319.2,353,264.1 color yellow radius 1
> marker #7 position 317.8,354.9,264.1 color yellow radius 1
> marker #7 position 317,352.7,265.3 color yellow radius 1
> marker #7 position 316.6,355.5,263.8 color yellow radius 1
> marker #7 position 315.6,356,263.1 color yellow radius 1
> marker #7 position 313.8,357.3,260.7 color yellow radius 1
> marker #7 position 315.3,357.8,261.4 color yellow radius 1
> marker #7 position 317.2,356.9,262.7 color yellow radius 1
> marker #7 position 319.4,357.2,261.6 color yellow radius 1
> hide #2 models
> marker #7 position 316.3,358.8,260.1 color yellow radius 1
> marker #7 position 314.6,359.1,258.7 color yellow radius 1
> marker #7 position 313.6,359.3,260.6 color yellow radius 1
> marker #7 position 313.4,359.2,261.6 color yellow radius 1
> marker #7 position 315.3,358.2,257.5 color yellow radius 1
> marker #7 position 315.2,356.1,256.2 color yellow radius 1
> marker #7 position 315.6,355.4,255.6 color yellow radius 1
> marker #7 position 316,357.3,255.5 color yellow radius 1
> marker #7 position 316.2,357.5,253.7 color yellow radius 1
> marker #7 position 316.9,357,251.3 color yellow radius 1
> marker #7 position 317.9,357.3,251.4 color yellow radius 1
> marker #7 position 316.7,359.1,253 color yellow radius 1
> marker #7 position 317.8,360.5,255.4 color yellow radius 1
> marker #7 position 320,364.6,258.4 color yellow radius 1
> marker #7 position 315.9,363.5,258.5 color yellow radius 1
> marker #7 position 314.9,365.6,259.7 color yellow radius 1
> marker #7 position 313.1,365.4,260.3 color yellow radius 1
> marker #7 position 311.2,365.4,261.1 color yellow radius 1
> marker #7 position 309.8,364,262.5 color yellow radius 1
> marker #7 position 307.5,362.9,263.1 color yellow radius 1
> marker #7 position 306.9,361.7,263.5 color yellow radius 1
> marker #7 position 306,359,263.3 color yellow radius 1
> marker #7 position 305.4,359.9,263.3 color yellow radius 1
> marker #7 position 303.4,361.1,259.8 color yellow radius 1
> marker #7 position 300.6,358.1,258.5 color yellow radius 1
> marker #7 position 300,357.3,256 color yellow radius 1
> marker #7 position 298.1,357.7,253.3 color yellow radius 1
> marker #7 position 298,358.2,252 color yellow radius 1
> volume #1 level 0.6361
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> marker #7 position 297.3,356.6,254.3 color yellow radius 1
> marker #7 position 295.4,355.7,255 color yellow radius 1
> marker #7 position 294.5,355.4,254.8 color yellow radius 1
> marker #7 position 295.6,355.3,254.1 color yellow radius 1
> marker #7 position 296,355.3,253.2 color yellow radius 1
> marker #7 position 295.4,354.9,252 color yellow radius 1
> marker #7 position 291.1,356.5,251.3 color yellow radius 1
> marker #7 position 293.5,355.7,250.9 color yellow radius 1
> marker #7 position 291.8,357.1,252.3 color yellow radius 1
> marker #7 position 296.5,354.7,250.7 color yellow radius 1
> marker #7 position 297.3,354.8,249.7 color yellow radius 1
> marker #7 position 298.1,355,249.2 color yellow radius 1
> marker #7 position 299,355.6,248.4 color yellow radius 1
> volume #1 level 0.5488
> volume #1 level 0.6696
> volume zone #1 nearAtoms #7 newMap true range 4
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #11, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32
> surface dust #6 size 13.7
> surface dust #8 size 13.7
> surface dust #11 size 13.7
> hide #7 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!8 models
> volume #11 level 0.4878
> select add #5
3716 atoms, 3815 bonds, 463 residues, 2 models selected
Alignment identifier is 5/A
> select clear
> hide #!6 models
> show #!6 models
> hide #!11 models
> hide #10 models
> hide #5 models
> show #5 models
> select add #5
3715 atoms, 3815 bonds, 462 residues, 1 model selected
> select add #6
3715 atoms, 3815 bonds, 462 residues, 3 models selected
> fitmap #5 inMap #6
Fit molecule PCH45_Gp25_BetaBulbFitted-coot-3.pdb (#5) to map
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) using 3715 atoms
average map value = 0.7312, steps = 48
shifted from previous position = 0.228
rotated from previous position = 0.24 degrees
atoms outside contour = 1174, contour level = 0.475
Position of PCH45_Gp25_BetaBulbFitted-coot-3.pdb (#5) relative to
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) coordinates:
Matrix rotation and translation
0.99999125 0.00384265 -0.00165212 -0.55305518
-0.00384246 0.99999261 0.00011850 1.29508340
0.00165256 -0.00011215 0.99999863 -0.46020967
