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Opened 11 months ago
Closed 11 months ago
#16373 closed defect (can't reproduce)
Crash in Sequence::rname3to1 drawing ribbons after restoring session
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000003513ab000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000320f77000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1134 in read
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1278 in recv_into
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py", line 706 in readinto
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 279 in _read_status
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 318 in begin
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1378 in getresponse
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1352 in do_open
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1391 in https_open
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 496 in _call_chain
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 536 in _open
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 519 in open
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 216 in urlopen
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/available.py", line 62 in load
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 465 in reload_available
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001fffc4c00 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1897 in polymers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 53 in _make_ribbon_graphics
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 630 in compute_ribbons
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 667 in _create_ribbon_graphics
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 357 in update_graphics_if_needed
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1906 in _update_graphics_if_needed
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 295 in check_for_drawing_change
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 76 in draw_new_frame
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 323 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1030 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1193 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, lxml._elementpath, lxml.etree, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio (total: 62)
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{
"uptime" : 180000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 10817,
"osVersion" : {
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"build" : "23F79",
"releaseType" : "User"
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"captureTime" : "2024-11-26 11:19:17.1794 +0100",
"codeSigningMonitor" : 1,
"incident" : "9CDDD835-71E0-4C41-93D3-79C2AAC9D858",
"pid" : 67738,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-26 11:19:13.8283 +0100",
"procStartAbsTime" : 4328542037434,
"procExitAbsTime" : 4328621764872,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0DB7D24A-30FC-5B07-8CDD-CBA90178D69C","thirdParty":true},
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"parentPid" : 1,
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"crashReporterKey" : "60BE7814-FB40-D022-C629-140BFE3D09F3",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 6584,
"sleepWakeUUID" : "E98FBD0F-9ED1-4EA1-8061-EB4F7F11D593",
"sip" : "enabled",
"vmRegionInfo" : "0x7f is not in any region. Bytes before following region: 4333830017\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102510000-102514000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000000007f","rawCodes":[1,127],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000007f"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":67738},
"vmregioninfo" : "0x7f is not in any region. Bytes before following region: 4333830017\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102510000-102514000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.9.dev202407020250 (2024-07-02)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/sramonabarua/Library/CloudStorage/GoogleDrive-
> sramona.barua@gmail.com/.shortcut-targets-by-
> id/1-02g7s2-HN7n0hHn5fFUKDRLRKY6fSx4/supercomplex/CV-
> Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
> Conf1/central_stalk/centralstalk_protein_version2_joinfragments.cxs
Log from Mon Nov 25 16:32:30 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/sramonabarua/Library/CloudStorage/GoogleDrive-
> sramona.barua@gmail.com/.shortcut-targets-by-
> id/1-02g7s2-HN7n0hHn5fFUKDRLRKY6fSx4/supercomplex/CV-
> Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
> Conf1/cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1.cif
Summary of feedback from opening
/Users/sramonabarua/Library/CloudStorage/GoogleDrive-
sramona.barua@gmail.com/.shortcut-targets-by-
id/1-02g7s2-HN7n0hHn5fFUKDRLRKY6fSx4/supercomplex/CV-
Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
Conf1/cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1.cif #1
---
Chain | Description
0 BX Bf CP | No description available
1 Bi CE DG | No description available
4 | No description available
5 | No description available
6 | No description available
8 | No description available
9 | No description available
A | No description available
A0 AA | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A9 | No description available
AB AN Bg | No description available
AC | No description available
AF | No description available
AG DX | No description available
AI | No description available
AJ | No description available
AK AQ Ba | No description available
AL | No description available
AM | No description available
AO Bn El | No description available
AP | No description available
AS | No description available
AT | No description available
AU B7 | No description available
AX Cx | No description available
AY Dz a | No description available
Aa | No description available
Ab | No description available
Ad | No description available
Ae Ds | No description available
Ai | No description available
Al | No description available
An | No description available
Ap | No description available
Ar | No description available
At | No description available
Au | No description available
Av | No description available
Aw CB | No description available
Ax | No description available
Az | No description available
B | No description available
B0 | No description available
B1 D6 DJ EC | No description available
B4 | No description available
B8 | No description available
B9 | No description available
BB | No description available
BC Cl | No description available
BD | No description available
BE | No description available
BG | No description available
BI | No description available
BM | No description available
BN | No description available
BO | No description available
BQ Cm ES | No description available
BR | No description available
BZ | No description available
Be | No description available
Bh | No description available
Bk | No description available
Bp | No description available
Br | No description available
Bs CF | No description available
Bt | No description available
Bv C6 | No description available
Bw | No description available
C | No description available
C4 | No description available
C8 | No description available
C9 | No description available
CL | No description available
CO FF | No description available
CQ | No description available
CR | No description available
CY DM | No description available
Ce | No description available
Ch | No description available
Ck | No description available
Cu | No description available
D | No description available
D0 | No description available
D2 | No description available
D4 i | No description available
