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Opened 17 months ago
Last modified 17 months ago
#15548 accepted defect
Crash in python_instances_of_class
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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
Current thread 0x00000001f19ccc00 (most recent call first):
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 52 in
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61 in
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61 in python_instances_of_class
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 162 in copy
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 65 in combine_cmd
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Users/rafaelrocha/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py", line 155 in
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 72 in _exec_python
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py", line 95 in open_python_script
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py", line 49 in runscript
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
(deleted to fit within ticket limits)
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 688K 33 \nColorSync 624K 31 \nCoreAnimation 2912K 180 \nCoreGraphics 64K 4 \nCoreGraphics (reserved) 16K 1 reserved VM address space (unallocated)\nCoreUI image data 5632K 46 \nDispatch continuations 96.0M 1 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 1.7G 599 \nMALLOC guard page 192K 12 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 992K 62 \nStack 183.1M 63 \nStack Guard 56.0M 1 \nVM_ALLOCATE 641.7M 306 \nVM_ALLOCATE (reserved) 512.0M 4 reserved VM address space (unallocated)\n__AUTH 2199K 404 \n__AUTH_CONST 31.7M 622 \n__CTF 824 1 \n__DATA 25.1M 876 \n__DATA_CONST 44.0M 877 \n__DATA_DIRTY 2024K 232 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 576.0M 250 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2199K 1 \n__TEXT 994.4M 894 \ndyld private memory 592K 8 \nmapped file 282.2M 59 \nshared memory 3248K 30 \n=========== ======= ======= \nTOTAL 5.1G 5613 \nTOTAL, minus reserved VM space 4.6G 5613 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "20fe21696ccfa98e4374b0190d0d0cd29a7e9ec4",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "6112d17137f5d11121dcd4e2",
"factorPackIds" : {
},
"deploymentId" : 240000565
}
],
"experiments" : [
{
"treatmentId" : "5d85d104-adc7-4ebf-8b7c-96d84fdad9cc",
"experimentId" : "6384d56b96e8d228551ec182",
"deploymentId" : 400000032
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000004
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> set selectionWidth 4
Done loading forcefield
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> runscript
> /Users/rafaelrocha/GitHub/KRSPs/modelangeloScripts/bondFragmentsFillGapsMutateForMultipleChains.py
Traceback (most recent call last):
File
"/Users/rafaelrocha/GitHub/KRSPs/modelangeloScripts/bondFragmentsFillGapsMutateForMultipleChains.py",
line 20, in
inpAligns = open("test.txt",'r').readlines()
^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'test.txt'
Error opening python file
/Users/rafaelrocha/GitHub/KRSPs/modelangeloScripts/bondFragmentsFillGapsMutateForMultipleChains.py
> cd /Users/rafaelrocha/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ
Current working directory is:
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/supercomplexV-
IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ
> open "/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
> rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
> Computer/supercomplex/supercomplexV-
> IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ/cryosparc_P43_J436_002_volume_map_sharp_NOSEQFixed.cif"
Summary of feedback from opening
/Users/rafaelrocha/Library/CloudStorage/GoogleDrive-
rafael.eduardo.oliveira.rocha@gmail.com/Other computers/My
Computer/supercomplex/supercomplexV-
IV2-II/cryosparc_P43_J436_002_volume_map_sharp_NOSEQ/cryosparc_P43_J436_002_volume_map_sharp_NOSEQFixed.cif
---
warnings | Unknown polymer entity '1' on line 1568
Unknown polymer entity '2' on line 1624
Unknown polymer entity '3' on line 1658
Unknown polymer entity '4' on line 1671
Unknown polymer entity '5' on line 1685
523 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for cryosparc_P43_J436_002_volume_map_sharp_NOSEQFixed.cif
#1
---
Chain | Description
2 | No description available
3 | No description available
4 Db Eh | No description available
5 D6 | No description available
6 | No description available
8 | No description available
9 | No description available
A0 | No description available
A1 | No description available
A3 BX GE | No description available
A4 | No description available
A7 | No description available
A8 | No description available
AA | No description available
AB | No description available
AD CF | No description available
AE | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ BT | No description available
AK | No description available
AL BS | No description available
AN | No description available
AO | No description available
AP | No description available
AR BM DJ Eu GD | No description available
AS | No description available
AT | No description available
AU | No description available
AW | No description available
AX Av BN CE D2 DK | No description available
AY | No description available
AZ | No description available
Ae CP EA | No description available
Af | No description available
Ag | No description available
Ah | No description available
Aj | No description available
Al | No description available
Am At CV CY EO | No description available
An | No description available
Ao | No description available
Ap BO | No description available
Ar GL r | No description available
As | No description available
Aw | No description available
Ax BD | No description available
Az Bl | No description available
B | No description available
B0 | No description available
B1 Ew | No description available
B4 | No description available
B5 | No description available
BB | No description available
BE | No description available
BF Eq | No description available
BG | No description available
BH | No description available
BJ | No description available
BL | No description available
BP | No description available
BR HQ | No description available
BV | No description available
BW | No description available
Ba DZ | No description available
Bb | No description available
Be | No description available
Bf | No description available
Bg | No description available
Bh | No description available
Bk | No description available
Bn | No description available
Bp | No description available
Br | No description available
Bv | No description available
Bw Ez | No description available
Bx | No description available
By | No description available
C | No description available
C0 | No description available
C1 | No description available
C2 | No description available