Axis -0.02756009 -0.39488584 -0.91831673
Axis point 329.20777673 145.20249896 0.00000000
Rotation angle (degrees) 0.23974591
Shift along axis -0.07354960
> select clear
> volume #6 level 0.6932
> select #5/A:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:333-387
427 atoms, 439 bonds, 55 residues, 1 model selected
> select #5/A:388
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:388-462
634 atoms, 653 bonds, 75 residues, 1 model selected
> volume zone #1 nearSel newMap true range 4
Expected a keyword
> volume zone #1 nearAtoms sel newMap true range 4
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #12, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32
> surface dust #6 size 13.7
> surface dust #12 size 13.7
> transparency #6.1#12.1 0
> transparency #6.1#12.1 50
> show #!1 models
> select clear
> hide #!1 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #5 models
> show #5 models
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/New Folder/PCH45_Gp25_BetaBulbFitted-coot-3.pdb"
Chain information for PCH45_Gp25_BetaBulbFitted-coot-3.pdb #13
---
Chain | Description
A | No description available
> select add #13
3715 atoms, 3815 bonds, 462 residues, 1 model selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 4 maps.
> select add #1
3715 atoms, 3815 bonds, 462 residues, 3 models selected
> fitmap #13 inMap #1
Fit molecule PCH45_Gp25_BetaBulbFitted-coot-3.pdb (#13) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 3715 atoms
average map value = 0.7437, steps = 48
shifted from previous position = 0.23
rotated from previous position = 0.258 degrees
atoms outside contour = 1733, contour level = 0.66964
Position of PCH45_Gp25_BetaBulbFitted-coot-3.pdb (#13) relative to
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99998985 0.00390379 -0.00224966 -0.43402769
-0.00390336 0.99999236 0.00019712 1.28620271
0.00225041 -0.00018834 0.99999745 -0.63077562
Axis -0.04273630 -0.49892866 -0.86558870
Axis point 319.42544666 112.85651605 0.00000000
Rotation angle (degrees) 0.25838968
Shift along axis -0.07718241
> select clear
> rename #13 Gp25BetaNotBulb-1-333AA
> select add #13
3715 atoms, 3815 bonds, 462 residues, 1 model selected
Alignment identifier is 13/A
> select #13/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1-169
1350 atoms, 1383 bonds, 169 residues, 1 model selected
> select #13/A:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:333-462
1061 atoms, 1093 bonds, 130 residues, 1 model selected
> delete sel
> select clear
> hide #5 models
> measure center #1
Center of mass grid index for PCH45_Neck_C6_3_40A_map_sharp.mrc = (208.00,
208.00, 140.90)
Center of mass xyz scene coordinates for PCH45_Neck_C6_3_40A_map_sharp.mrc =
(284.19, 284.19, 192.51)
> sym #13 C6 center 284.19, 284.19, 192.51
Made 6 copies for Gp25BetaNotBulb-1-333AA symmetry C6
> select add #1
2 models selected
> ui mousemode right "crop volume"
> volume sel showOutlineBox true
> volume #6 region 0,0,0,415,415,415
> select clear
> volume #!1,6,9,12 showOutlineBox false
> close #14
> show #13 models
> select #13/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1-31
244 atoms, 248 bonds, 31 residues, 1 model selected
> hide #!9 models
> delete sel
> sym #13 C6 center 284.19, 284.19, 192.51
Made 6 copies for Gp25BetaNotBulb-1-333AA symmetry C6
> volume zone #1 nearAtoms #14 newMap true range 4
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #15, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32
> surface dust #6 size 13.7
> surface dust #12 size 13.7
> surface dust #15 size 13.7
> rename #15 Gp25Beta_NotBulb_33-333AA_VZr4
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!12 models
> hide #!14 models
> hide #!6 models
> show #!6 models
> volume #* level .65
> show #!9 models
> hide #!9 models
> show #!1 models
> vop subtract #1 #15
Opened volume difference as #16, grid size 416,416,416, pixel 1.37, shown at
step 1, values float32
> surface dust #6 size 13.7
> surface dust #16 size 13.7
> transparency #6.1#16.1 0
> transparency #6.1#16.1 50
> hide #!6 models
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_GP25alpha/PCH45_Gp25alpha_1-200AA fit-coot-2.pdb"
Chain information for PCH45_Gp25alpha_1-200AA fit-coot-2.pdb #17
---
Chain | Description
A | No description available
> sym #17 C6 center 284.19, 284.19, 192.51
Made 6 copies for PCH45_Gp25alpha_1-200AA fit-coot-2.pdb symmetry C6
> volume zone #1 nearAtoms #18 newMap true range 4