DO | No description available
DR | No description available
DT | No description available
DZ | No description available
Di | No description available
Dm | No description available
Dp | No description available
Dy | No description available
E | No description available
ET | No description available
EW | No description available
EY | No description available
Ea | No description available
Eh | No description available
Em | No description available
F | No description available
F0 | No description available
F1 | No description available
F2 | No description available
F3 | No description available
F4 | No description available
F5 | No description available
F6 | No description available
F7 | No description available
F8 | No description available
F9 | No description available
FB | No description available
FZ | No description available
Fa | No description available
Fb | No description available
Fh | No description available
Fi | No description available
Fj | No description available
Fk | No description available
Fl | No description available
Fm | No description available
Fn | No description available
Fo | No description available
Fp | No description available
Fq | No description available
Fr | No description available
Fs | No description available
Ft | No description available
Fu | No description available
Fv | No description available
Fw | No description available
Fx | No description available
Fy | No description available
Fz | No description available
G | No description available
G0 | No description available
G1 | No description available
G2 | No description available
G3 | No description available
G4 | No description available
G5 | No description available
G6 | No description available
G7 | No description available
G8 | No description available
G9 | No description available
GA | No description available
GB | No description available
GC | No description available
GD | No description available
GE | No description available
GF | No description available
GG | No description available
GH | No description available
GI | No description available
GJ | No description available
GK | No description available
GL | No description available
GM | No description available
GN | No description available
GO | No description available
GP | No description available
GQ | No description available
GR | No description available
GS | No description available
GT | No description available
GU | No description available
GV | No description available
GW | No description available
GX | No description available
GY | No description available
GZ | No description available
Ga | No description available
Gb | No description available
Gc | No description available
Gd | No description available
Ge | No description available
Gf | No description available
Gg | No description available
Gh | No description available
Gi | No description available
Gj | No description available
Gk | No description available
Gl | No description available
Gm | No description available
Gn | No description available
Go | No description available
Gp | No description available
Gq | No description available
Gr | No description available
Gs | No description available
Gt | No description available
Gu | No description available
Gv | No description available
Gw | No description available
Gx | No description available
Gy | No description available
Gz | No description available
H | No description available
H0 | No description available
H1 | No description available
H2 | No description available
H3 | No description available
H4 | No description available
H5 | No description available
H6 | No description available
H7 | No description available
H8 | No description available
H9 | No description available
HA | No description available
HB | No description available
HC | No description available
HD | No description available
HE | No description available
HF | No description available
HG | No description available
HH | No description available
HI | No description available
HJ | No description available
HK | No description available
HL | No description available
HM | No description available
HN | No description available
HO | No description available
HP | No description available
HQ | No description available
HR | No description available
HS | No description available
HT | No description available
HU | No description available
HV | No description available
HW | No description available
HX | No description available
HY | No description available
HZ | No description available
Ha | No description available
Hb | No description available
Hc | No description available
Hd | No description available
He | No description available
Hf | No description available
Hg | No description available
Hh | No description available
Hi | No description available
Hj | No description available
Hk | No description available
Hl | No description available
Hm | No description available
Hn | No description available
Ho | No description available
Hp | No description available
Hq | No description available
Hr | No description available
Hs | No description available
Ht | No description available
Hu | No description available
Hv | No description available
Hw | No description available
Hx | No description available
Hy | No description available
Hz | No description available
I | No description available
I0 | No description available
I1 | No description available
I2 | No description available
I3 | No description available
I4 | No description available
I5 | No description available
I6 | No description available
I7 | No description available
I8 | No description available
I9 | No description available
IA | No description available
IB | No description available
IC | No description available
ID | No description available
IE | No description available
IF | No description available
IG | No description available
IH | No description available
II | No description available
IJ | No description available
IK | No description available
IL | No description available
IM | No description available
IN | No description available
IO | No description available
IP | No description available
IQ | No description available
IR | No description available
IS | No description available
IT | No description available
IU | No description available
IV | No description available
IW | No description available
IX | No description available
IY | No description available
IZ | No description available
Ia | No description available
Ib | No description available
Ic | No description available
Id | No description available
Ie | No description available
If | No description available
Ig | No description available
Ih | No description available
Ii | No description available
Ij | No description available
Ik | No description available
Il | No description available
Im | No description available
In | No description available
Io | No description available
Ip | No description available
Iq | No description available
Ir | No description available
Is | No description available
It | No description available
Iu | No description available
Iv | No description available
Iw | No description available
Ix | No description available
Iy | No description available
Iz | No description available
J | No description available
JA | No description available
JB | No description available
JC | No description available
JD | No description available
JE | No description available
JF | No description available
JG | No description available
JH | No description available
JI | No description available
JJ | No description available
JK | No description available
JL | No description available
JM | No description available
JN | No description available
JO | No description available
JP | No description available
JQ | No description available
JR | No description available