C4 G6 | No description available
C5 | No description available
C7 | No description available
C8 | No description available
CA DQ HZ | No description available
CC FX | No description available
CD | No description available
CJ | No description available
CK Ff | No description available
CL Cg EV | No description available
CQ | No description available
CR | No description available
CS | No description available
CU | No description available
CW | No description available
Ca | No description available
Cb | No description available
Cd | No description available
Ce | No description available
Cf EF | No description available
Ci | No description available
Cj | No description available
Cl | No description available
Cm | No description available
Cp | No description available
Cr | No description available
Cs En | No description available
Cv | No description available
Cy | No description available
D | No description available
D1 | No description available
D3 Ds | No description available
D4 | No description available
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DA | No description available
DD | No description available
DF | No description available
DM | No description available
DO F4 | No description available
DT E3 | No description available
DU | No description available
DV | No description available
Dm Dp | No description available
Dr | No description available
Dv Et | No description available
E4 | No description available
E6 | No description available
E8 | No description available
ED | No description available
EG | No description available
EQ | No description available
Ea | No description available
Ed | No description available
Eg | No description available
Ek FS G0 | No description available
Eo | No description available
Er | No description available
Ey | No description available
F | No description available
F0 | No description available
F1 | No description available
FA | No description available
Fq | No description available
Fs IL | No description available
Ft | No description available
G | No description available
GF | No description available
H | No description available
H2 | No description available
HB | No description available
HH | No description available
I | No description available
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IK | No description available
IS | 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
J0 | No description available
J1 | No description available
J2 | No description available
J3 | No description available
J4 | No description available
J5 | No description available
J6 | No description available
J7 | No description available
J8 | No description available
J9 | 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
JW | No description available
JX | No description available
JY | No description available
JZ | 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
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
Jw | No description available
Jx | No description available
Jy | No description available
Jz | No description available
K | No description available
K0 | No description available
K1 | No description available
K2 | No description available
K3 | No description available
K4 | No description available
K5 | No description available
K6 | No description available
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KA | No description available
KB | No description available
KC | No description available
KD | No description available
KE | No description available
KF | No description available
KG | No description available
KH | No description available
KI | No description available
KJ | No description available
KK | No description available
KL | No description available
KM | No description available
KN | No description available
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KP | No description available
KQ | No description available
KR | No description available
KS | No description available
KT | No description available
KU | No description available
KV | No description available
KW | No description available
KX | No description available
KY | No description available
KZ | No description available
Ka | No description available
Kb | No description available
Kc | No description available
Kd | No description available
Ke | No description available
Kf | No description available
Kg | No description available
Kh | No description available
Ki | No description available
Kj | No description available
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Kl | No description available
Km | No description available
Kn | No description available
Ko | No description available
Kp | No description available
Kq | No description available
Kr | No description available
Ks | No description available
Kt | No description available
Ku | No description available
Kv | No description available
Kw | No description available
Kx | No description available
Ky | No description available
Kz | No description available
L | No description available
L0 | No description available
L1 | No description available
L2 | No description available
L3 | No description available
L4 | No description available
L5 | No description available
L6 | No description available
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LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LK | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lq | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Lu | No description available
Lv | No description available
Lw | No description available
Lx | No description available
Ly | No description available
Lz | No description available
M | No description available
M0 | No description available
M1 | No description available
M2 | No description available
M3 | No description available
M4 | No description available
M5 | No description available
M6 | No description available
M7 | No description available
M8 | No description available
M9 | No description available
MA | No description available
MB | No description available
MC | No description available
MD | No description available
ME | No description available
MF | No description available
MG | No description available
MH | No description available
MI | No description available
MJ | No description available
MK | No description available
ML | No description available
MM | No description available
MN | No description available
MO | No description available
MP | No description available
MQ | No description available
MR | No description available
MS | No description available
MT | No description available
MU | No description available
MV | No description available
MW | No description available
MX | No description available
MY | No description available
MZ | No description available
Ma | No description available
Mb | No description available
Mc | No description available
Md | No description available
Me | No description available
Mf | No description available
Mg | No description available
Mh | No description available