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #19, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32
> surface dust #16 size 13.7
> surface dust #19 size 13.7
> vop subtract #16 #19
Opened volume difference as #20, grid size 416,416,416, pixel 1.37, shown at
step 1, values float32
> surface dust #20 size 13.7
> hide #!18 models
> show #10 models
> rename #20 BulbconfirmationsDensity_Subtractions
> show #!6 models
> hide #!6 models
> show #!6 models
> transparency #6.1#20.1 0
> transparency #6.1#20.1 50
> show #5 models
> volume #6 level 0.65
> hide #!6 models
> show #!1 models
> volume #1 level 0.5963
> volume #1 level 0.556
> volume #1 level 0.6433
> hide #5 models
> show #5 models
> hide #5 models
> hide #10 models
> transparency #1.1#20.1 0
> transparency #1.1#20.1 50
> show #5 models
> select #5/A:387
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:328-387
474 atoms, 486 bonds, 60 residues, 1 model selected
> select #5/A:434
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:434
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:387
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:387-390
30 atoms, 30 bonds, 4 residues, 1 model selected
> select #5/A:398
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:398-400
25 atoms, 25 bonds, 3 residues, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #5/A:322
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:322-328
61 atoms, 63 bonds, 7 residues, 1 model selected
> select #5/A:333
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:333-384
402 atoms, 412 bonds, 52 residues, 1 model selected
> select #5/A:385
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:333-385
414 atoms, 425 bonds, 53 residues, 1 model selected
> color sel lime
> select clear
> select #5/A:386
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:386-397
100 atoms, 103 bonds, 12 residues, 1 model selected
> select #5/A:386-387
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/A:386-407
188 atoms, 194 bonds, 22 residues, 1 model selected
> select #5/A:386
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:386-410
211 atoms, 217 bonds, 25 residues, 1 model selected
> color sel cyan
> select clear
> show #!1 models
> select #5/A:411-412
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/A:411-462
436 atoms, 449 bonds, 52 residues, 1 model selected
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25_411_462/fold_pch45_gp25_411_462_model_0.cif"
Chain information for fold_pch45_gp25_411_462_model_0.cif #21
---
Chain | Description
A | .
Computing secondary structure
> select add #21
872 atoms, 898 bonds, 104 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #21 to #5
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 PCH45_Gp25_BetaBulbFitted-coot-3.pdb, chain A (#5) with
fold_pch45_gp25_411_462_model_0.cif, chain A (#21), sequence alignment score =
271.8
RMSD between 34 pruned atom pairs is 0.624 angstroms; (across all 52 pairs:
5.646)
> select clear
> select add #21
436 atoms, 449 bonds, 52 residues, 1 model selected
> select add #1
436 atoms, 449 bonds, 52 residues, 3 models selected
> fitmap #21 inMap #1
Fit molecule fold_pch45_gp25_411_462_model_0.cif (#21) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 436 atoms
average map value = 0.7079, steps = 68
shifted from previous position = 1.05
rotated from previous position = 4.89 degrees
atoms outside contour = 216, contour level = 0.64329
Position of fold_pch45_gp25_411_462_model_0.cif (#21) relative to
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.89277032 0.01270563 -0.45033290 358.86819646
-0.29285807 0.74321667 0.60155061 305.50715641
0.34233799 0.66893015 -0.65980084 233.72255583
Axis 0.07906588 -0.93015201 -0.35856077
Axis point 178.95533192 0.00000000 104.36154798
Rotation angle (degrees) 154.77984855
Shift along axis -339.59760619
> select clear
> hide #!1 models
> hide #!20 models
> select add #21
436 atoms, 449 bonds, 52 residues, 1 model selected
> select clear
> show #!1 models
> hide #!1 models
> show #!6 models
> select add #6
2 models selected
> select add #21
436 atoms, 449 bonds, 52 residues, 3 models selected
> fitmap #21 inMap #6
Fit molecule fold_pch45_gp25_411_462_model_0.cif (#21) to map
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) using 436 atoms
average map value = 0.708, steps = 60
shifted from previous position = 0.00659
rotated from previous position = 0.0789 degrees
atoms outside contour = 216, contour level = 0.65