JS | No description available
JT | No description available
JU | No description available
JV | No description available
K | No description available
L | No description available
M | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> cd /Users/sramonabarua/Library/CloudStorage/GoogleDrive-
> sramona.barua@gmail.com/.shortcut-targets-by-
> id/1-02g7s2-HN7n0hHn5fFUKDRLRKY6fSx4/supercomplex/CV-
> Full/cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1
Current working directory is:
/Users/sramonabarua/Library/CloudStorage/GoogleDrive-
sramona.barua@gmail.com/.shortcut-targets-by-
id/1-02g7s2-HN7n0hHn5fFUKDRLRKY6fSx4/supercomplex/CV-
Full/cryosparc_P31_J281_004_volume_map_sharp--VC-Conf1
> runscript ../../scripts/renameAndRenumberChainsChimeraX.py #1
> ./central_stalk/Mod_copy.txt
['7', '58']
['7', '58']
['1', '9']
['1', '9']
['12']
['1', '2']
['1', '18']
['1', '18']
['12']
['1', '2']
['1', '21']
['1', '21']
['1', '3']
['1', '3']
['1', '3']
['1', '3']
['1', '29']
['1', '29']
['1', '8']
['1', '8']
['1', '8']
['1', '8']
['1', '8']
['1', '8']
['2', '28']
['2', '28']
['1', '53']
['1', '53']
['1', '8']
['1', '8']
['1', '5']
['1', '5']
['1', '8']
['1', '8']
['4', '22']
['4', '22']
['12']
['1', '2']
['1', '18']
['1', '18']
['1', '3']
['1', '3']
['1', '8']
['1', '8']
['1', '10']
['1', '10']
['1', '5']
['1', '5']
['2', '23']
['2', '23']
['1', '15']
['1', '15']
['1', '4']
['1', '4']
['1', '4']
['1', '4']
['12']
['1', '2']
['1', '4']
['1', '4']
['12']
['1', '2']
['1', '24']
['1', '24']
['12']
['1', '2']
['1', '3']
['1', '3']
['6', '13']
['6', '13']
['1', '3']
['1', '3']
['12']
['1', '2']
['1', '4']
['1', '4']
['1', '3']
['1', '3']
['12']
['1', '2']
['1', '6']
['1', '6']
LtaP21.2100.mRNA
LtaP30.3640.mRNA
LtaP36.0640.mRNA
> combine #1 close false name renamedAndRenumberedModel
Renumering chain LtaP21.2100.mRNA
> delete #2/IY:14
> delete #2/IY:37
> renumber #2/IY:15-9999999 start 14
50 residues renumbered
> renumber #2/IY:37-9999999 start 36
28 residues renumbered
> renumber #2/IY:18-9999999 start 19
46 residues renumbered
> ~bond #2/IY:17@C #2/IY:19@N
['7', '55']
> select #2/IY
523 atoms, 530 bonds, 3 pseudobonds, 63 residues, 2 models selected
0
2
>2
> renumber #2/IY start 2
63 residues renumbered
['1', '9']
> select #2/GE
71 atoms, 72 bonds, 9 residues, 1 model selected
65
64
>-1
> delete #2/GE:2
> delete #2/GE:1
> renumber #2/GE start 66
7 residues renumbered
> changechains #2/GE IY
Chain IDs of 7 residues changed
['1', '2']
> select #2/DT
15 atoms, 14 bonds, 2 residues, 1 model selected
72
76
>4
> renumber #2/DT start 76
2 residues renumbered
> changechains #2/DT IY
Chain IDs of 2 residues changed
['1', '18']
> select #2/H2
128 atoms, 129 bonds, 18 residues, 1 model selected
77
78
>1
> renumber #2/H2 start 78
18 residues renumbered
> changechains #2/H2 IY
Chain IDs of 18 residues changed
['1', '2']
> select #2/DJ
8 atoms, 7 bonds, 2 residues, 1 model selected
95
96
>1
> renumber #2/DJ start 96
2 residues renumbered
> changechains #2/DJ IY
Chain IDs of 2 residues changed
['1', '21']
> select #2/Iw
170 atoms, 172 bonds, 21 residues, 1 model selected
97
98
>1
> renumber #2/Iw start 98
21 residues renumbered
> changechains #2/Iw IY
Chain IDs of 21 residues changed
['1', '3']
> select #2/t
25 atoms, 24 bonds, 3 residues, 1 model selected
118
119
>1
> renumber #2/t start 119
3 residues renumbered
> changechains #2/t IY
Chain IDs of 3 residues changed
['1', '3']
> select #2/IZ
24 atoms, 24 bonds, 3 residues, 1 model selected
121
122
>1
> renumber #2/IZ start 122
3 residues renumbered
> changechains #2/IZ IY
Chain IDs of 3 residues changed
['1', '29']
> select #2/G6
231 atoms, 236 bonds, 29 residues, 1 model selected
124
125
>1
> renumber #2/G6 start 125
29 residues renumbered
> changechains #2/G6 IY
Chain IDs of 29 residues changed
['1', '8']
> select #2/L
77 atoms, 79 bonds, 8 residues, 1 model selected
153
154
>1
> renumber #2/L start 154
8 residues renumbered
> changechains #2/L IY
Chain IDs of 8 residues changed
['1', '8']
> select #2/GN
57 atoms, 57 bonds, 8 residues, 1 model selected
161
162
>1
> renumber #2/GN start 162
8 residues renumbered
> changechains #2/GN IY
Chain IDs of 8 residues changed
['1', '8']
> select #2/Z
69 atoms, 72 bonds, 8 residues, 1 model selected
169
171
>2
> renumber #2/Z start 171
8 residues renumbered
> changechains #2/Z IY
Chain IDs of 8 residues changed
['2', '28']
> select #2/Fy
319 atoms, 324 bonds, 38 residues, 1 model selected
178
178
>0
> delete #2/Fy:1
> renumber #2/Fy start 179
37 residues renumbered
> changechains #2/Fy IY
Chain IDs of 37 residues changed
['1', '53']
> select #2/V
564 atoms, 567 bonds, 70 residues, 1 model selected
215
216
>1
> renumber #2/V start 216
70 residues renumbered
> changechains #2/V IY
Chain IDs of 70 residues changed
['1', '8']
> select #2/Iv
69 atoms, 69 bonds, 8 residues, 1 model selected
285
288
>3
> renumber #2/Iv start 288
8 residues renumbered
> changechains #2/Iv IY
Chain IDs of 8 residues changed
Renumering chain LtaP30.3640.mRNA
['1', '5']
> select #2/JC
43 atoms, 44 bonds, 5 residues, 1 model selected
0
22
>22
> renumber #2/JC start 22
5 residues renumbered
['1', '8']
> select #2/R
63 atoms, 63 bonds, 8 residues, 1 model selected
26
26
>0
> delete #2/R:1
> renumber #2/R start 27
7 residues renumbered
> changechains #2/R JC
Chain IDs of 7 residues changed
['4', '22']
> select #2/G9
197 atoms, 201 bonds, 24 residues, 1 model selected
33
34
>1
> renumber #2/G9 start 34
24 residues renumbered
> changechains #2/G9 JC
Chain IDs of 24 residues changed
['1', '2']
> select #2/B1
8 atoms, 7 bonds, 2 residues, 1 model selected
57
58
>1
> renumber #2/B1 start 58
2 residues renumbered
> changechains #2/B1 JC
Chain IDs of 2 residues changed
['1', '18']
> select #2/I3
143 atoms, 145 bonds, 18 residues, 1 model selected
59
60
>1
> renumber #2/I3 start 60
18 residues renumbered
> changechains #2/I3 JC
Chain IDs of 18 residues changed
['1', '3']
> select #2/r
20 atoms, 19 bonds, 3 residues, 1 model selected
77
77
>0
> delete #2/r:1
> renumber #2/r start 78
2 residues renumbered
> changechains #2/r JC
Chain IDs of 2 residues changed
['1', '8']
> select #2/HX
62 atoms, 61 bonds, 8 residues, 1 model selected
79
80
>1
> renumber #2/HX start 80
8 residues renumbered
> changechains #2/HX JC
Chain IDs of 8 residues changed
['1', '10']
> select #2/P
79 atoms, 80 bonds, 10 residues, 1 model selected
87
88
>1
> renumber #2/P start 88
10 residues renumbered
> changechains #2/P JC
Chain IDs of 10 residues changed
['1', '5']
> select #2/Q
38 atoms, 37 bonds, 5 residues, 1 model selected
97
98
>1
> renumber #2/Q start 98
5 residues renumbered
> changechains #2/Q JC
Chain IDs of 5 residues changed
['2', '23']
> select #2/He
206 atoms, 210 bonds, 26 residues, 1 model selected
102
101
>-1
> delete #2/He:2
> delete #2/He:1
> renumber #2/He start 103
24 residues renumbered
> changechains #2/He JC
Chain IDs of 24 residues changed
['1', '15']
> select #2/IE
116 atoms, 118 bonds, 15 residues, 1 model selected
126
127
>1
> renumber #2/IE start 127
15 residues renumbered
> changechains #2/IE JC
Chain IDs of 15 residues changed
['1', '4']
> select #2/GZ
30 atoms, 29 bonds, 4 residues, 1 model selected
141
143
>2
> renumber #2/GZ start 143
4 residues renumbered
> changechains #2/GZ JC
Chain IDs of 4 residues changed
['1', '4']
> select #2/I
28 atoms, 27 bonds, 4 residues, 1 model selected
146
148
>2
> renumber #2/I start 148
4 residues renumbered
> changechains #2/I JC
Chain IDs of 4 residues changed
['1', '2']
> select #2/BC
17 atoms, 16 bonds, 2 residues, 1 model selected
151
152
>1
> renumber #2/BC start 152
2 residues renumbered
> changechains #2/BC JC
Chain IDs of 2 residues changed
['1', '4']
> select #2/AM