Mi | No description available
Mj | No description available
Mk | No description available
Ml | No description available
Mm | No description available
Mn | No description available
Mo | No description available
Mp | No description available
Mq | No description available
Mr | No description available
Ms | No description available
Mt | No description available
Mu | No description available
Mv | No description available
Mw | No description available
Mx | No description available
My | No description available
Mz | No description available
N | No description available
NA | No description available
NB | No description available
NC | No description available
ND | No description available
NE | No description available
NF | No description available
NG | No description available
NH | No description available
NI | No description available
NJ | No description available
NK | No description available
NL | No description available
NM | No description available
NN | No description available
NO | No description available
NP | No description available
NQ | No description available
NR | No description available
NS | No description available
NT | No description available
NU | No description available
NV | No description available
NW | No description available
NX | No description available
NY | No description available
NZ | No description available
Na | No description available
Nb | No description available
Nc | No description available
Nd | No description available
Ne | No description available
Nf | No description available
Ng | No description available
Nh | No description available
Ni | No description available
Nj | No description available
Nk | No description available
Nl | No description available
Nm | No description available
Nn | No description available
No | No description available
Np | No description available
Nq | No description available
Nr | 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
TA | No description available
TB | 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
a | No description available
b | No description available
d | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
s | No description available
t | No description available
u | No description available
v | No description available
x | No description available
y | No description available
z | No description available
> runscript
> /Users/rafaelrocha/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py
> #1 alignmentsModCorrected.txt
['4', '91']
['4', '91']
['1', '23']
['1', '23']
['1', '33']
['1', '33']
['3', '12']
['3', '12']
['1', '84']
['1', '84']
['3', '6']
['3', '6']
['3', '93']
['3', '93']
['5', '38']
['5', '38']
['1', '38']
['1', '38']
['3', '101']
['3', '101']
['2', '12']
['2', '12']
['1', '13']
['1', '13']
['1', '45']
['1', '45']
['1', '9']
['1', '9']
['11']
['1', '1']
['2', '17']
['2', '17']
['1', '3']
['1', '3']
['1', '59']
['1', '59']
['1', '34']
['1', '34']
['4', '57']
['4', '57']
['12']
['1', '2']
['11']
['1', '1']
['1', '4']
['1', '4']
['4', '10']
['4', '10']
['1', '39']
['1', '39']
['1', '127']
['1', '127']
['1', '4']
['1', '4']
['8', '304']
['8', '304']
['7', '17']
['7', '17']
['1', '68']
['1', '68']
['3', '92']
['3', '92']
['1', '25']
['1', '25']
['1', '47']
['1', '47']
['3', '53']
['3', '53']
['1', '11']
['1', '11']
['7', '43']
['7', '43']
['2', '11']
['2', '11']
['1', '7']
['1', '7']
['1', '8']
['1', '8']
['1', '3']
['1', '3']
['1', '20']
['1', '20']
['1', '16']
['1', '16']
['1', '26']
['1', '26']
['4', '35']
['4', '35']
['1', '4']
['1', '4']
['11']
['1', '1']
['12']
['1', '2']
['1', '3']
['1', '3']
['12']
['1', '2']
['11']
['1', '1']
['4', '59']
['4', '59']
['1', '17']
['1', '17']
['1', '11']
['1', '11']
['1', '6']
['1', '6']
['1', '8']
['1', '8']
['12']
['1', '2']
['1', '5']
['1', '5']
['1', '5']
['1', '5']
['1', '5']
['1', '5']
['1', '3']
['1', '3']
['1', '10']
['1', '10']
['1', '17']
['1', '17']
['1', '3']
['1', '3']
['1', '18']
['1', '18']
['1', '15']
['1', '15']
['1', '3']
['1', '3']
['1', '9']
['1', '9']
['3', '33']
['3', '33']
['1', '16']
['1', '16']
['1', '20']
['1', '20']
['1', '5']
['1', '5']
['11']
['1', '1']
['11']
['1', '1']
['11']
['1', '1']
['11']
['1', '1']
['1', '11']
['1', '11']
['4', '24']
['4', '24']
['1', '13']
['1', '13']
['12']
['1', '2']
['1', '4']
['1', '4']
['1', '6']
['1', '6']
['1', '12']
['1', '12']
['2', '46']
['2', '46']
['1', '25']
['1', '25']
['1', '64']
['1', '64']
['9', '13']
['9', '13']
['1', '43']
['1', '43']
['25', '72']
['25', '72']
['1', '6']
['1', '6']
['4', '41']
['4', '41']
['1', '159']
['1', '159']
['1', '24']
['1', '24']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['11']
['1', '1']
['1', '6']
['1', '6']
['1', '24']
['1', '24']
['1', '6']
['1', '6']
['11']
['1', '1']
['11']
['1', '1']
['11']
['1', '1']
['1', '19']
['1', '19']
['1', '21']
['1', '21']
['2', '12']
['2', '12']
['1', '12']
['1', '12']
['1', '128']
['1', '128']
['1', '44']
['1', '44']
['1', '48']
['1', '48']
['2', '32']
['2', '32']
['1', '13']
['1', '13']
['1', '14']
['1', '14']
['1', '6']
['1', '6']
['1', '4']
['1', '4']
['1', '3']
['1', '3']
['11']
['1', '1']
['11']
['1', '1']
['4', '21']
['4', '21']
['1', '46']
['1', '46']
['4', '24']
['4', '24']
['1', '3']
['1', '3']
['2', '16']
['2', '16']
['1', '4']
['1', '4']
['1', '49']
['1', '49']
['11']
['1', '1']
['11']
['1', '1']
['1', '6']
['1', '6']
['2', '92']
['2', '92']
['1', '3']
['1', '3']
['1', '5']
['1', '5']
['11']
['1', '1']
['1', '108']
['1', '108']
['2', '40']
['2', '40']
['1316']
['1', '3', '1', '6']
['1', '50']
['1', '50']
['1', '12']
['1', '12']
['3', '14']
['3', '14']
['1', '7']
['1', '7']
['1', '4']
['1', '4']
['1', '14']
['1', '14']
['1', '20']
['1', '20']
['2', '55']
['2', '55']
['8', '43']
['8', '43']
['7', '52']
['7', '52']
['1', '5']
['1', '5']
['3', '37']
['3', '37']
['2', '41']
['2', '41']
['1', '49']
['1', '49']
['2', '105']
['2', '105']
['3', '29']
['3', '29']
['3', '33']
['3', '33']
['1', '5']
['1', '5']
['1', '8']
['1', '8']
['5', '25']
['5', '25']
['1', '4']
['1', '4']
['9', '30']
['9', '30']
['1', '16']
['1', '16']
['11']
['1', '1']
['4', '36']
['4', '36']
['11']
['1', '1']
['1', '3']
['1', '3']
['1', '6']
['1', '6']
['2', '80']
['2', '80']
['1', '78']
['1', '78']
['1', '6']
['1', '6']
['309', '337']
['309', '337']
['4', '22']
['4', '22']
['6', '62']
['6', '62']
['1', '9']
['1', '9']
['1', '5']
['1', '5']
['1', '27']
['1', '27']
['1', '16']
['1', '16']
['2', '20']
['2', '20']
['11']
['1', '1']
['11']
['1', '1']
['11']
['1', '1']
['1', '7']
['1', '7']
['2', '8']
['2', '8']
['1', '13']
['1', '13']
['1', '10']
['1', '10']
['1', '6']
['1', '6']
['1', '11']
['1', '11']
['1', '26']
['1', '26']
['1', '12']
['1', '12']
['12']
['1', '2']
['1', '12']
['1', '12']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['1', '60']
['1', '60']
['1', '4']
['1', '4']
['12']
['1', '2']
['2', '30']
['2', '30']
['1', '20']
['1', '20']
['12']
['1', '2']
['1', '11']
['1', '11']
['12']
['1', '2']
['1', '6']
['1', '6']