Position of fold_pch45_gp25_411_462_model_0.cif (#21) relative to
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) coordinates:
Matrix rotation and translation
-0.89309837 0.01155333 -0.44971304 358.87465433
-0.29329821 0.74303671 0.60155849 305.50641600
0.34110330 0.66915093 -0.66021630 233.72486139
Axis 0.07949887 -0.93011879 -0.35855119
Axis point 179.05599943 0.00000000 104.26268979
Rotation angle (degrees) 154.84200817
Shift along axis -339.42945811
> select clear
> select add #21
436 atoms, 449 bonds, 52 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.87033,-0.041317,-0.49074,358.7,-0.40491,0.62723,0.6653,305.5,0.28032,0.77774,-0.56263,234.11
> view matrix models
> #21,-0.83765,0.014748,-0.546,358.72,-0.43034,0.59779,0.67635,305.5,0.33637,0.80152,-0.49439,234.11
> view matrix models
> #21,-0.83765,0.014748,-0.546,357.9,-0.43034,0.59779,0.67635,306.2,0.33637,0.80152,-0.49439,233.78
> view matrix models
> #21,-0.82144,0.051881,-0.56794,357.93,-0.42967,0.59852,0.67613,306.2,0.375,0.79943,-0.46935,233.73
> view matrix models
> #21,-0.82144,0.051881,-0.56794,357.52,-0.42967,0.59852,0.67613,307.9,0.375,0.79943,-0.46935,233.56
> fitmap #21 inMap #6
Fit molecule fold_pch45_gp25_411_462_model_0.cif (#21) to map
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) using 436 atoms
average map value = 0.708, steps = 132
shifted from previous position = 2.55
rotated from previous position = 14.1 degrees
atoms outside contour = 216, contour level = 0.65
Position of fold_pch45_gp25_411_462_model_0.cif (#21) relative to
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) coordinates:
Matrix rotation and translation
-0.89298122 0.01168575 -0.44994220 358.87161135
-0.29333815 0.74308848 0.60147505 305.50321627
0.34137555 0.66909114 -0.66013618 233.72537056
Axis 0.07947713 -0.93012867 -0.35853041
Axis point 179.04075764 0.00000000 104.29777173
Rotation angle (degrees) 154.82523086
Shift along axis -339.43286569
> view matrix models
> #21,-0.62342,-0.11768,-0.77298,357.85,-0.70758,0.50556,0.4937,305.72,0.33269,0.85473,-0.39844,234.57
> fitmap #21 inMap #6
Fit molecule fold_pch45_gp25_411_462_model_0.cif (#21) to map
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) using 436 atoms
average map value = 0.7081, steps = 120
shifted from previous position = 0.778
rotated from previous position = 30 degrees
atoms outside contour = 215, contour level = 0.65
Position of fold_pch45_gp25_411_462_model_0.cif (#21) relative to
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) coordinates:
Matrix rotation and translation
-0.89235317 0.01274596 -0.45115781 358.86164988
-0.29340057 0.74319042 0.60131864 305.51334753
0.34296054 0.66895855 -0.65944865 233.70326901
Axis 0.07922489 -0.93013046 -0.35858158
Axis point 178.95150405 0.00000000 104.44700249
Rotation angle (degrees) 154.72993418
Shift along axis -339.53818078
> select clear
> select add #21
436 atoms, 449 bonds, 52 residues, 1 model selected
> sym #21 C12 center 284.19, 284.19, 192.51
Made 12 copies for fold_pch45_gp25_411_462_model_0.cif symmetry C12
> show #!1 models
> show #21 models
> hide #21 models
> hide #!22 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!1 models
> vop subtract #20 #22
volume subtract operation requires exactly two volumes
> volume zone #1 nearAtoms #22 newMap true range 4
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #23, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32
> surface dust #6 size 13.7
> surface dust #20 size 13.7
> surface dust #23 size 13.7
> vop subtract #20 #23
Opened volume difference as #24, grid size 416,416,416, pixel 1.37, shown at
step 1, values float32
> surface dust #6 size 13.7
> surface dust #24 size 13.7
> show #!23 models
> hide #!23 models
> show #!23 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!19 models
> hide #!19 models
> show #!19 models
> show #17 models
> hide #17 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #5 models
> show #5 models
> transparency #6.1#15.1#19.1#20.1#23.1#24.1 0
> transparency #6.1#15.1#19.1#20.1#23.1#24.1 50
> hide #!23 models
> hide #!20 models
> show #7 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #7 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!23 models
> hide #!9 models
> show #!1 models
> volume #1 level 0.5963
> volume #1 level 0.5292
> show #!18 models
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_0.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_0.cif #25
---
Chain | Description
A | .