28 atoms, 27 bonds, 4 residues, 1 model selected
153
154
>1
> renumber #2/AM start 154
4 residues renumbered
> changechains #2/AM JC
Chain IDs of 4 residues changed
['1', '2']
> select #2/B9
10 atoms, 9 bonds, 2 residues, 1 model selected
157
158
>1
> renumber #2/B9 start 158
2 residues renumbered
> changechains #2/B9 JC
Chain IDs of 2 residues changed
['1', '24']
> select #2/H7
196 atoms, 195 bonds, 24 residues, 1 model selected
159
160
>1
> renumber #2/H7 start 160
24 residues renumbered
> changechains #2/H7 JC
Chain IDs of 24 residues changed
Renumering chain LtaP36.0640.mRNA
['1', '2']
> select #2/D6
8 atoms, 7 bonds, 2 residues, 1 model selected
0
7
>7
> renumber #2/D6 start 7
2 residues renumbered
['1', '3']
> select #2/C8
23 atoms, 22 bonds, 3 residues, 1 model selected
8
9
>1
> renumber #2/C8 start 9
3 residues renumbered
> changechains #2/C8 D6
Chain IDs of 3 residues changed
['6', '13']
> select #2/Hd
202 atoms, 201 bonds, 26 residues, 1 model selected
11
14
>3
> renumber #2/Hd start 14
26 residues renumbered
> changechains #2/Hd D6
Chain IDs of 26 residues changed
['1', '3']
> select #2/JV
25 atoms, 24 bonds, 3 residues, 1 model selected
39
41
>2
> renumber #2/JV start 41
3 residues renumbered
> changechains #2/JV D6
Chain IDs of 3 residues changed
['1', '2']
> select #2/At
16 atoms, 15 bonds, 2 residues, 1 model selected
43
44
>1
> renumber #2/At start 44
2 residues renumbered
> changechains #2/At D6
Chain IDs of 2 residues changed
['1', '4']
> select #2/6
33 atoms, 34 bonds, 4 residues, 1 model selected
45
46
>1
> renumber #2/6 start 46
4 residues renumbered
> changechains #2/6 D6
Chain IDs of 4 residues changed
['1', '3']
> select #2/Io
20 atoms, 20 bonds, 3 residues, 1 model selected
49
50
>1
> renumber #2/Io start 50
3 residues renumbered
> changechains #2/Io D6
Chain IDs of 3 residues changed
['1', '2']
> select #2/BN
16 atoms, 15 bonds, 2 residues, 1 model selected
52
63
>11
> renumber #2/BN start 63
2 residues renumbered
> changechains #2/BN D6
Chain IDs of 2 residues changed
['1', '6']
> select #2/I5
44 atoms, 43 bonds, 6 residues, 1 model selected
64
65
>1
> renumber #2/I5 start 65
6 residues renumbered
> changechains #2/I5 D6
Chain IDs of 6 residues changed
> hide #1 models
> select add #2
48037 atoms, 48351 bonds, 3 pseudobonds, 6078 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> runscript ../../scripts/bondFragmentsAndFillGapsMultipleChains.py #2 3
> ./central_stalk/Mod_copy.txt
> combine #2 close false name gapsFilledModel
> color #3 gray
> select #3/IY
2331 atoms, 2357 bonds, 3 pseudobonds, 287 residues, 2 models 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 start"
FYI: command is replacing existing command: "bond"
FYI: command is replacing existing command: "~bond"
FYI: command is replacing existing command: "bond length"
> build start peptide #3 Y 1,1 position
> 283.6507980671056,299.2096922474093,284.9317073958794 chainId zz
> delete #3/zz:1@OXT
> renumber #3/zz start 19
1 residues renumbered
> changechains #3/zz IY
Chain IDs of 1 residues changed
> bond #3/IY:19@C #3/IY:20@N reasonable false
Created 1 bond
> bond #3/IY:18@C #3/IY:19@N reasonable false
Created 1 bond
> color #3/IY:19-19@C* red
> build start peptide #3 PVM 1,1 1,1 1,1 position
> 268.4778101337697,293.5020375253132,299.18008777153227 chainId zz
> delete #3/zz:3@OXT
> renumber #3/zz start 73
3 residues renumbered
> changechains #3/zz IY
Chain IDs of 3 residues changed
> bond #3/IY:75@C #3/IY:76@N reasonable false
Created 1 bond
> bond #3/IY:72@C #3/IY:73@N reasonable false
Created 1 bond
> color #3/IY:73-75@C* red
> build start peptide #3 Q 1,1 position
> 277.8905614257111,284.7191156752,312.0360418859748 chainId zz
> delete #3/zz:1@OXT
> renumber #3/zz start 170
1 residues renumbered
> changechains #3/zz IY
Chain IDs of 1 residues changed
> bond #3/IY:170@C #3/IY:171@N reasonable false
Created 1 bond
> bond #3/IY:169@C #3/IY:170@N reasonable false
Created 1 bond
> color #3/IY:170-170@C* red
> build start peptide #3 NA 1,1 1,1 position
> 303.7947658745627,282.8651265547019,230.76316856057028 chainId zz
> delete #3/zz:2@OXT
> renumber #3/zz start 286
2 residues renumbered
> changechains #3/zz IY
Chain IDs of 2 residues changed
> bond #3/IY:287@C #3/IY:288@N reasonable false
Created 1 bond
> bond #3/IY:285@C #3/IY:286@N reasonable false
Created 1 bond
> color #3/IY:286-287@C* red
> bond #3/IY:154@C #3/IY:155@N reasonable false
Created 0 bonds
> bond #3/IY:155@C #3/IY:156@N reasonable false
Created 0 bonds
> bond #3/IY:156@C #3/IY:157@N reasonable false
Created 0 bonds
> bond #3/IY:157@C #3/IY:158@N reasonable false
Created 0 bonds
> bond #3/IY:158@C #3/IY:159@N reasonable false
Created 0 bonds
> bond #3/IY:159@C #3/IY:160@N reasonable false
Created 0 bonds
> bond #3/IY:160@C #3/IY:161@N reasonable false
Created 0 bonds
> bond #3/IY:161@C #3/IY:162@N reasonable false
Created 1 bond
> bond #3/IY:216@C #3/IY:217@N reasonable false
Created 0 bonds
> bond #3/IY:217@C #3/IY:218@N reasonable false
Created 0 bonds
> bond #3/IY:218@C #3/IY:219@N reasonable false
Created 0 bonds
> bond #3/IY:219@C #3/IY:220@N reasonable false
Created 0 bonds
> bond #3/IY:220@C #3/IY:221@N reasonable false
Created 0 bonds
> bond #3/IY:221@C #3/IY:222@N reasonable false
Created 0 bonds
> bond #3/IY:222@C #3/IY:223@N reasonable false
Created 0 bonds
> bond #3/IY:223@C #3/IY:224@N reasonable false
Created 0 bonds
> bond #3/IY:224@C #3/IY:225@N reasonable false
Created 0 bonds
> bond #3/IY:225@C #3/IY:226@N reasonable false
Created 0 bonds
> bond #3/IY:226@C #3/IY:227@N reasonable false
Created 0 bonds
> bond #3/IY:227@C #3/IY:228@N reasonable false
Created 0 bonds
> bond #3/IY:228@C #3/IY:229@N reasonable false
Created 0 bonds
> bond #3/IY:229@C #3/IY:230@N reasonable false
Created 0 bonds
> bond #3/IY:230@C #3/IY:231@N reasonable false
Created 0 bonds
> bond #3/IY:231@C #3/IY:232@N reasonable false
Created 0 bonds
> bond #3/IY:232@C #3/IY:233@N reasonable false
Created 0 bonds
> bond #3/IY:233@C #3/IY:234@N reasonable false
Created 0 bonds
> bond #3/IY:234@C #3/IY:235@N reasonable false
Created 0 bonds
> bond #3/IY:235@C #3/IY:236@N reasonable false
Created 0 bonds
> bond #3/IY:236@C #3/IY:237@N reasonable false
Created 0 bonds
> bond #3/IY:237@C #3/IY:238@N reasonable false
Created 0 bonds
> bond #3/IY:238@C #3/IY:239@N reasonable false
Created 0 bonds
> bond #3/IY:239@C #3/IY:240@N reasonable false
Created 0 bonds
> bond #3/IY:240@C #3/IY:241@N reasonable false
Created 0 bonds
> bond #3/IY:241@C #3/IY:242@N reasonable false
Created 0 bonds
> bond #3/IY:242@C #3/IY:243@N reasonable false
Created 0 bonds
> bond #3/IY:243@C #3/IY:244@N reasonable false
Created 0 bonds
> bond #3/IY:244@C #3/IY:245@N reasonable false
Created 0 bonds
> bond #3/IY:245@C #3/IY:246@N reasonable false
Created 0 bonds
> bond #3/IY:246@C #3/IY:247@N reasonable false
Created 0 bonds
> bond #3/IY:247@C #3/IY:248@N reasonable false
Created 0 bonds
> bond #3/IY:248@C #3/IY:249@N reasonable false
Created 0 bonds
> bond #3/IY:249@C #3/IY:250@N reasonable false
Created 0 bonds
> bond #3/IY:250@C #3/IY:251@N reasonable false
Created 0 bonds
> bond #3/IY:251@C #3/IY:252@N reasonable false
Created 0 bonds
> bond #3/IY:252@C #3/IY:253@N reasonable false
Created 0 bonds
> bond #3/IY:253@C #3/IY:254@N reasonable false
Created 0 bonds
> bond #3/IY:254@C #3/IY:255@N reasonable false
Created 0 bonds
> bond #3/IY:255@C #3/IY:256@N reasonable false
Created 0 bonds
> bond #3/IY:256@C #3/IY:257@N reasonable false
Created 0 bonds
> bond #3/IY:257@C #3/IY:258@N reasonable false
Created 0 bonds
> bond #3/IY:258@C #3/IY:259@N reasonable false
Created 0 bonds
> bond #3/IY:259@C #3/IY:260@N reasonable false
Created 0 bonds
> bond #3/IY:260@C #3/IY:261@N reasonable false