['1', '8']
['1', '8']
['12']
['1', '2']
['19', '23']
['19', '23']
['5', '68']
['5', '68']
['2', '112']
['2', '112']
['2', '29']
['2', '29']
['1', '88']
['1', '88']
['1', '8']
['1', '8']
['12']
['1', '2']
['1', '9']
['1', '9']
['1', '3']
['1', '3']
['4', '80']
['4', '80']
['2', '25']
['2', '25']
['12']
['1', '2']
['12']
['1', '2']
['1', '10']
['1', '10']
['1', '33']
['1', '33']
['1', '24']
['1', '24']
['1', '27']
['1', '27']
['1', '49']
['1', '49']
['2', '25']
['2', '25']
['1', '24']
['1', '24']
['1', '4']
['1', '4']
['12']
['1', '2']
['1', '4']
['1', '4']
['1', '14']
['1', '14']
['2', '37']
['2', '37']
['12']
['1', '2']
['12']
['1', '2']
['1', '175']
['1', '175']
['5', '199']
['5', '199']
['1', '36']
['1', '36']
['4', '30']
['4', '30']
['1', '18']
['1', '18']
['12', '64']
['12', '64']
['1', '30']
['1', '30']
['1', '7']
['1', '7']
['1', '50']
['1', '50']
['1', '308']
['1', '308']
['1', '8']
['1', '8']
['1', '4']
['1', '4']
['1', '44']
['1', '44']
['1', '43']
['1', '43']
['12']
['1', '2']
['1', '16']
['1', '16']
['1', '3']
['1', '3']
['2', '66']
['2', '66']
['1', '5']
['1', '5']
['18', '97']
['18', '97']
['1', '10']
['1', '10']
['12', '92']
['12', '92']
['1', '13']
['1', '13']
['11']
['1', '1']
['11']
['1', '1']
['1', '79']
['1', '79']
['1', '5']
['1', '5']
['1', '21']
['1', '21']
['1', '18']
['1', '18']
['1', '3']
['1', '3']
['11']
['1', '1']
['1', '8']
['1', '8']
['1', '21']
['1', '21']
['1', '8']
['1', '8']
['3', '27']
['3', '27']
['1', '10']
['1', '10']
['1', '7']
['1', '7']
['2', '278']
['2', '278']
['2', '15']
['2', '15']
['1', '29']
['1', '29']
LtaP21.2040.mRNA-A
LtaP21.2040.mRNA-B
LtaP33.2260.mRNA-A
LtaP33.2260.mRNA-B
LtaP31.2040.mRNA
LtaP15.1010.mRNA
LtaP36.1760.mRNA-A
LtaP36.1760.mRNA-B
sp|P14544.1|COX1_LEITA-A
sp|P14544.1|COX1_LEITA-B
LtaP36.7290.mRNA-A
LtaP36.7290.mRNA-B
LtaP24.1770.mRNA
LtaP33.1170.mRNA-A
LtaP33.1170.mRNA-B
LtaP29.0960.mRNA
LtaP21.1790.mRNA
AAA31876.1-A
AAA31876.1-B
LtaP23.1700.mRNA
LtaP03.0910.mRNA
LtaP04.0630.mRNA-A
LtaP04.0630.mRNA-B
LtaP05.0500.mRNA
LtaP05.1110.mRNA
LtaP25.1190.mRNA-A
LtaP25.1190.mRNA-B
LtaP09.0030.mRNA-A
LtaP09.0030.mRNA-B
LtaP16.0500.mRNA
LtaP30.2840.mRNA
LtaP34.3980.mRNA
LtaP33.1260.mRNA
LtaP27.2160.mRNA
LtaP05.0800.mRNA
LtaP23.0450.mRNA
AAA31882.1
LtaP25.2210.mRNA
LtaP26.1720.mRNA
LtaP36.0470.mRNA
LtaP25.1690.mRNA
LtaP14.1460.mRNA
LtaP34.1060.mRNA
LtaP12.0690.mRNA
LtaP24.1430.mRNA
LtaP04.1180.mRNA
LtaP08.0840.mRNA
LdBPK_301100.1ReplacementOfLtaP30.1150.mRNA
LtaP32.0010.mRNA
LtaP27.0660.mRNA
AAA31877.1
LtaP22.1610.mRNA
> combine #1 close false name renamedAndRenumberedModel
Renumering chain LtaP21.2040.mRNA-A
['4', '91']
> select #2/Ks
820 atoms, 851 bonds, 91 residues, 1 model selected
0
4
>4
> renumber #2/Ks start 4
91 residues renumbered
> delete #2/Jz:16
> renumber #2/Jz:17-9999999 start 16
7 residues renumbered
> bond #2/Jz:15@C #2/Jz:16@N reasonable false
Created 1 bond
['1', '22']
> select #2/Jz
190 atoms, 195 bonds, 22 residues, 1 model selected
94
95
>1
> renumber #2/Jz start 95
22 residues renumbered
> changechains #2/Jz Ks
Chain IDs of 22 residues changed
['1', '33']
> select #2/I3
341 atoms, 354 bonds, 40 residues, 1 model selected
116
117
>1
> renumber #2/I3 start 117
40 residues renumbered
> changechains #2/I3 Ks
Chain IDs of 40 residues changed
Renumering chain LtaP21.2040.mRNA-B
['3', '12']
> select #2/Ik
123 atoms, 129 bonds, 14 residues, 1 model selected
0
19
>19
> renumber #2/Ik start 19
14 residues renumbered
['1', '84']
> select #2/It
731 atoms, 761 bonds, 84 residues, 1 model selected
32
33
>1
> renumber #2/It start 33
84 residues renumbered
> changechains #2/It Ik
Chain IDs of 84 residues changed
['3', '6']
> select #2/MB
253 atoms, 258 bonds, 29 residues, 1 model selected
116
129
>13
> renumber #2/MB start 129
29 residues renumbered
> changechains #2/MB Ik
Chain IDs of 29 residues changed
Renumering chain LtaP33.2260.mRNA-A
['3', '93']
> select #2/Iy
745 atoms, 757 bonds, 94 residues, 1 model selected
0
22
>22
> renumber #2/Iy start 22
94 residues renumbered
Renumering chain LtaP33.2260.mRNA-B
> delete #2/Le:13
> renumber #2/Le:14-9999999 start 13
30 residues renumbered
> bond #2/Le:12@C #2/Le:13@N reasonable false
Created 1 bond
> renumber #2/Le:11-9999999 start 12
32 residues renumbered
> ~bond #2/Le:10@C #2/Le:12@N
['5', '36']
> select #2/Le
344 atoms, 347 bonds, 1 pseudobond, 42 residues, 2 models selected
0
31
>31
> renumber #2/Le start 31
42 residues renumbered
['1', '38']
> select #2/M0
325 atoms, 329 bonds, 40 residues, 1 model selected
73
76
>3
> renumber #2/M0 start 76
40 residues renumbered
> changechains #2/M0 Le
Chain IDs of 40 residues changed
Renumering chain LtaP31.2040.mRNA
['3', '101']
> select #2/Ix
896 atoms, 930 bonds, 102 residues, 1 model selected
0
152
>152
> renumber #2/Ix start 152
102 residues renumbered
> delete #2/KR:9
> renumber #2/KR:10-9999999 start 9
3 residues renumbered
> bond #2/KR:8@C #2/KR:9@N reasonable false
Created 1 bond
['2', '11']
> select #2/KR
96 atoms, 99 bonds, 11 residues, 1 model selected
253
255
>2
> renumber #2/KR start 255
11 residues renumbered
> changechains #2/KR Ix
Chain IDs of 11 residues changed
['1', '13']
> select #2/Je
97 atoms, 98 bonds, 13 residues, 1 model selected
265
267
>2
> renumber #2/Je start 267
13 residues renumbered
> changechains #2/Je Ix
Chain IDs of 13 residues changed
Renumering chain LtaP15.1010.mRNA
['1', '45']
> select #2/Kp
368 atoms, 376 bonds, 45 residues, 1 model selected
0
53
>53
> renumber #2/Kp start 53
45 residues renumbered
['1', '9']
> select #2/L5
80 atoms, 83 bonds, 9 residues, 1 model selected
97
98
>1
> renumber #2/L5 start 98
9 residues renumbered
> changechains #2/L5 Kp
Chain IDs of 9 residues changed
['1', '1']
> select #2/Bj
12 atoms, 12 bonds, 1 residue, 1 model selected
106
109
>3
> renumber #2/Bj start 109
1 residues renumbered
> changechains #2/Bj Kp
Chain IDs of 1 residues changed
['2', '17']
> select #2/m
155 atoms, 157 bonds, 18 residues, 1 model selected
109
110
>1
> renumber #2/m start 110
18 residues renumbered
> changechains #2/m Kp
Chain IDs of 18 residues changed
['1', '3']
> select #2/6
22 atoms, 21 bonds, 3 residues, 1 model selected
127
128
>1
> renumber #2/6 start 128
3 residues renumbered
> changechains #2/6 Kp
Chain IDs of 3 residues changed
['1', '59']
> select #2/LF
495 atoms, 508 bonds, 60 residues, 1 model selected
130
131
>1
> renumber #2/LF start 131
60 residues renumbered
> changechains #2/LF Kp
Chain IDs of 60 residues changed
['1', '34']
> select #2/Io
250 atoms, 253 bonds, 34 residues, 1 model selected
190
191
>1
> renumber #2/Io start 191
34 residues renumbered
> changechains #2/Io Kp
Chain IDs of 34 residues changed
Renumering chain LtaP36.1760.mRNA-A
['4', '57']
> select #2/Il
502 atoms, 519 bonds, 58 residues, 1 model selected
0
26
>26
> renumber #2/Il start 26
58 residues renumbered
['1', '2']
> select #2/B0
16 atoms, 16 bonds, 2 residues, 1 model selected
83
84
>1