Computing secondary structure
> select #5/A:201
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/A:201-462
2120 atoms, 2182 bonds, 262 residues, 1 model selected
> select clear
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25_201_462/fold_pch45_gp25_201_462_model_0.cif"
Chain information for fold_pch45_gp25_201_462_model_0.cif #26
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #26 to #5
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 PCH45_Gp25_BetaBulbFitted-coot-3.pdb, chain A (#5) with
fold_pch45_gp25_201_462_model_0.cif, chain A (#26), sequence alignment score =
1199.3
RMSD between 205 pruned atom pairs is 0.779 angstroms; (across all 262 pairs:
3.618)
> hide #5 models
> select add #26
2120 atoms, 2182 bonds, 262 residues, 1 model selected
> select add #1
2120 atoms, 2182 bonds, 262 residues, 3 models selected
> fitmap #26 inMap #1
Fit molecule fold_pch45_gp25_201_462_model_0.cif (#26) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 2120 atoms
average map value = 0.6306, steps = 52
shifted from previous position = 0.301
rotated from previous position = 2.29 degrees
atoms outside contour = 921, contour level = 0.52919
Position of fold_pch45_gp25_201_462_model_0.cif (#26) relative to
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.60407289 -0.55734931 0.56961188 355.41912124
-0.29798826 -0.50493974 -0.81008571 307.08307748
0.73912038 -0.65908847 0.13893686 246.20306853
Axis 0.43808475 -0.49179104 0.75247812
Axis point 82.93716909 249.69918501 0.00000000
Rotation angle (degrees) 170.07622060
Shift along axis 189.94541365
> select clear
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #!22 models
> select add #1
2 models selected
> volume #1 level 0.348
> volume #1 level 0.5091
> hide #!1 models
> hide #26 models
> show #26 models
> hide #!15 models
> hide #!18 models
> show #!18 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.6567
> volume #1 level 0.8044
> select clear
> hide #26 models
> show #26 models
> select add #26
2120 atoms, 2182 bonds, 262 residues, 1 model selected
> ui tool show "Model Loops"
Populating font family aliases took 78 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> modeller refine 5/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> select clear
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp025/fold_pch45_gp025_model_0.cif"
Chain information for fold_pch45_gp025_model_0.cif #27
---
Chain | Description
A | .
Computing secondary structure
> select add #27
3715 atoms, 3815 bonds, 462 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #27 to #17
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 PCH45_Gp25alpha_1-200AA fit-coot-2.pdb, chain A (#17) with
fold_pch45_gp025_model_0.cif, chain A (#27), sequence alignment score = 879.3
RMSD between 107 pruned atom pairs is 0.766 angstroms; (across all 200 pairs:
25.924)
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!24 models
> show #!1 models
> select add #27
3715 atoms, 3815 bonds, 462 residues, 1 model selected
> select clear
> select add #27
3715 atoms, 3815 bonds, 462 residues, 1 model selected
> select clear
> select #13/A:32-132
794 atoms, 811 bonds, 101 residues, 1 model selected
> select clear
> select #13/A:32-230
1615 atoms, 1656 bonds, 199 residues, 1 model selected
> select add #27
5330 atoms, 5471 bonds, 661 residues, 2 models selected
> select clear
> select #13/A:201-332
1059 atoms, 1088 bonds, 132 residues, 1 model selected
> select add #27
4774 atoms, 4903 bonds, 594 residues, 2 models selected
> select clear
> select add #27
3715 atoms, 3815 bonds, 462 residues, 1 model selected
Alignment identifier is 27/A
> select #27/A:462
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #27/A:201-462
2120 atoms, 2182 bonds, 262 residues, 1 model selected
> volume gaussian #1 sDev 2
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc gaussian as #28, grid size
416,416,416, pixel 1.37, shown at step 1, values float32
> surface dust #6 size 13.7
> surface dust #19 size 13.7
> surface dust #28 size 13.7
> transparency #6.1#19.1#28.1 0
> lighting simple
> help fit in map
> ui tool show "Fit in Map"
> fitmap sel inMap #28 moveWholeMolecules false
Fit molecule fold_pch45_gp025_model_0.cif (#27) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc gaussian (#28) using 2120 atoms
average map value = 0.3277, steps = 328
shifted from previous position = 39
rotated from previous position = 54.7 degrees
atoms outside contour = 1095, contour level = 0.34651
> hide #!28 models
> hide #27 models
> show #27 models
> hide #27 models
> show #27 models
> show #!28 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> hide #27 models
> show #27 models
> hide #27 models
> show #27 models
> hide #!19 models
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp025/fold_pch45_gp025_model_0.cif"
Chain information for fold_pch45_gp025_model_0.cif #29
---
Chain | Description
A | .