Created 0 bonds
> bond #3/IY:261@C #3/IY:262@N reasonable false
Created 0 bonds
> bond #3/IY:262@C #3/IY:263@N reasonable false
Created 0 bonds
> bond #3/IY:263@C #3/IY:264@N reasonable false
Created 0 bonds
> bond #3/IY:264@C #3/IY:265@N reasonable false
Created 0 bonds
> bond #3/IY:265@C #3/IY:266@N reasonable false
Created 0 bonds
> bond #3/IY:266@C #3/IY:267@N reasonable false
Created 0 bonds
> bond #3/IY:267@C #3/IY:268@N reasonable false
Created 0 bonds
> bond #3/IY:268@C #3/IY:269@N reasonable false
Created 0 bonds
> bond #3/IY:269@C #3/IY:270@N reasonable false
Created 0 bonds
> bond #3/IY:270@C #3/IY:271@N reasonable false
Created 0 bonds
> bond #3/IY:271@C #3/IY:272@N reasonable false
Created 0 bonds
> bond #3/IY:272@C #3/IY:273@N reasonable false
Created 0 bonds
> bond #3/IY:273@C #3/IY:274@N reasonable false
Created 0 bonds
> bond #3/IY:274@C #3/IY:275@N reasonable false
Created 0 bonds
> bond #3/IY:275@C #3/IY:276@N reasonable false
Created 0 bonds
> bond #3/IY:276@C #3/IY:277@N reasonable false
Created 0 bonds
> bond #3/IY:277@C #3/IY:278@N reasonable false
Created 0 bonds
> bond #3/IY:278@C #3/IY:279@N reasonable false
Created 0 bonds
> bond #3/IY:279@C #3/IY:280@N reasonable false
Created 0 bonds
> bond #3/IY:280@C #3/IY:281@N reasonable false
Created 0 bonds
> bond #3/IY:281@C #3/IY:282@N reasonable false
Created 0 bonds
> bond #3/IY:282@C #3/IY:283@N reasonable false
Created 0 bonds
> bond #3/IY:283@C #3/IY:284@N reasonable false
Created 0 bonds
> bond #3/IY:284@C #3/IY:285@N reasonable false
Created 0 bonds
> bond #3/IY:171@C #3/IY:172@N reasonable false
Created 0 bonds
> bond #3/IY:172@C #3/IY:173@N reasonable false
Created 0 bonds
> bond #3/IY:173@C #3/IY:174@N reasonable false
Created 0 bonds
> bond #3/IY:174@C #3/IY:175@N reasonable false
Created 0 bonds
> bond #3/IY:175@C #3/IY:176@N reasonable false
Created 0 bonds
> bond #3/IY:176@C #3/IY:177@N reasonable false
Created 0 bonds
> bond #3/IY:177@C #3/IY:178@N reasonable false
Created 0 bonds
> bond #3/IY:178@C #3/IY:179@N reasonable false
Created 1 bond
> bond #3/IY:119@C #3/IY:120@N reasonable false
Created 0 bonds
> bond #3/IY:120@C #3/IY:121@N reasonable false
Created 0 bonds
> bond #3/IY:121@C #3/IY:122@N reasonable false
Created 1 bond
> bond #3/IY:96@C #3/IY:97@N reasonable false
Created 0 bonds
> bond #3/IY:97@C #3/IY:98@N reasonable false
Created 1 bond
> bond #3/IY:76@C #3/IY:77@N reasonable false
Created 0 bonds
> bond #3/IY:77@C #3/IY:78@N reasonable false
Created 1 bond
> bond #3/IY:179@C #3/IY:180@N reasonable false
Created 0 bonds
> bond #3/IY:180@C #3/IY:181@N reasonable false
Created 0 bonds
> bond #3/IY:181@C #3/IY:182@N reasonable false
Created 0 bonds
> bond #3/IY:182@C #3/IY:183@N reasonable false
Created 0 bonds
> bond #3/IY:183@C #3/IY:184@N reasonable false
Created 0 bonds
> bond #3/IY:184@C #3/IY:185@N reasonable false
Created 0 bonds
> bond #3/IY:185@C #3/IY:186@N reasonable false
Created 0 bonds
> bond #3/IY:186@C #3/IY:187@N reasonable false
Created 0 bonds
> bond #3/IY:187@C #3/IY:188@N reasonable false
Created 0 bonds
> bond #3/IY:188@C #3/IY:189@N reasonable false
Created 0 bonds
> bond #3/IY:189@C #3/IY:190@N reasonable false
Created 0 bonds
> bond #3/IY:190@C #3/IY:191@N reasonable false
Created 0 bonds
> bond #3/IY:191@C #3/IY:192@N reasonable false
Created 0 bonds
> bond #3/IY:192@C #3/IY:193@N reasonable false
Created 0 bonds
> bond #3/IY:193@C #3/IY:194@N reasonable false
Created 0 bonds
> bond #3/IY:194@C #3/IY:195@N reasonable false
Created 0 bonds
> bond #3/IY:195@C #3/IY:196@N reasonable false
Created 0 bonds
> bond #3/IY:196@C #3/IY:197@N reasonable false
Created 0 bonds
> bond #3/IY:197@C #3/IY:198@N reasonable false
Created 0 bonds
> bond #3/IY:198@C #3/IY:199@N reasonable false
Created 0 bonds
> bond #3/IY:199@C #3/IY:200@N reasonable false
Created 0 bonds
> bond #3/IY:200@C #3/IY:201@N reasonable false
Created 0 bonds
> bond #3/IY:201@C #3/IY:202@N reasonable false
Created 0 bonds
> bond #3/IY:202@C #3/IY:203@N reasonable false
Created 0 bonds
> bond #3/IY:203@C #3/IY:204@N reasonable false
Created 0 bonds
> bond #3/IY:204@C #3/IY:205@N reasonable false
Created 0 bonds
> bond #3/IY:205@C #3/IY:206@N reasonable false
Created 0 bonds
> bond #3/IY:206@C #3/IY:207@N reasonable false
Created 0 bonds
> bond #3/IY:207@C #3/IY:208@N reasonable false
Created 0 bonds
> bond #3/IY:208@C #3/IY:209@N reasonable false
Created 0 bonds
> bond #3/IY:209@C #3/IY:210@N reasonable false
Created 0 bonds
> bond #3/IY:210@C #3/IY:211@N reasonable false
Created 0 bonds
> bond #3/IY:211@C #3/IY:212@N reasonable false
Created 0 bonds
> bond #3/IY:212@C #3/IY:213@N reasonable false
Created 0 bonds
> bond #3/IY:213@C #3/IY:214@N reasonable false
Created 0 bonds
> bond #3/IY:214@C #3/IY:215@N reasonable false
Created 0 bonds
> bond #3/IY:215@C #3/IY:216@N reasonable false
Created 1 bond
> bond #3/IY:66@C #3/IY:67@N reasonable false
Created 0 bonds
> bond #3/IY:67@C #3/IY:68@N reasonable false
Created 0 bonds
> bond #3/IY:68@C #3/IY:69@N reasonable false
Created 0 bonds
> bond #3/IY:69@C #3/IY:70@N reasonable false
Created 0 bonds
> bond #3/IY:70@C #3/IY:71@N reasonable false
Created 0 bonds
> bond #3/IY:71@C #3/IY:72@N reasonable false
Created 0 bonds
> bond #3/IY:162@C #3/IY:163@N reasonable false
Created 0 bonds
> bond #3/IY:163@C #3/IY:164@N reasonable false
Created 0 bonds
> bond #3/IY:164@C #3/IY:165@N reasonable false
Created 0 bonds
> bond #3/IY:165@C #3/IY:166@N reasonable false
Created 0 bonds
> bond #3/IY:166@C #3/IY:167@N reasonable false
Created 0 bonds
> bond #3/IY:167@C #3/IY:168@N reasonable false
Created 0 bonds
> bond #3/IY:168@C #3/IY:169@N reasonable false
Created 0 bonds
> bond #3/IY:125@C #3/IY:126@N reasonable false
Created 0 bonds
> bond #3/IY:126@C #3/IY:127@N reasonable false
Created 0 bonds
> bond #3/IY:127@C #3/IY:128@N reasonable false
Created 0 bonds
> bond #3/IY:128@C #3/IY:129@N reasonable false
Created 0 bonds
> bond #3/IY:129@C #3/IY:130@N reasonable false
Created 0 bonds
> bond #3/IY:130@C #3/IY:131@N reasonable false
Created 0 bonds
> bond #3/IY:131@C #3/IY:132@N reasonable false
Created 0 bonds
> bond #3/IY:132@C #3/IY:133@N reasonable false
Created 0 bonds
> bond #3/IY:133@C #3/IY:134@N reasonable false
Created 0 bonds
> bond #3/IY:134@C #3/IY:135@N reasonable false
Created 0 bonds
> bond #3/IY:135@C #3/IY:136@N reasonable false
Created 0 bonds
> bond #3/IY:136@C #3/IY:137@N reasonable false
Created 0 bonds
> bond #3/IY:137@C #3/IY:138@N reasonable false
Created 0 bonds
> bond #3/IY:138@C #3/IY:139@N reasonable false
Created 0 bonds
> bond #3/IY:139@C #3/IY:140@N reasonable false
Created 0 bonds
> bond #3/IY:140@C #3/IY:141@N reasonable false
Created 0 bonds
> bond #3/IY:141@C #3/IY:142@N reasonable false
Created 0 bonds
> bond #3/IY:142@C #3/IY:143@N reasonable false
Created 0 bonds
> bond #3/IY:143@C #3/IY:144@N reasonable false
Created 0 bonds
> bond #3/IY:144@C #3/IY:145@N reasonable false
Created 0 bonds
> bond #3/IY:145@C #3/IY:146@N reasonable false
Created 0 bonds
> bond #3/IY:146@C #3/IY:147@N reasonable false
Created 0 bonds
> bond #3/IY:147@C #3/IY:148@N reasonable false
Created 0 bonds
> bond #3/IY:148@C #3/IY:149@N reasonable false
Created 0 bonds
> bond #3/IY:149@C #3/IY:150@N reasonable false
Created 0 bonds
> bond #3/IY:150@C #3/IY:151@N reasonable false
Created 0 bonds
> bond #3/IY:151@C #3/IY:152@N reasonable false
Created 0 bonds
> bond #3/IY:152@C #3/IY:153@N reasonable false
Created 0 bonds
> bond #3/IY:153@C #3/IY:154@N reasonable false
Created 1 bond
> bond #3/IY:78@C #3/IY:79@N reasonable false
Created 0 bonds
> bond #3/IY:79@C #3/IY:80@N reasonable false
Created 0 bonds