> renumber #2/B0 start 84
2 residues renumbered
> changechains #2/B0 Il
Chain IDs of 2 residues changed
['1', '1']
> select #2/G7
11 atoms, 10 bonds, 1 residue, 1 model selected
85
86
>1
> renumber #2/G7 start 86
1 residues renumbered
> changechains #2/G7 Il
Chain IDs of 1 residues changed
['1', '4']
> select #2/H
33 atoms, 34 bonds, 4 residues, 1 model selected
86
87
>1
> renumber #2/H start 87
4 residues renumbered
> changechains #2/H Il
Chain IDs of 4 residues changed
['4', '10']
> select #2/LJ
119 atoms, 122 bonds, 14 residues, 1 model selected
90
91
>1
> renumber #2/LJ start 91
14 residues renumbered
> changechains #2/LJ Il
Chain IDs of 14 residues changed
Renumering chain LtaP36.1760.mRNA-B
> delete #2/Kf:30
> renumber #2/Kf:31-9999999 start 30
9 residues renumbered
> bond #2/Kf:29@C #2/Kf:30@N reasonable false
Created 1 bond
['1', '38']
> select #2/Kf
341 atoms, 350 bonds, 38 residues, 1 model selected
0
43
>43
> renumber #2/Kf start 43
38 residues renumbered
Renumering chain sp|P14544.1|COX1_LEITA-A
> delete #2/JJ:48
> renumber #2/JJ:49-9999999 start 48
79 residues renumbered
> bond #2/JJ:47@C #2/JJ:48@N reasonable false
Created 1 bond
['1', '126']
> select #2/JJ
1023 atoms, 1055 bonds, 126 residues, 1 model selected
0
1
>1
> renumber #2/JJ start 1
0 residues renumbered
['1', '4']
> select #2/Kq
32 atoms, 35 bonds, 4 residues, 1 model selected
126
127
>1
> renumber #2/Kq start 127
4 residues renumbered
> changechains #2/Kq JJ
Chain IDs of 4 residues changed
['8', '304']
> select #2/JW
2510 atoms, 2588 bonds, 305 residues, 1 model selected
130
131
>1
> renumber #2/JW start 131
305 residues renumbered
> changechains #2/JW JJ
Chain IDs of 305 residues changed
['7', '17']
> select #2/j
383 atoms, 398 bonds, 44 residues, 1 model selected
435
436
>1
> renumber #2/j start 436
44 residues renumbered
> changechains #2/j JJ
Chain IDs of 44 residues changed
['1', '68']
> select #2/JX
638 atoms, 667 bonds, 69 residues, 1 model selected
479
481
>2
> renumber #2/JX start 481
69 residues renumbered
> changechains #2/JX JJ
Chain IDs of 69 residues changed
Renumering chain sp|P14544.1|COX1_LEITA-B
['3', '92']
> select #2/LQ
737 atoms, 758 bonds, 92 residues, 1 model selected
0
4
>4
> renumber #2/LQ start 4
92 residues renumbered
['1', '25']
> select #2/O
221 atoms, 230 bonds, 27 residues, 1 model selected
95
97
>2
> renumber #2/O start 97
27 residues renumbered
> changechains #2/O LQ
Chain IDs of 27 residues changed
['1', '47']
> select #2/J3
386 atoms, 395 bonds, 47 residues, 1 model selected
123
129
>6
> renumber #2/J3 start 129
47 residues renumbered
> changechains #2/J3 LQ
Chain IDs of 47 residues changed
Renumering chain LtaP36.7290.mRNA-A
> delete #2/Mr:38
> renumber #2/Mr:39-9999999 start 38
17 residues renumbered
> bond #2/Mr:37@C #2/Mr:38@N reasonable false
Created 1 bond
['3', '52']
> select #2/Mr
435 atoms, 447 bonds, 54 residues, 1 model selected
0
38
>38
> renumber #2/Mr start 38
54 residues renumbered
['1', '11']
> select #2/NX
86 atoms, 87 bonds, 11 residues, 1 model selected
91
92
>1
> renumber #2/NX start 92
11 residues renumbered
> changechains #2/NX Mr
Chain IDs of 11 residues changed
> renumber #2/Lt:8-9999999 start 9
36 residues renumbered
> ~bond #2/Lt:7@C #2/Lt:9@N
['7', '42']
> select #2/Lt
335 atoms, 343 bonds, 1 pseudobond, 43 residues, 2 models selected
102
104
>2
> renumber #2/Lt start 104
43 residues renumbered
> changechains #2/Lt Mr
Chain IDs of 43 residues changed
Renumering chain LtaP36.7290.mRNA-B
['2', '11']
> select #2/MV
84 atoms, 86 bonds, 11 residues, 1 model selected
0
120
>120
> renumber #2/MV start 120
11 residues renumbered
Renumering chain LtaP24.1770.mRNA
['1', '7']
> select #2/K5
63 atoms, 63 bonds, 7 residues, 1 model selected
0
14
>14
> renumber #2/K5 start 14
7 residues renumbered
['1', '8']
> select #2/If
61 atoms, 61 bonds, 8 residues, 1 model selected
20
21
>1
> renumber #2/If start 21
8 residues renumbered
> changechains #2/If K5
Chain IDs of 8 residues changed
['1', '3']
> select #2/KY
14 atoms, 13 bonds, 3 residues, 1 model selected
28
29
>1
> renumber #2/KY start 29
3 residues renumbered
> changechains #2/KY K5
Chain IDs of 3 residues changed
['1', '20']
> select #2/I8
145 atoms, 146 bonds, 21 residues, 1 model selected
31
32
>1
> renumber #2/I8 start 32
21 residues renumbered
> changechains #2/I8 K5
Chain IDs of 21 residues changed
['1', '16']
> select #2/I9
119 atoms, 122 bonds, 16 residues, 1 model selected
52
53
>1
> renumber #2/I9 start 53
16 residues renumbered
> changechains #2/I9 K5
Chain IDs of 16 residues changed
['1', '26']
> select #2/LC
202 atoms, 206 bonds, 26 residues, 1 model selected
68
69
>1
> renumber #2/LC start 69
26 residues renumbered
> changechains #2/LC K5
Chain IDs of 26 residues changed
['4', '35']
> select #2/KN
284 atoms, 290 bonds, 35 residues, 1 model selected
94
95
>1
> renumber #2/KN start 95
35 residues renumbered
> changechains #2/KN K5
Chain IDs of 35 residues changed
['1', '4']
> select #2/CD
38 atoms, 37 bonds, 4 residues, 1 model selected
129
130
>1
> renumber #2/CD start 130
4 residues renumbered
> changechains #2/CD K5
Chain IDs of 4 residues changed
['1', '1']
> select #2/Bd
7 atoms, 6 bonds, 1 residue, 1 model selected
133
134
>1
> renumber #2/Bd start 134
1 residues renumbered
> changechains #2/Bd K5
Chain IDs of 1 residues changed
['1', '2']
> select #2/GL
16 atoms, 16 bonds, 2 residues, 1 model selected
134
135
>1
> renumber #2/GL start 135
2 residues renumbered
> changechains #2/GL K5
Chain IDs of 2 residues changed
['1', '3']
> select #2/C1
24 atoms, 25 bonds, 3 residues, 1 model selected
136
136
>0
> delete #2/C1:1
> renumber #2/C1 start 137
2 residues renumbered
> changechains #2/C1 K5
Chain IDs of 2 residues changed
['1', '2']
> select #2/CR
15 atoms, 14 bonds, 2 residues, 1 model selected
138
143
>5
> renumber #2/CR start 143
2 residues renumbered
> changechains #2/CR K5
Chain IDs of 2 residues changed
['1', '1']
> select #2/FE
12 atoms, 12 bonds, 1 residue, 1 model selected
144
145
>1
> renumber #2/FE start 145
1 residues renumbered
> changechains #2/FE K5
Chain IDs of 1 residues changed
['4', '59']
> select #2/LL
472 atoms, 481 bonds, 59 residues, 1 model selected
145
147
>2
> renumber #2/LL start 147
59 residues renumbered
> changechains #2/LL K5
Chain IDs of 59 residues changed
['1', '17']
> select #2/MQ
128 atoms, 129 bonds, 17 residues, 1 model selected
205
206
>1
> renumber #2/MQ start 206
17 residues renumbered
> changechains #2/MQ K5
Chain IDs of 17 residues changed
['1', '11']
> select #2/KL
81 atoms, 83 bonds, 11 residues, 1 model selected
222
223
>1
> renumber #2/KL start 223
11 residues renumbered
> changechains #2/KL K5
Chain IDs of 11 residues changed
['1', '6']
> select #2/KA
37 atoms, 36 bonds, 6 residues, 1 model selected
233
234
>1
> renumber #2/KA start 234
6 residues renumbered
> changechains #2/KA K5
Chain IDs of 6 residues changed
['1', '8']
> select #2/JK