Computing secondary structure
> hide #27 models
> ui tool show Matchmaker
> matchmaker #29 to #17
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 PCH45_Gp25alpha_1-200AA fit-coot-2.pdb, chain A (#17) with
fold_pch45_gp025_model_0.cif, chain A (#29), sequence alignment score = 879.3
RMSD between 107 pruned atom pairs is 0.766 angstroms; (across all 200 pairs:
25.924)
> select add #29
5835 atoms, 5997 bonds, 724 residues, 2 models selected
Alignment identifier is 1
> select #27/A:76-77 #29/A:76-77
40 atoms, 38 bonds, 4 residues, 2 models selected
> select #27/A:76-90 #29/A:76-90
270 atoms, 272 bonds, 30 residues, 2 models selected
. [ID: 1] region 2 chains [76-90] RMSD: 0.000
> select #27/A:462 #29/A:462
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #27/A:196-462 #29/A:196-462
4316 atoms, 4440 bonds, 534 residues, 2 models selected
. [ID: 1] region 2 chains [196-462] RMSD: 41.732
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecules fold_pch45_gp025_model_0.cif (#27), fold_pch45_gp025_model_0.cif
(#29) to map PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 4316 atoms
average map value = 0.2734, steps = 68
shifted from previous position = 2.4
rotated from previous position = 9.53 degrees
atoms outside contour = 3724, contour level = 0.80437
> show #4 models
> hide #4 models
> show #!1 models
> select clear
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> hide #!1 models
> show #!1 models
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25_201_462/fold_pch45_gp25_201_462_model_0.cif"
Chain information for fold_pch45_gp25_201_462_model_0.cif #30
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #30 to #21
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 fold_pch45_gp25_411_462_model_0.cif, chain A (#21) with
fold_pch45_gp25_201_462_model_0.cif, chain A (#30), sequence alignment score =
271.8
RMSD between 34 pruned atom pairs is 0.677 angstroms; (across all 52 pairs:
5.408)
> transparency #1.1#6.1 0
> transparency #1.1#6.1 50
> hide #30 models
> show #30 models
> hide #30 models
> show #30 models
> hide #30 models
> show #30 models
> hide #30 models
> show #30 models
> select add #30
2120 atoms, 2182 bonds, 262 residues, 1 model selected
> select add #1
2120 atoms, 2182 bonds, 262 residues, 3 models selected
> fitmap #30 inMap #1
Fit molecule fold_pch45_gp25_201_462_model_0.cif (#30) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 2120 atoms
average map value = 0.6307, steps = 68
shifted from previous position = 0.628
rotated from previous position = 3.48 degrees
atoms outside contour = 1304, contour level = 0.80437
Position of fold_pch45_gp25_201_462_model_0.cif (#30) relative to
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.60384333 -0.55765393 0.56955714 355.42581166
-0.29831444 -0.50450676 -0.81023541 307.07191066
0.73917639 -0.65916237 0.13828682 246.21080457
Axis 0.43821382 -0.49201033 0.75225959
Axis point 82.88471712 249.76377171 0.00000000
Rotation angle (degrees) 170.07414215
Shift along axis 189.88438816
> hide #30 models
> show #30 models
> fitmap #30 inMap #1
Fit molecule fold_pch45_gp25_201_462_model_0.cif (#30) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 2120 atoms
average map value = 0.6307, steps = 48
shifted from previous position = 0.0112
rotated from previous position = 0.0145 degrees
atoms outside contour = 1304, contour level = 0.80437
Position of fold_pch45_gp25_201_462_model_0.cif (#30) relative to
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.60383134 -0.55768962 0.56953490 355.41865279
-0.29811090 -0.50465267 -0.81021946 307.07448850
0.73926829 -0.65902047 0.13847174 246.20239156
Axis 0.43820887 -0.49192573 0.75231780
Axis point 82.87189607 249.75343465 0.00000000
Rotation angle (degrees) 170.06566978
Shift along axis 189.91220412
> select clear
> hide #30 models
> show #30 models
> hide #30 models
> hide #26 models
> show #30 models
> hide #30 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> show #30 models
> sym #30 C12 center 284.19, 284.19, 192.51
Made 12 copies for fold_pch45_gp25_201_462_model_0.cif symmetry C12
> hide #31.2 models
> show #31.2 models
> hide #31.1 models
> show #31.1 models
> hide #31.1 models
> show #31.1 models
> hide #31.2 models
> show #31.2 models
> hide #31.3 models
> hide #31.4 models
> hide #31.1 models
> hide #31.5 models
> hide #31.6 models
> hide #31.7 models
> hide #31.8 models
> hide #31.9 models
> hide #31.10 models
> hide #31.11 models
> hide #31.12 models
> hide #31.2 models
> show #31.2 models
> help combine
> volume zone #1 nearAtoms 31.2 newMap true range 4
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #1 nearAtoms #31.2 newMap true range 4