> bond #3/IY:80@C #3/IY:81@N reasonable false
Created 0 bonds
> bond #3/IY:81@C #3/IY:82@N reasonable false
Created 0 bonds
> bond #3/IY:82@C #3/IY:83@N reasonable false
Created 0 bonds
> bond #3/IY:83@C #3/IY:84@N reasonable false
Created 0 bonds
> bond #3/IY:84@C #3/IY:85@N reasonable false
Created 0 bonds
> bond #3/IY:85@C #3/IY:86@N reasonable false
Created 0 bonds
> bond #3/IY:86@C #3/IY:87@N reasonable false
Created 0 bonds
> bond #3/IY:87@C #3/IY:88@N reasonable false
Created 0 bonds
> bond #3/IY:88@C #3/IY:89@N reasonable false
Created 0 bonds
> bond #3/IY:89@C #3/IY:90@N reasonable false
Created 0 bonds
> bond #3/IY:90@C #3/IY:91@N reasonable false
Created 0 bonds
> bond #3/IY:91@C #3/IY:92@N reasonable false
Created 0 bonds
> bond #3/IY:92@C #3/IY:93@N reasonable false
Created 0 bonds
> bond #3/IY:93@C #3/IY:94@N reasonable false
Created 0 bonds
> bond #3/IY:94@C #3/IY:95@N reasonable false
Created 0 bonds
> bond #3/IY:95@C #3/IY:96@N reasonable false
Created 1 bond
> bond #3/IY:2@C #3/IY:3@N reasonable false
Created 0 bonds
> bond #3/IY:3@C #3/IY:4@N reasonable false
Created 0 bonds
> bond #3/IY:4@C #3/IY:5@N reasonable false
Created 0 bonds
> bond #3/IY:5@C #3/IY:6@N reasonable false
Created 0 bonds
> bond #3/IY:6@C #3/IY:7@N reasonable false
Created 0 bonds
> bond #3/IY:7@C #3/IY:8@N reasonable false
Created 0 bonds
> bond #3/IY:8@C #3/IY:9@N reasonable false
Created 0 bonds
> bond #3/IY:9@C #3/IY:10@N reasonable false
Created 0 bonds
> bond #3/IY:10@C #3/IY:11@N reasonable false
Created 0 bonds
> bond #3/IY:11@C #3/IY:12@N reasonable false
Created 0 bonds
> bond #3/IY:12@C #3/IY:13@N reasonable false
Created 0 bonds
> bond #3/IY:13@C #3/IY:14@N reasonable false
Created 0 bonds
> bond #3/IY:14@C #3/IY:15@N reasonable false
Created 1 bond
> bond #3/IY:15@C #3/IY:16@N reasonable false
Created 0 bonds
> bond #3/IY:16@C #3/IY:17@N reasonable false
Created 0 bonds
> bond #3/IY:17@C #3/IY:18@N reasonable false
Created 0 bonds
> bond #3/IY:20@C #3/IY:21@N reasonable false
Created 0 bonds
> bond #3/IY:21@C #3/IY:22@N reasonable false
Created 0 bonds
> bond #3/IY:22@C #3/IY:23@N reasonable false
Created 0 bonds
> bond #3/IY:23@C #3/IY:24@N reasonable false
Created 0 bonds
> bond #3/IY:24@C #3/IY:25@N reasonable false
Created 0 bonds
> bond #3/IY:25@C #3/IY:26@N reasonable false
Created 0 bonds
> bond #3/IY:26@C #3/IY:27@N reasonable false
Created 0 bonds
> bond #3/IY:27@C #3/IY:28@N reasonable false
Created 0 bonds
> bond #3/IY:28@C #3/IY:29@N reasonable false
Created 0 bonds
> bond #3/IY:29@C #3/IY:30@N reasonable false
Created 0 bonds
> bond #3/IY:30@C #3/IY:31@N reasonable false
Created 0 bonds
> bond #3/IY:31@C #3/IY:32@N reasonable false
Created 0 bonds
> bond #3/IY:32@C #3/IY:33@N reasonable false
Created 0 bonds
> bond #3/IY:33@C #3/IY:34@N reasonable false
Created 0 bonds
> bond #3/IY:34@C #3/IY:35@N reasonable false
Created 0 bonds
> bond #3/IY:35@C #3/IY:36@N reasonable false
Created 0 bonds
> bond #3/IY:36@C #3/IY:37@N reasonable false
Created 0 bonds
> bond #3/IY:37@C #3/IY:38@N reasonable false
Created 1 bond
> bond #3/IY:38@C #3/IY:39@N reasonable false
Created 0 bonds
> bond #3/IY:39@C #3/IY:40@N reasonable false
Created 0 bonds
> bond #3/IY:40@C #3/IY:41@N reasonable false
Created 0 bonds
> bond #3/IY:41@C #3/IY:42@N reasonable false
Created 0 bonds
> bond #3/IY:42@C #3/IY:43@N reasonable false
Created 0 bonds
> bond #3/IY:43@C #3/IY:44@N reasonable false
Created 0 bonds
> bond #3/IY:44@C #3/IY:45@N reasonable false
Created 0 bonds
> bond #3/IY:45@C #3/IY:46@N reasonable false
Created 0 bonds
> bond #3/IY:46@C #3/IY:47@N reasonable false
Created 0 bonds
> bond #3/IY:47@C #3/IY:48@N reasonable false
Created 0 bonds
> bond #3/IY:48@C #3/IY:49@N reasonable false
Created 0 bonds
> bond #3/IY:49@C #3/IY:50@N reasonable false
Created 0 bonds
> bond #3/IY:50@C #3/IY:51@N reasonable false
Created 0 bonds
> bond #3/IY:51@C #3/IY:52@N reasonable false
Created 0 bonds
> bond #3/IY:52@C #3/IY:53@N reasonable false
Created 0 bonds
> bond #3/IY:53@C #3/IY:54@N reasonable false
Created 0 bonds
> bond #3/IY:54@C #3/IY:55@N reasonable false
Created 0 bonds
> bond #3/IY:55@C #3/IY:56@N reasonable false
Created 0 bonds
> bond #3/IY:56@C #3/IY:57@N reasonable false
Created 0 bonds
> bond #3/IY:57@C #3/IY:58@N reasonable false
Created 0 bonds
> bond #3/IY:58@C #3/IY:59@N reasonable false
Created 0 bonds
> bond #3/IY:59@C #3/IY:60@N reasonable false
Created 0 bonds
> bond #3/IY:60@C #3/IY:61@N reasonable false
Created 0 bonds
> bond #3/IY:61@C #3/IY:62@N reasonable false
Created 0 bonds
> bond #3/IY:62@C #3/IY:63@N reasonable false
Created 0 bonds
> bond #3/IY:63@C #3/IY:64@N reasonable false
Created 0 bonds
> bond #3/IY:64@C #3/IY:65@N reasonable false
Created 0 bonds
> bond #3/IY:65@C #3/IY:66@N reasonable false
Created 1 bond
> bond #3/IY:122@C #3/IY:123@N reasonable false
Created 0 bonds
> bond #3/IY:123@C #3/IY:124@N reasonable false
Created 0 bonds
> bond #3/IY:124@C #3/IY:125@N reasonable false
Created 1 bond
> bond #3/IY:288@C #3/IY:289@N reasonable false
Created 0 bonds
> bond #3/IY:289@C #3/IY:290@N reasonable false
Created 0 bonds
> bond #3/IY:290@C #3/IY:291@N reasonable false
Created 0 bonds
> bond #3/IY:291@C #3/IY:292@N reasonable false
Created 0 bonds
> bond #3/IY:292@C #3/IY:293@N reasonable false
Created 0 bonds
> bond #3/IY:293@C #3/IY:294@N reasonable false
Created 0 bonds
> bond #3/IY:294@C #3/IY:295@N reasonable false
Created 0 bonds
> bond #3/IY:98@C #3/IY:99@N reasonable false
Created 0 bonds
> bond #3/IY:99@C #3/IY:100@N reasonable false
Created 0 bonds
> bond #3/IY:100@C #3/IY:101@N reasonable false
Created 0 bonds
> bond #3/IY:101@C #3/IY:102@N reasonable false
Created 0 bonds
> bond #3/IY:102@C #3/IY:103@N reasonable false
Created 0 bonds
> bond #3/IY:103@C #3/IY:104@N reasonable false
Created 0 bonds
> bond #3/IY:104@C #3/IY:105@N reasonable false
Created 0 bonds
> bond #3/IY:105@C #3/IY:106@N reasonable false
Created 0 bonds
> bond #3/IY:106@C #3/IY:107@N reasonable false
Created 0 bonds
> bond #3/IY:107@C #3/IY:108@N reasonable false
Created 0 bonds
> bond #3/IY:108@C #3/IY:109@N reasonable false
Created 0 bonds
> bond #3/IY:109@C #3/IY:110@N reasonable false
Created 0 bonds
> bond #3/IY:110@C #3/IY:111@N reasonable false
Created 0 bonds
> bond #3/IY:111@C #3/IY:112@N reasonable false
Created 0 bonds
> bond #3/IY:112@C #3/IY:113@N reasonable false
Created 0 bonds
> bond #3/IY:113@C #3/IY:114@N reasonable false
Created 0 bonds
> bond #3/IY:114@C #3/IY:115@N reasonable false
Created 0 bonds
> bond #3/IY:115@C #3/IY:116@N reasonable false
Created 0 bonds
> bond #3/IY:116@C #3/IY:117@N reasonable false
Created 0 bonds
> bond #3/IY:117@C #3/IY:118@N reasonable false
Created 0 bonds
> bond #3/IY:118@C #3/IY:119@N reasonable false
Created 1 bond
> select #3/JC
1259 atoms, 1263 bonds, 160 residues, 1 model selected
\---------------------************************************************************************************************************************-****-**********************************
> build start peptide #3 E 1,1 position
> 253.26145227640222,323.16895561049313,318.93294617572474 chainId zz
> delete #3/zz:1@OXT
> renumber #3/zz start 142
1 residues renumbered
> changechains #3/zz JC
Chain IDs of 1 residues changed
> bond #3/JC:142@C #3/JC:143@N reasonable false
Created 1 bond
> bond #3/JC:141@C #3/JC:142@N reasonable false
Created 1 bond
> color #3/JC:142-142@C* red
> build start peptide #3 Q 1,1 position
> 245.88878959150833,318.9809337422343,316.345575943639 chainId zz
> delete #3/zz:1@OXT
> renumber #3/zz start 147
1 residues renumbered
> changechains #3/zz JC
Chain IDs of 1 residues changed
> bond #3/JC:147@C #3/JC:148@N reasonable false