57 atoms, 57 bonds, 8 residues, 1 model selected
239
240
>1
> renumber #2/JK start 240
8 residues renumbered
> changechains #2/JK K5
Chain IDs of 8 residues changed
['1', '2']
> select #2/Ae
12 atoms, 11 bonds, 2 residues, 1 model selected
247
249
>2
> renumber #2/Ae start 249
2 residues renumbered
> changechains #2/Ae K5
Chain IDs of 2 residues changed
['1', '5']
> select #2/h
47 atoms, 48 bonds, 5 residues, 1 model selected
250
252
>2
> renumber #2/h start 252
5 residues renumbered
> changechains #2/h K5
Chain IDs of 5 residues changed
['1', '5']
> select #2/Nq
49 atoms, 49 bonds, 5 residues, 1 model selected
256
258
>2
> renumber #2/Nq start 258
5 residues renumbered
> changechains #2/Nq K5
Chain IDs of 5 residues changed
['1', '5']
> select #2/Mb
37 atoms, 36 bonds, 5 residues, 1 model selected
262
264
>2
> renumber #2/Mb start 264
5 residues renumbered
> changechains #2/Mb K5
Chain IDs of 5 residues changed
['1', '3']
> select #2/NC
17 atoms, 16 bonds, 3 residues, 1 model selected
268
299
>31
> renumber #2/NC start 299
3 residues renumbered
> changechains #2/NC K5
Chain IDs of 3 residues changed
['1', '10']
> select #2/NG
75 atoms, 74 bonds, 10 residues, 1 model selected
301
302
>1
> renumber #2/NG start 302
10 residues renumbered
> changechains #2/NG K5
Chain IDs of 10 residues changed
['1', '17']
> select #2/KS
139 atoms, 141 bonds, 17 residues, 1 model selected
311
338
>27
> renumber #2/KS start 338
17 residues renumbered
> changechains #2/KS K5
Chain IDs of 17 residues changed
['1', '3']
> select #2/C2
18 atoms, 17 bonds, 3 residues, 1 model selected
354
361
>7
> renumber #2/C2 start 361
3 residues renumbered
> changechains #2/C2 K5
Chain IDs of 3 residues changed
['1', '18']
> select #2/NA
128 atoms, 131 bonds, 18 residues, 1 model selected
363
366
>3
> renumber #2/NA start 366
18 residues renumbered
> changechains #2/NA K5
Chain IDs of 18 residues changed
> delete #2/JV:6
> renumber #2/JV:7-9999999 start 6
10 residues renumbered
> bond #2/JV:5@C #2/JV:6@N reasonable false
Created 1 bond
> renumber #2/JV:2-9999999 start 3
14 residues renumbered
> ~bond #2/JV:1@C #2/JV:3@N
> renumber #2/JV:1-9999999 start 2
15 residues renumbered
> ~bond #2/JV:0@C #2/JV:2@N
['1', '12']
> select #2/JV
105 atoms, 108 bonds, 1 pseudobond, 15 residues, 2 models selected
383
382
>-1
> delete #2/JV:2
> delete #2/JV:1
> renumber #2/JV start 384
14 residues renumbered
> changechains #2/JV K5
Chain IDs of 14 residues changed
['1', '3']
> select #2/g
15 atoms, 14 bonds, 3 residues, 1 model selected
398
401
>3
> renumber #2/g start 401
3 residues renumbered
> changechains #2/g K5
Chain IDs of 3 residues changed
['1', '9']
> select #2/NJ
68 atoms, 70 bonds, 9 residues, 1 model selected
403
405
>2
> renumber #2/NJ start 405
9 residues renumbered
> changechains #2/NJ K5
Chain IDs of 9 residues changed
['3', '33']
> select #2/JY
257 atoms, 261 bonds, 33 residues, 1 model selected
413
414
>1
> renumber #2/JY start 414
33 residues renumbered
> changechains #2/JY K5
Chain IDs of 33 residues changed
['1', '16']
> select #2/J7
136 atoms, 137 bonds, 16 residues, 1 model selected
446
448
>2
> renumber #2/J7 start 448
16 residues renumbered
> changechains #2/J7 K5
Chain IDs of 16 residues changed
['1', '20']
> select #2/L0
161 atoms, 163 bonds, 20 residues, 1 model selected
463
465
>2
> renumber #2/L0 start 465
20 residues renumbered
> changechains #2/L0 K5
Chain IDs of 20 residues changed
['1', '5']
> select #2/Kz
37 atoms, 36 bonds, 5 residues, 1 model selected
484
490
>6
> renumber #2/Kz start 490
5 residues renumbered
> changechains #2/Kz K5
Chain IDs of 5 residues changed
['1', '1']
> select #2/Bc
9 atoms, 8 bonds, 1 residue, 1 model selected
494
495
>1
> renumber #2/Bc start 495
1 residues renumbered
> changechains #2/Bc K5
Chain IDs of 1 residues changed
['1', '1']
> select #2/EP
5 atoms, 4 bonds, 1 residue, 1 model selected
495
496
>1
> renumber #2/EP start 496
1 residues renumbered
> changechains #2/EP K5
Chain IDs of 1 residues changed
['1', '1']
> select #2/B9
8 atoms, 7 bonds, 1 residue, 1 model selected
496
497
>1
> renumber #2/B9 start 497
1 residues renumbered
> changechains #2/B9 K5
Chain IDs of 1 residues changed
['1', '1']
> select #2/IA
9 atoms, 8 bonds, 1 residue, 1 model selected
497
498
>1
> renumber #2/IA start 498
1 residues renumbered
> changechains #2/IA K5
Chain IDs of 1 residues changed
['1', '11']
> select #2/Jf
105 atoms, 106 bonds, 11 residues, 1 model selected
498
499
>1
> renumber #2/Jf start 499
11 residues renumbered
> changechains #2/Jf K5
Chain IDs of 11 residues changed
['4', '24']
> select #2/MU
268 atoms, 274 bonds, 34 residues, 1 model selected
509
513
>4
> renumber #2/MU start 513
34 residues renumbered
> changechains #2/MU K5
Chain IDs of 34 residues changed
['1', '13']
> select #2/Nn
114 atoms, 116 bonds, 13 residues, 1 model selected
546
567
>21
> renumber #2/Nn start 567
13 residues renumbered
> changechains #2/Nn K5
Chain IDs of 13 residues changed
['1', '2']
> select #2/CQ
14 atoms, 13 bonds, 2 residues, 1 model selected
579
580
>1
> renumber #2/CQ start 580
2 residues renumbered
> changechains #2/CQ K5
Chain IDs of 2 residues changed
['1', '4']
> select #2/AS
35 atoms, 35 bonds, 4 residues, 1 model selected
581
582
>1
> renumber #2/AS start 582
4 residues renumbered
> changechains #2/AS K5
Chain IDs of 4 residues changed
['1', '6']
> select #2/Mm
49 atoms, 49 bonds, 6 residues, 1 model selected
585
585
>0
> delete #2/Mm:1
> renumber #2/Mm start 586
5 residues renumbered
> changechains #2/Mm K5
Chain IDs of 5 residues changed
['1', '12']
> select #2/Jb
90 atoms, 92 bonds, 12 residues, 1 model selected
590
591
>1
> renumber #2/Jb start 591
12 residues renumbered
> changechains #2/Jb K5
Chain IDs of 12 residues changed
Renumering chain LtaP33.1170.mRNA-A
['2', '46']
> select #2/I0
383 atoms, 398 bonds, 46 residues, 1 model selected
0
160
>160
> renumber #2/I0 start 160
46 residues renumbered
['1', '25']
> select #2/JD
230 atoms, 240 bonds, 26 residues, 1 model selected
205
206
>1
> renumber #2/JD start 206
26 residues renumbered
> changechains #2/JD I0
Chain IDs of 26 residues changed
['1', '64']
> select #2/JE
547 atoms, 565 bonds, 65 residues, 1 model selected
231
231
>0
> delete #2/JE:1
> renumber #2/JE start 232
64 residues renumbered
> changechains #2/JE I0
Chain IDs of 64 residues changed
['9', '13']
> select #2/JF
191 atoms, 195 bonds, 22 residues, 1 model selected
295
296
>1
> renumber #2/JF start 296
22 residues renumbered
> changechains #2/JF I0
Chain IDs of 22 residues changed
['1', '43']
> select #2/Im
545 atoms, 555 bonds, 65 residues, 1 model selected
317
319
>2
> renumber #2/Im start 319
65 residues renumbered
> changechains #2/Im I0
Chain IDs of 65 residues changed
Renumering chain LtaP33.1170.mRNA-B
['25', '72']
> select #2/KM
613 atoms, 630 bonds, 72 residues, 1 model selected
0
244
>244
> renumber #2/KM start 244
72 residues renumbered