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #32, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32
> surface dust #6 size 13.7
> surface dust #32 size 13.7
> save "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_Gp25AlphaCombine201-462SegmapTest.mrc" models #32
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_Gp25AlphaCombine201-462SegmapTest.mrc"
Opened PCH45_Gp25AlphaCombine201-462SegmapTest.mrc as #33, grid size
416,416,416, pixel 1.37, shown at level 7.63e-05, step 2, values float32
> save "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_GP25Alpha_CombineFitted200-462Test.pdb" models #31.2
> relModel #33
> hide #18.4 models
> show #18.4 models
> hide #18.4 models
> hide #18.3 models
> hide #18.2 models
> hide #18.1 models
> hide #18.6 models
> show #18.6 models
> hide #18.5 models
> volume zone #1 nearAtoms #18.6 newMap true range 4
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #34, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32
> surface dust #6 size 13.7
> surface dust #32 size 13.7
> surface dust #33 size 13.7
> surface dust #34 size 13.7
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> vop add #33 #34
Opened volume sum as #35, grid size 416,416,416, pixel 1.37, shown at step 1,
values float32
> select add #35
2 models selected
> volume #35 level 0.4228
> surface dust #35 size 13.7
> volume #35 level 0.4705
> save "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_GP25AlphaWHoleMapCombineTestCOot.mrc" models #35
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_GP25AlphaWHoleMapCombineTestCOot.mrc"
Opened PCH45_GP25AlphaWHoleMapCombineTestCOot.mrc as #36, grid size
416,416,416, pixel 1.37, shown at level 0.000214, step 2, values float32
> volume #36 step 1
> select add #31.2
2120 atoms, 2182 bonds, 262 residues, 3 models selected
> save "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/GP25AlphaCootFitPt200-462.pdb" models #31.2 relModel #36
> save "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45Alpha1-200fit.pdb" relModel #36
> save "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_Gp25Alpha1-200TestCoot2.pdb" models #18.6 relModel #36
> hide #!36 models
> hide #35.1 models
> hide #!32 models
> select clear
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp025/fold_pch45_gp025_model_0.cif"
Chain information for fold_pch45_gp025_model_0.cif #37
---
Chain | Description
A | .
Computing secondary structure
> hide #37 models
> show #37 models
> ui tool show Matchmaker
> matchmaker #37 to #31.2
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 fold_pch45_gp25_201_462_model_0.cif, chain A (#31.2) with
fold_pch45_gp025_model_0.cif, chain A (#37), sequence alignment score = 1282.7
RMSD between 223 pruned atom pairs is 0.453 angstroms; (across all 262 pairs:
2.831)
> help match
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> select add #37
3715 atoms, 3815 bonds, 462 residues, 1 model selected
Alignment identifier is 37/A
> select #37/A:264
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #37/A:1-264
2117 atoms, 2173 bonds, 264 residues, 1 model selected
> select #37/A:199
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:1-199
1587 atoms, 1624 bonds, 199 residues, 1 model selected
> select #37/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #37/A:1-200
1595 atoms, 1632 bonds, 200 residues, 1 model selected
> matchAtoms sel #18.6
Unknown command: matchAtoms sel #18.6
> matchAtoms
Unknown command: matchAtoms
> matchatom
Unknown command: matchatom
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> matchAtoms #37/A:1-200 #18.6
Unknown command: matchAtoms #37/A:1-200 #18.6
> matchmaker #37/A:1-200 #18.6
Missing required "to" argument
> matchmaker #37/A:1-200 to #18.6
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 PCH45_Gp25alpha_1-200AA fit-coot-2.pdb, chain A (#18.6) with
fold_pch45_gp025_model_0.cif, chain A (#37), sequence alignment score = 879.3
RMSD between 107 pruned atom pairs is 0.766 angstroms; (across all 200 pairs:
25.924)
> select clear
> hide #!35 models
> show #!35 models
> show #!36 models
> hide #!36 models
> show #!36 models
> volume #36 level 0.4161
> surface dust #6 size 13.7
> surface dust #36 size 13.7
> volume gaussian #36 sDev 2
Opened PCH45_GP25AlphaWHoleMapCombineTestCOot.mrc gaussian as #38, grid size
416,416,416, pixel 1.37, shown at step 1, values float32
> volume #38 level 0.2722
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp025/fold_pch45_gp025_model_0.cif"
Chain information for fold_pch45_gp025_model_0.cif #39
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #39 to #31.2
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 fold_pch45_gp25_201_462_model_0.cif, chain A (#31.2) with