Created 1 bond
> bond #3/JC:146@C #3/JC:147@N reasonable false
Created 1 bond
> color #3/JC:147-147@C* red
> bond #3/JC:148@C #3/JC:149@N reasonable false
Created 0 bonds
> bond #3/JC:149@C #3/JC:150@N reasonable false
Created 0 bonds
> bond #3/JC:150@C #3/JC:151@N reasonable false
Created 0 bonds
> bond #3/JC:151@C #3/JC:152@N reasonable false
Created 1 bond
> bond #3/JC:88@C #3/JC:89@N reasonable false
Created 0 bonds
> bond #3/JC:89@C #3/JC:90@N reasonable false
Created 0 bonds
> bond #3/JC:90@C #3/JC:91@N reasonable false
Created 0 bonds
> bond #3/JC:91@C #3/JC:92@N reasonable false
Created 0 bonds
> bond #3/JC:92@C #3/JC:93@N reasonable false
Created 0 bonds
> bond #3/JC:93@C #3/JC:94@N reasonable false
Created 0 bonds
> bond #3/JC:94@C #3/JC:95@N reasonable false
Created 0 bonds
> bond #3/JC:95@C #3/JC:96@N reasonable false
Created 0 bonds
> bond #3/JC:96@C #3/JC:97@N reasonable false
Created 0 bonds
> bond #3/JC:97@C #3/JC:98@N reasonable false
Created 1 bond
> bond #3/JC:98@C #3/JC:99@N reasonable false
Created 0 bonds
> bond #3/JC:99@C #3/JC:100@N reasonable false
Created 0 bonds
> bond #3/JC:100@C #3/JC:101@N reasonable false
Created 0 bonds
> bond #3/JC:101@C #3/JC:102@N reasonable false
Created 0 bonds
> bond #3/JC:102@C #3/JC:103@N reasonable false
Created 1 bond
> bond #3/JC:27@C #3/JC:28@N reasonable false
Created 0 bonds
> bond #3/JC:28@C #3/JC:29@N reasonable false
Created 0 bonds
> bond #3/JC:29@C #3/JC:30@N reasonable false
Created 0 bonds
> bond #3/JC:30@C #3/JC:31@N reasonable false
Created 0 bonds
> bond #3/JC:31@C #3/JC:32@N reasonable false
Created 0 bonds
> bond #3/JC:32@C #3/JC:33@N reasonable false
Created 0 bonds
> bond #3/JC:33@C #3/JC:34@N reasonable false
Created 1 bond
> bond #3/JC:78@C #3/JC:79@N reasonable false
Created 0 bonds
> bond #3/JC:79@C #3/JC:80@N reasonable false
Created 1 bond
> bond #3/JC:154@C #3/JC:155@N reasonable false
Created 0 bonds
> bond #3/JC:155@C #3/JC:156@N reasonable false
Created 0 bonds
> bond #3/JC:156@C #3/JC:157@N reasonable false
Created 0 bonds
> bond #3/JC:157@C #3/JC:158@N reasonable false
Created 1 bond
> bond #3/JC:152@C #3/JC:153@N reasonable false
Created 0 bonds
> bond #3/JC:153@C #3/JC:154@N reasonable false
Created 1 bond
> bond #3/JC:58@C #3/JC:59@N reasonable false
Created 0 bonds
> bond #3/JC:59@C #3/JC:60@N reasonable false
Created 1 bond
> bond #3/JC:158@C #3/JC:159@N reasonable false
Created 0 bonds
> bond #3/JC:159@C #3/JC:160@N reasonable false
Created 1 bond
> bond #3/JC:143@C #3/JC:144@N reasonable false
Created 0 bonds
> bond #3/JC:144@C #3/JC:145@N reasonable false
Created 0 bonds
> bond #3/JC:145@C #3/JC:146@N reasonable false
Created 0 bonds
> bond #3/JC:34@C #3/JC:35@N reasonable false
Created 0 bonds
> bond #3/JC:35@C #3/JC:36@N reasonable false
Created 0 bonds
> bond #3/JC:36@C #3/JC:37@N reasonable false
Created 0 bonds
> bond #3/JC:37@C #3/JC:38@N reasonable false
Created 0 bonds
> bond #3/JC:38@C #3/JC:39@N reasonable false
Created 0 bonds
> bond #3/JC:39@C #3/JC:40@N reasonable false
Created 0 bonds
> bond #3/JC:40@C #3/JC:41@N reasonable false
Created 0 bonds
> bond #3/JC:41@C #3/JC:42@N reasonable false
Created 0 bonds
> bond #3/JC:42@C #3/JC:43@N reasonable false
Created 0 bonds
> bond #3/JC:43@C #3/JC:44@N reasonable false
Created 0 bonds
> bond #3/JC:44@C #3/JC:45@N reasonable false
Created 0 bonds
> bond #3/JC:45@C #3/JC:46@N reasonable false
Created 0 bonds
> bond #3/JC:46@C #3/JC:47@N reasonable false
Created 0 bonds
> bond #3/JC:47@C #3/JC:48@N reasonable false
Created 0 bonds
> bond #3/JC:48@C #3/JC:49@N reasonable false
Created 0 bonds
> bond #3/JC:49@C #3/JC:50@N reasonable false
Created 0 bonds
> bond #3/JC:50@C #3/JC:51@N reasonable false
Created 0 bonds
> bond #3/JC:51@C #3/JC:52@N reasonable false
Created 0 bonds
> bond #3/JC:52@C #3/JC:53@N reasonable false
Created 0 bonds
> bond #3/JC:53@C #3/JC:54@N reasonable false
Created 0 bonds
> bond #3/JC:54@C #3/JC:55@N reasonable false
Created 0 bonds
> bond #3/JC:55@C #3/JC:56@N reasonable false
Created 0 bonds
> bond #3/JC:56@C #3/JC:57@N reasonable false
Created 0 bonds
> bond #3/JC:57@C #3/JC:58@N reasonable false
Created 1 bond
> bond #3/JC:80@C #3/JC:81@N reasonable false
Created 0 bonds
> bond #3/JC:81@C #3/JC:82@N reasonable false
Created 0 bonds
> bond #3/JC:82@C #3/JC:83@N reasonable false
Created 0 bonds
> bond #3/JC:83@C #3/JC:84@N reasonable false
Created 0 bonds
> bond #3/JC:84@C #3/JC:85@N reasonable false
Created 0 bonds
> bond #3/JC:85@C #3/JC:86@N reasonable false
Created 0 bonds
> bond #3/JC:86@C #3/JC:87@N reasonable false
Created 0 bonds
> bond #3/JC:87@C #3/JC:88@N reasonable false
Created 1 bond
> bond #3/JC:103@C #3/JC:104@N reasonable false
Created 0 bonds
> bond #3/JC:104@C #3/JC:105@N reasonable false
Created 0 bonds
> bond #3/JC:105@C #3/JC:106@N reasonable false
Created 0 bonds
> bond #3/JC:106@C #3/JC:107@N reasonable false
Created 0 bonds
> bond #3/JC:107@C #3/JC:108@N reasonable false
Created 0 bonds
> bond #3/JC:108@C #3/JC:109@N reasonable false
Created 0 bonds
> bond #3/JC:109@C #3/JC:110@N reasonable false
Created 0 bonds
> bond #3/JC:110@C #3/JC:111@N reasonable false
Created 0 bonds
> bond #3/JC:111@C #3/JC:112@N reasonable false
Created 0 bonds
> bond #3/JC:112@C #3/JC:113@N reasonable false
Created 0 bonds
> bond #3/JC:113@C #3/JC:114@N reasonable false
Created 0 bonds
> bond #3/JC:114@C #3/JC:115@N reasonable false
Created 0 bonds
> bond #3/JC:115@C #3/JC:116@N reasonable false
Created 0 bonds
> bond #3/JC:116@C #3/JC:117@N reasonable false
Created 0 bonds
> bond #3/JC:117@C #3/JC:118@N reasonable false
Created 0 bonds
> bond #3/JC:118@C #3/JC:119@N reasonable false
Created 0 bonds
> bond #3/JC:119@C #3/JC:120@N reasonable false
Created 0 bonds
> bond #3/JC:120@C #3/JC:121@N reasonable false
Created 0 bonds
> bond #3/JC:121@C #3/JC:122@N reasonable false
Created 0 bonds
> bond #3/JC:122@C #3/JC:123@N reasonable false
Created 0 bonds
> bond #3/JC:123@C #3/JC:124@N reasonable false
Created 0 bonds
> bond #3/JC:124@C #3/JC:125@N reasonable false
Created 0 bonds
> bond #3/JC:125@C #3/JC:126@N reasonable false
Created 0 bonds
> bond #3/JC:126@C #3/JC:127@N reasonable false
Created 1 bond
> bond #3/JC:160@C #3/JC:161@N reasonable false
Created 0 bonds
> bond #3/JC:161@C #3/JC:162@N reasonable false
Created 0 bonds
> bond #3/JC:162@C #3/JC:163@N reasonable false
Created 0 bonds
> bond #3/JC:163@C #3/JC:164@N reasonable false
Created 0 bonds
> bond #3/JC:164@C #3/JC:165@N reasonable false
Created 0 bonds
> bond #3/JC:165@C #3/JC:166@N reasonable false
Created 0 bonds
> bond #3/JC:166@C #3/JC:167@N reasonable false
Created 0 bonds
> bond #3/JC:167@C #3/JC:168@N reasonable false
Created 0 bonds
> bond #3/JC:168@C #3/JC:169@N reasonable false
Created 0 bonds
> bond #3/JC:169@C #3/JC:170@N reasonable false
Created 0 bonds
> bond #3/JC:170@C #3/JC:171@N reasonable false
Created 0 bonds
> bond #3/JC:171@C #3/JC:172@N reasonable false
Created 0 bonds
> bond #3/JC:172@C #3/JC:173@N reasonable false
Created 0 bonds
> bond #3/JC:173@C #3/JC:174@N reasonable false
Created 0 bonds
> bond #3/JC:174@C #3/JC:175@N reasonable false
Created 0 bonds
> bond #3/JC:175@C #3/JC:176@N reasonable false
Created 0 bonds
> bond #3/JC:176@C #3/JC:177@N reasonable false
Created 0 bonds
> bond #3/JC:177@C #3/JC:178@N reasonable false
Created 0 bonds
> bond #3/JC:178@C #3/JC:179@N reasonable false
Created 0 bonds
> bond #3/JC:179@C #3/JC:180@N reasonable false
Created 0 bonds
> bond #3/JC:180@C #3/JC:181@N reasonable false
Created 0 bonds
> bond #3/JC:181@C #3/JC:182@N reasonable false
Created 0 bonds
> bond #3/JC:182@C #3/JC:183@N reasonable false
Created 0 bonds
> bond #3/JC:127@C #3/JC:128@N reasonable false