Renumering chain LtaP29.0960.mRNA
['1', '6']
> select #2/JI
43 atoms, 44 bonds, 6 residues, 1 model selected
0
11
>11
> renumber #2/JI start 11
6 residues renumbered
> delete #2/KQ:19
> renumber #2/KQ:20-9999999 start 19
22 residues renumbered
> bond #2/KQ:18@C #2/KQ:19@N reasonable false
Created 1 bond
['4', '40']
> select #2/KQ
309 atoms, 311 bonds, 40 residues, 1 model selected
16
17
>1
> renumber #2/KQ start 17
40 residues renumbered
> changechains #2/KQ JI
Chain IDs of 40 residues changed
['1', '159']
> select #2/Lc
1296 atoms, 1320 bonds, 159 residues, 1 model selected
56
58
>2
> renumber #2/Lc start 58
159 residues renumbered
> changechains #2/Lc JI
Chain IDs of 159 residues changed
> delete #2/Jg:12
> delete #2/Jg:21
> renumber #2/Jg:13-9999999 start 12
11 residues renumbered
> bond #2/Jg:11@C #2/Jg:12@N reasonable false
Created 1 bond
> renumber #2/Jg:21-9999999 start 20
3 residues renumbered
> bond #2/Jg:19@C #2/Jg:20@N reasonable false
Created 1 bond
['1', '22']
> select #2/Jg
149 atoms, 152 bonds, 22 residues, 1 model selected
216
220
>4
> renumber #2/Jg start 220
22 residues renumbered
> changechains #2/Jg JI
Chain IDs of 22 residues changed
['1', '2']
> select #2/C0
18 atoms, 17 bonds, 2 residues, 1 model selected
241
242
>1
> renumber #2/C0 start 242
2 residues renumbered
> changechains #2/C0 JI
Chain IDs of 2 residues changed
['1', '1']
> select #2/DL
5 atoms, 4 bonds, 1 residue, 1 model selected
243
244
>1
> renumber #2/DL start 244
1 residues renumbered
> changechains #2/DL JI
Chain IDs of 1 residues changed
['1', '1']
> select #2/Bu
7 atoms, 6 bonds, 1 residue, 1 model selected
244
245
>1
> renumber #2/Bu start 245
1 residues renumbered
> changechains #2/Bu JI
Chain IDs of 1 residues changed
['1', '1']
> select #2/CH
9 atoms, 8 bonds, 1 residue, 1 model selected
245
246
>1
> renumber #2/CH start 246
1 residues renumbered
> changechains #2/CH JI
Chain IDs of 1 residues changed
['1', '6']
> select #2/J8
53 atoms, 53 bonds, 6 residues, 1 model selected
246
247
>1
> renumber #2/J8 start 247
6 residues renumbered
> changechains #2/J8 JI
Chain IDs of 6 residues changed
> delete #2/KE:18
> renumber #2/KE:19-9999999 start 18
6 residues renumbered
> bond #2/KE:17@C #2/KE:18@N reasonable false
Created 1 bond
['1', '23']
> select #2/KE
187 atoms, 189 bonds, 23 residues, 1 model selected
252
259
>7
> renumber #2/KE start 259
23 residues renumbered
> changechains #2/KE JI
Chain IDs of 23 residues changed
['1', '6']
> select #2/Kc
48 atoms, 50 bonds, 6 residues, 1 model selected
281
282
>1
> renumber #2/Kc start 282
6 residues renumbered
> changechains #2/Kc JI
Chain IDs of 6 residues changed
['1', '1']
> select #2/FU
12 atoms, 12 bonds, 1 residue, 1 model selected
287
288
>1
> renumber #2/FU start 288
1 residues renumbered
> changechains #2/FU JI
Chain IDs of 1 residues changed
['1', '1']
> select #2/Ay
7 atoms, 7 bonds, 1 residue, 1 model selected
288
289
>1
> renumber #2/Ay start 289
1 residues renumbered
> changechains #2/Ay JI
Chain IDs of 1 residues changed
['1', '1']
> select #2/Cu
9 atoms, 8 bonds, 1 residue, 1 model selected
289
290
>1
> renumber #2/Cu start 290
1 residues renumbered
> changechains #2/Cu JI
Chain IDs of 1 residues changed
['1', '19']
> select #2/Jv
165 atoms, 166 bonds, 20 residues, 1 model selected
290
291
>1
> renumber #2/Jv start 291
20 residues renumbered
> changechains #2/Jv JI
Chain IDs of 20 residues changed
['1', '21']
> select #2/Mu
178 atoms, 179 bonds, 21 residues, 1 model selected
310
312
>2
> renumber #2/Mu start 312
21 residues renumbered
> changechains #2/Mu JI
Chain IDs of 21 residues changed
['2', '12']
> select #2/N
106 atoms, 105 bonds, 13 residues, 1 model selected
332
333
>1
> renumber #2/N start 333
13 residues renumbered
> changechains #2/N JI
Chain IDs of 13 residues changed
['1', '12']
> select #2/MH
102 atoms, 104 bonds, 12 residues, 1 model selected
345
349
>4
> renumber #2/MH start 349
12 residues renumbered
> changechains #2/MH JI
Chain IDs of 12 residues changed
['1', '128']
> select #2/Lj
1029 atoms, 1045 bonds, 129 residues, 1 model selected
360
363
>3
> renumber #2/Lj start 363
129 residues renumbered
> changechains #2/Lj JI
Chain IDs of 129 residues changed
Renumering chain LtaP21.1790.mRNA
> delete #2/Lr:29
> renumber #2/Lr:30-9999999 start 29
15 residues renumbered
> bond #2/Lr:28@C #2/Lr:29@N reasonable false
Created 1 bond
['1', '43']
> select #2/Lr
378 atoms, 386 bonds, 43 residues, 1 model selected
0
1
>1
> renumber #2/Lr start 1
0 residues renumbered
['1', '48']
> select #2/KB
415 atoms, 426 bonds, 51 residues, 1 model selected
43
79
>36
> renumber #2/KB start 79
51 residues renumbered
> changechains #2/KB Lr
Chain IDs of 51 residues changed
['2', '32']
> select #2/MJ
301 atoms, 311 bonds, 34 residues, 1 model selected
129
136
>7
> renumber #2/MJ start 136
34 residues renumbered
> changechains #2/MJ Lr
Chain IDs of 34 residues changed
['1', '13']
> select #2/KZ
100 atoms, 103 bonds, 13 residues, 1 model selected
169
167
>-2
> delete #2/KZ:3
> delete #2/KZ:2
> delete #2/KZ:1
> renumber #2/KZ start 170
10 residues renumbered
> changechains #2/KZ Lr
Chain IDs of 10 residues changed
['1', '14']
> select #2/JT
123 atoms, 129 bonds, 14 residues, 1 model selected
179
179
>0
> delete #2/JT:1
> renumber #2/JT start 180
13 residues renumbered
> changechains #2/JT Lr
Chain IDs of 13 residues changed
['1', '6']
> select #2/Ju
42 atoms, 41 bonds, 6 residues, 1 model selected
192
193
>1
> renumber #2/Ju start 193
6 residues renumbered
> changechains #2/Ju Lr
Chain IDs of 6 residues changed
['1', '4']
> select #2/JO
34 atoms, 34 bonds, 4 residues, 1 model selected
198
198
>0
> delete #2/JO:1
> renumber #2/JO start 199
3 residues renumbered
> changechains #2/JO Lr
Chain IDs of 3 residues changed
['1', '3']
> select #2/A7
29 atoms, 29 bonds, 3 residues, 1 model selected
201
202
>1
> renumber #2/A7 start 202
3 residues renumbered
> changechains #2/A7 Lr
Chain IDs of 3 residues changed
['1', '1']
> select #2/BK
9 atoms, 8 bonds, 1 residue, 1 model selected
204
206
>2
> renumber #2/BK start 206
1 residues renumbered
> changechains #2/BK Lr
Chain IDs of 1 residues changed
['1', '1']
> select #2/Bz
11 atoms, 11 bonds, 1 residue, 1 model selected
206
207
>1
> renumber #2/Bz start 207
1 residues renumbered
> changechains #2/Bz Lr
Chain IDs of 1 residues changed
['4', '21']
> select #2/NP
190 atoms, 195 bonds, 21 residues, 1 model selected
207
208
>1
> renumber #2/NP start 208
21 residues renumbered
> changechains #2/NP Lr
Chain IDs of 21 residues changed
> delete #2/NB:29
> renumber #2/NB:30-9999999 start 29
17 residues renumbered
> bond #2/NB:28@C #2/NB:29@N reasonable false
Created 1 bond
['1', '45']
> select #2/NB
394 atoms, 404 bonds, 45 residues, 1 model selected
228
230
>2
> renumber #2/NB start 230
45 residues renumbered
> changechains #2/NB Lr
Chain IDs of 45 residues changed
['4', '24']
> select #2/JS