fold_pch45_gp025_model_0.cif, chain A (#39), sequence alignment score = 1282.7
RMSD between 223 pruned atom pairs is 0.453 angstroms; (across all 262 pairs:
2.831)
> ui tool show "Fit in Map"
> select clear
> select add #39
3715 atoms, 3815 bonds, 462 residues, 1 model selected
Alignment identifier is 39/A
> select #39/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:1-207
1661 atoms, 1702 bonds, 207 residues, 1 model selected
> select #39/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:1-200
1595 atoms, 1632 bonds, 200 residues, 1 model selected
> fitmap #39 inMap #38 moveWholeMolecules false
Fit molecule fold_pch45_gp025_model_0.cif (#39) to map
PCH45_GP25AlphaWHoleMapCombineTestCOot.mrc gaussian (#38) using 3715 atoms
average map value = 0.2251, steps = 240
shifted from previous position = 8.84
rotated from previous position = 33.7 degrees
atoms outside contour = 2261, contour level = 0.27224
> hide #!38 models
> hide #37 models
> show #37 models
> hide #37 models
> select add #39
3715 atoms, 3815 bonds, 462 residues, 1 model selected
> select subtract #39
Nothing selected
> hide #39 models
> show #39 models
> hide #39 models
> show #39 models
> combine #31.2 #18.6
Remapping chain ID 'A' in PCH45_Gp25alpha_1-200AA fit-coot-2.pdb #18.6 to 'B'
> hide #18.6 models
> show #18.6 models
> hide #18.6 models
> show #18.6 models
> hide #18.6 models
> show #18.6 models
> hide #40 models
> show #40 models
> hide #40 models
> hide #31.2 models
> hide #18.6 models
> show #40 models
> hide #40 models
> show #40 models
> bone
Unknown command: bone
> bond
Missing or invalid "atoms" argument: empty atom specifier
> help bond
> helpbond
Unknown command: helpbond
> hide #40 models
> show #40 models
> ui tool show "Model Panel"
> view #40 clip false
> ui tool show "Build Structure"
No atoms selected
> show #31.2 models
> hide #31.2 models
> select add #40
3716 atoms, 3815 bonds, 462 residues, 1 model selected
FYI: command is replacing existing command: "build invert"
FYI: command is replacing existing command: "build join peptide"
FYI: command is replacing existing command: "build join bond"
FYI: command is replacing existing command: "build modify"
FYI: command is replacing existing command: "build replace"
FYI: command is replacing existing command: "build start"
FYI: command is replacing existing command: "bond"
FYI: command is replacing existing command: "~bond"
FYI: command is replacing existing command: "bond length"
> build join peptide sel length 1.33 omega 180 phi -120 move small
Multiple N- and C-terminii in atoms
> select clear
> select add #40
3716 atoms, 3815 bonds, 462 residues, 1 model selected
> select subtract #40
Nothing selected
> select #40/A:1
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #40/B:200
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #40/A:1
23 atoms, 23 bonds, 2 residues, 1 model selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
Atoms must be in different models
> select add #40
3717 atoms, 3816 bonds, 462 residues, 1 model selected
> hide #40 models
> show #40 models
> hide #40 models
> select subtract #40
Nothing selected
> show #31.2 models
> show #18.6 models
> select #31.2/A:1
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #18.6/A:200
23 atoms, 23 bonds, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/New Folder/GP25AlphaCootFitPt200-462-coot-0[True Test].pdb"
Chain information for GP25AlphaCootFitPt200-462-coot-0[True Test].pdb #41
---
Chain | Description
A | No description available
B | No description available
> hide #!18 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> hide #41 models
> show #41 models
> select clear
> select #41/A:1
14 atoms, 15 bonds, 1 residue, 1 model selected
> view matrix models
> #41,0.99998,0.0044456,-0.0043127,-0.53243,-0.0044611,0.99998,-0.0035795,2.3082,0.0042967,0.0035987,0.99998,-2.6602
Drag select of 2 residues
> build join peptide sel length 1.33 omega 180 phi -120 move small
Atoms must be in different models
> save "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_GP25alpha/FucksSake.cxs" includeMaps true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,3
Model Number: Z1C80004VX/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.1.2
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.1 (24G231)
Kernel Version: Darwin 24.6.0
Time since boot: 3 hours, 2 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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: Yes
Connection Type: Internal
VN2410C:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 144.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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