Created 0 bonds
> bond #3/JC:128@C #3/JC:129@N reasonable false
Created 0 bonds
> bond #3/JC:129@C #3/JC:130@N reasonable false
Created 0 bonds
> bond #3/JC:130@C #3/JC:131@N reasonable false
Created 0 bonds
> bond #3/JC:131@C #3/JC:132@N reasonable false
Created 0 bonds
> bond #3/JC:132@C #3/JC:133@N reasonable false
Created 0 bonds
> bond #3/JC:133@C #3/JC:134@N reasonable false
Created 0 bonds
> bond #3/JC:134@C #3/JC:135@N reasonable false
Created 0 bonds
> bond #3/JC:135@C #3/JC:136@N reasonable false
Created 0 bonds
> bond #3/JC:136@C #3/JC:137@N reasonable false
Created 0 bonds
> bond #3/JC:137@C #3/JC:138@N reasonable false
Created 0 bonds
> bond #3/JC:138@C #3/JC:139@N reasonable false
Created 0 bonds
> bond #3/JC:139@C #3/JC:140@N reasonable false
Created 0 bonds
> bond #3/JC:140@C #3/JC:141@N reasonable false
Created 0 bonds
> bond #3/JC:60@C #3/JC:61@N reasonable false
Created 0 bonds
> bond #3/JC:61@C #3/JC:62@N reasonable false
Created 0 bonds
> bond #3/JC:62@C #3/JC:63@N reasonable false
Created 0 bonds
> bond #3/JC:63@C #3/JC:64@N reasonable false
Created 0 bonds
> bond #3/JC:64@C #3/JC:65@N reasonable false
Created 0 bonds
> bond #3/JC:65@C #3/JC:66@N reasonable false
Created 0 bonds
> bond #3/JC:66@C #3/JC:67@N reasonable false
Created 0 bonds
> bond #3/JC:67@C #3/JC:68@N reasonable false
Created 0 bonds
> bond #3/JC:68@C #3/JC:69@N reasonable false
Created 0 bonds
> bond #3/JC:69@C #3/JC:70@N reasonable false
Created 0 bonds
> bond #3/JC:70@C #3/JC:71@N reasonable false
Created 0 bonds
> bond #3/JC:71@C #3/JC:72@N reasonable false
Created 0 bonds
> bond #3/JC:72@C #3/JC:73@N reasonable false
Created 0 bonds
> bond #3/JC:73@C #3/JC:74@N reasonable false
Created 0 bonds
> bond #3/JC:74@C #3/JC:75@N reasonable false
Created 0 bonds
> bond #3/JC:75@C #3/JC:76@N reasonable false
Created 0 bonds
> bond #3/JC:76@C #3/JC:77@N reasonable false
Created 0 bonds
> bond #3/JC:77@C #3/JC:78@N reasonable false
Created 1 bond
> bond #3/JC:22@C #3/JC:23@N reasonable false
Created 0 bonds
> bond #3/JC:23@C #3/JC:24@N reasonable false
Created 0 bonds
> bond #3/JC:24@C #3/JC:25@N reasonable false
Created 0 bonds
> bond #3/JC:25@C #3/JC:26@N reasonable false
Created 0 bonds
> bond #3/JC:26@C #3/JC:27@N reasonable false
Created 1 bond
> select #3/D6
387 atoms, 381 bonds, 51 residues, 1 model selected
\------*****--**************************-************----------********---
> build start peptide #3 RD 1,1 1,1 position
> 240.95136576070178,300.84769718569873,326.9298774506158 chainId zz
> delete #3/zz:2@OXT
> renumber #3/zz start 12
2 residues renumbered
> changechains #3/zz D6
Chain IDs of 2 residues changed
> bond #3/D6:13@C #3/D6:14@N reasonable false
Created 1 bond
> bond #3/D6:11@C #3/D6:12@N reasonable false
Created 1 bond
> color #3/D6:12-13@C* red
> build start peptide #3 K 1,1 position
> 265.73153028549467,312.79277069016905,316.5874818354688 chainId zz
> delete #3/zz:1@OXT
> renumber #3/zz start 40
1 residues renumbered
> changechains #3/zz D6
Chain IDs of 1 residues changed
> bond #3/D6:40@C #3/D6:41@N reasonable false
Created 1 bond
> bond #3/D6:39@C #3/D6:40@N reasonable false
Created 1 bond
> color #3/D6:40-40@C* red
> bond #3/D6:46@C #3/D6:47@N reasonable false
Created 0 bonds
> bond #3/D6:47@C #3/D6:48@N reasonable false
Created 0 bonds
> bond #3/D6:48@C #3/D6:49@N reasonable false
Created 0 bonds
> bond #3/D6:49@C #3/D6:50@N reasonable false
Created 1 bond
> bond #3/D6:44@C #3/D6:45@N reasonable false
Created 0 bonds
> bond #3/D6:45@C #3/D6:46@N reasonable false
Created 1 bond
> bond #3/D6:63@C #3/D6:64@N reasonable false
Created 0 bonds
> bond #3/D6:64@C #3/D6:65@N reasonable false
Created 1 bond
> bond #3/D6:9@C #3/D6:10@N reasonable false
Created 0 bonds
> bond #3/D6:10@C #3/D6:11@N reasonable false
Created 0 bonds
> bond #3/D6:7@C #3/D6:8@N reasonable false
Created 0 bonds
> bond #3/D6:8@C #3/D6:9@N reasonable false
Created 1 bond
> bond #3/D6:14@C #3/D6:15@N reasonable false
Created 0 bonds
> bond #3/D6:15@C #3/D6:16@N reasonable false
Created 0 bonds
> bond #3/D6:16@C #3/D6:17@N reasonable false
Created 0 bonds
> bond #3/D6:17@C #3/D6:18@N reasonable false
Created 0 bonds
> bond #3/D6:18@C #3/D6:19@N reasonable false
Created 0 bonds
> bond #3/D6:19@C #3/D6:20@N reasonable false
Created 0 bonds
> bond #3/D6:20@C #3/D6:21@N reasonable false
Created 0 bonds
> bond #3/D6:21@C #3/D6:22@N reasonable false
Created 0 bonds
> bond #3/D6:22@C #3/D6:23@N reasonable false
Created 0 bonds
> bond #3/D6:23@C #3/D6:24@N reasonable false
Created 0 bonds
> bond #3/D6:24@C #3/D6:25@N reasonable false
Created 0 bonds
> bond #3/D6:25@C #3/D6:26@N reasonable false
Created 0 bonds
> bond #3/D6:26@C #3/D6:27@N reasonable false
Created 0 bonds
> bond #3/D6:27@C #3/D6:28@N reasonable false
Created 0 bonds
> bond #3/D6:28@C #3/D6:29@N reasonable false
Created 0 bonds
> bond #3/D6:29@C #3/D6:30@N reasonable false
Created 0 bonds
> bond #3/D6:30@C #3/D6:31@N reasonable false
Created 0 bonds
> bond #3/D6:31@C #3/D6:32@N reasonable false
Created 0 bonds
> bond #3/D6:32@C #3/D6:33@N reasonable false
Created 0 bonds
> bond #3/D6:33@C #3/D6:34@N reasonable false
Created 0 bonds
> bond #3/D6:34@C #3/D6:35@N reasonable false
Created 0 bonds
> bond #3/D6:35@C #3/D6:36@N reasonable false
Created 0 bonds
> bond #3/D6:36@C #3/D6:37@N reasonable false
Created 0 bonds
> bond #3/D6:37@C #3/D6:38@N reasonable false
Created 0 bonds
> bond #3/D6:38@C #3/D6:39@N reasonable false
Created 0 bonds
> bond #3/D6:50@C #3/D6:51@N reasonable false
Created 0 bonds
> bond #3/D6:51@C #3/D6:52@N reasonable false
Created 0 bonds
> bond #3/D6:65@C #3/D6:66@N reasonable false
Created 0 bonds
> bond #3/D6:66@C #3/D6:67@N reasonable false
Created 0 bonds
> bond #3/D6:67@C #3/D6:68@N reasonable false
Created 0 bonds
> bond #3/D6:68@C #3/D6:69@N reasonable false
Created 0 bonds
> bond #3/D6:69@C #3/D6:70@N reasonable false
Created 0 bonds
> bond #3/D6:41@C #3/D6:42@N reasonable false
Created 0 bonds
> bond #3/D6:42@C #3/D6:43@N reasonable false
Created 0 bonds
> bond #3/D6:43@C #3/D6:44@N reasonable false
Created 1 bond
> save "/Users/sramonabarua/Google Drive/My Drive/supercomplex/CV-
> Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
> Conf1/central_stalk/centralstalk_protein_version1_renumbered model.cif"
> models #2
Not saving entity_poly_seq for non-authoritative sequences
> save "/Users/sramonabarua/Google Drive/My Drive/supercomplex/CV-
> Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
> Conf1/central_stalk/centralstalk_protein_version1_renumbered model.cxs"
> save "/Users/sramonabarua/Google Drive/My Drive/supercomplex/CV-
> Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
> Conf1/central_stalk/centralstalk_protein_version2_joinfragments.cif" models
> #3
Not saving entity_poly_seq for non-authoritative sequences
> save "/Users/sramonabarua/Google Drive/My Drive/supercomplex/CV-
> Full/cryosparc_P31_J281_004_volume_map_sharp--VC-
> Conf1/central_stalk/centralstalk_protein_version2_joinfragments.cxs"
——— End of log from Mon Nov 25 16:32:30 2024 ———
opened ChimeraX session
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,3
Model Number: Z1C8000ANFN/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 5 days, 22 hours, 8 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: No
Connection Type: Internal
DELL U2723QE:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.0
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 11 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in Sequence::rname3to1 drawing ribbons after restoring session |
comment:2 by , 11 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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