216 atoms, 219 bonds, 26 residues, 1 model selected
274
277
>3
> renumber #2/JS start 277
26 residues renumbered
> changechains #2/JS Lr
Chain IDs of 26 residues changed
['1', '3']
> select #2/Ce
25 atoms, 24 bonds, 3 residues, 1 model selected
302
303
>1
> renumber #2/Ce start 303
3 residues renumbered
> changechains #2/Ce Lr
Chain IDs of 3 residues changed
['2', '16']
> select #2/Lx
147 atoms, 149 bonds, 18 residues, 1 model selected
305
308
>3
> renumber #2/Lx start 308
18 residues renumbered
> changechains #2/Lx Lr
Chain IDs of 18 residues changed
['1', '4']
> select #2/T
36 atoms, 38 bonds, 4 residues, 1 model selected
325
326
>1
> renumber #2/T start 326
4 residues renumbered
> changechains #2/T Lr
Chain IDs of 4 residues changed
> delete #2/JQ:12
> renumber #2/JQ:13-9999999 start 12
37 residues renumbered
> bond #2/JQ:11@C #2/JQ:12@N reasonable false
Created 1 bond
['1', '48']
> select #2/JQ
401 atoms, 406 bonds, 48 residues, 1 model selected
329
330
>1
> renumber #2/JQ start 330
48 residues renumbered
> changechains #2/JQ Lr
Chain IDs of 48 residues changed
['1', '1']
> select #2/Bq
11 atoms, 10 bonds, 1 residue, 1 model selected
377
378
>1
> renumber #2/Bq start 378
1 residues renumbered
> changechains #2/Bq Lr
Chain IDs of 1 residues changed
['1', '1']
> select #2/EI
9 atoms, 8 bonds, 1 residue, 1 model selected
378
379
>1
> renumber #2/EI start 379
1 residues renumbered
> changechains #2/EI Lr
Chain IDs of 1 residues changed
['1', '6']
> select #2/KH
50 atoms, 49 bonds, 6 residues, 1 model selected
379
380
>1
> renumber #2/KH start 380
6 residues renumbered
> changechains #2/KH Lr
Chain IDs of 6 residues changed
Renumering chain AAA31876.1-A
['2', '92']
> select #2/Y
778 atoms, 803 bonds, 93 residues, 1 model selected
0
1
>1
> renumber #2/Y start 1
0 residues renumbered
['1', '3']
> select #2/Ja
24 atoms, 23 bonds, 3 residues, 1 model selected
93
94
>1
> renumber #2/Ja start 94
3 residues renumbered
> changechains #2/Ja Y
Chain IDs of 3 residues changed
['1', '5']
> select #2/D
38 atoms, 38 bonds, 5 residues, 1 model selected
96
97
>1
> renumber #2/D start 97
5 residues renumbered
> changechains #2/D Y
Chain IDs of 5 residues changed
['1', '1']
> select #2/H8
14 atoms, 15 bonds, 1 residue, 1 model selected
101
102
>1
> renumber #2/H8 start 102
1 residues renumbered
> changechains #2/H8 Y
Chain IDs of 1 residues changed
> delete #2/Ir:53
> renumber #2/Ir:54-9999999 start 53
56 residues renumbered
> bond #2/Ir:52@C #2/Ir:53@N reasonable false
Created 1 bond
['1', '107']
> select #2/Ir
860 atoms, 879 bonds, 108 residues, 1 model selected
102
103
>1
> renumber #2/Ir start 103
108 residues renumbered
> changechains #2/Ir Y
Chain IDs of 108 residues changed
Renumering chain AAA31876.1-B
['2', '40']
> select #2/JC
331 atoms, 338 bonds, 41 residues, 1 model selected
0
2
>2
> renumber #2/JC start 2
41 residues renumbered
['1', '3', '1', '6']
> select #2/Iv
435 atoms, 443 bonds, 56 residues, 1 model selected
42
29
>-13
> delete #2/Iv:14
> delete #2/Iv:13
> delete #2/Iv:12
> delete #2/Iv:11
> delete #2/Iv:10
> delete #2/Iv:9
> delete #2/Iv:8
> delete #2/Iv:7
> delete #2/Iv:6
> delete #2/Iv:5
> delete #2/Iv:4
> delete #2/Iv:3
> delete #2/Iv:2
> delete #2/Iv:1
> renumber #2/Iv start 43
42 residues renumbered
> changechains #2/Iv JC
Chain IDs of 42 residues changed
['1', '50']
> select #2/M3
421 atoms, 434 bonds, 50 residues, 1 model selected
84
44
>-40
> delete #2/M3:41
> delete #2/M3:40
> delete #2/M3:39
> delete #2/M3:38
> delete #2/M3:37
> delete #2/M3:36
> delete #2/M3:35
> delete #2/M3:34
> delete #2/M3:33
> delete #2/M3:32
> delete #2/M3:31
> delete #2/M3:30
> delete #2/M3:29
> delete #2/M3:28
> delete #2/M3:27
> delete #2/M3:26
> delete #2/M3:25
> delete #2/M3:24
> delete #2/M3:23
> delete #2/M3:22
> delete #2/M3:21
> delete #2/M3:20
> delete #2/M3:19
> delete #2/M3:18
> delete #2/M3:17
> delete #2/M3:16
> delete #2/M3:15
> delete #2/M3:14
> delete #2/M3:13
> delete #2/M3:12
> delete #2/M3:11
> delete #2/M3:10
> delete #2/M3:9
> delete #2/M3:8
> delete #2/M3:7
> delete #2/M3:6
> delete #2/M3:5
> delete #2/M3:4
> delete #2/M3:3
> delete #2/M3:2
> delete #2/M3:1
> renumber #2/M3 start 85
9 residues renumbered
> changechains #2/M3 JC
Chain IDs of 9 residues changed
['1', '12']
> select #2/JP
160 atoms, 167 bonds, 18 residues, 1 model selected
93
103
>10
> renumber #2/JP start 103
18 residues renumbered
> changechains #2/JP JC
Chain IDs of 18 residues changed
Renumering chain LtaP23.1700.mRNA
['3', '14']
> select #2/NF
128 atoms, 130 bonds, 15 residues, 1 model selected
0
30
>30
> renumber #2/NF start 30
15 residues renumbered
['1', '7']
> select #2/Id
67 atoms, 69 bonds, 7 residues, 1 model selected
44
46
>2
> renumber #2/Id start 46
7 residues renumbered
> changechains #2/Id NF
Chain IDs of 7 residues changed
['1', '4']
> select #2/Nd
34 atoms, 33 bonds, 4 residues, 1 model selected
52
53
>1
> renumber #2/Nd start 53
4 residues renumbered
> changechains #2/Nd NF
Chain IDs of 4 residues changed
['1', '14']
> select #2/Lz
106 atoms, 105 bonds, 14 residues, 1 model selected
56
56
>0
> delete #2/Lz:1
> renumber #2/Lz start 57
13 residues renumbered
> changechains #2/Lz NF
Chain IDs of 13 residues changed
['1', '20']
> select #2/LU
165 atoms, 168 bonds, 20 residues, 1 model selected
69
66
>-3
> delete #2/LU:4
> delete #2/LU:3
> delete #2/LU:2
> delete #2/LU:1
> renumber #2/LU start 70
16 residues renumbered
> changechains #2/LU NF
Chain IDs of 16 residues changed
['2', '55']
> select #2/NQ
454 atoms, 469 bonds, 55 residues, 1 model selected
85
85
>0
> delete #2/NQ:1
> renumber #2/NQ start 86
54 residues renumbered
> changechains #2/NQ NF
Chain IDs of 54 residues changed
['8', '43']
> select #2/JB
372 atoms, 374 bonds, 45 residues, 1 model selected
139
139
>0
> delete #2/JB:1
> renumber #2/JB start 140
44 residues renumbered
> changechains #2/JB NF
Chain IDs of 44 residues changed
['7', '52']
> select #2/Ic
458 atoms, 461 bonds, 58 residues, 1 model selected
183
189
>6
> renumber #2/Ic start 189
58 residues renumbered
> changechains #2/Ic NF
Chain IDs of 58 residues changed
Renumering chain LtaP03.0910.mRNA
['1', '5']
> select #2/Mx
52 atoms, 54 bonds, 5 residues, 1 model selected
0
2
>2
> renumber #2/Mx start 2
5 residues renumbered
['3', '37']
> select #2/JU
309 atoms, 317 bonds, 37 residues, 1 model selected
6
7
>1
> renumber #2/JU start 7
37 residues renumbered
> changechains #2/JU Mx
Chain IDs of 37 residues changed
Renumering chain LtaP04.0630.mRNA-A
['2', '41']
> select #2/J6
320 atoms, 330 bonds, 41 residues, 1 model selected
0
2
>2
> renumber #2/J6 start 2
41 residues renumbered
['1', '49']
> select #2/Kj
424 atoms, 433 bonds, 50 residues, 1 model selected
42
44
>2
> renumber #2/Kj start 44
50 residues renumbered
> changechains #2/Kj J6
Chain IDs of 50 residues changed
['2', '105']
> select #2/Ip
893 atoms, 917 bonds, 105 residues, 1 model selected
93
95
>2
> renumber #2/Ip start 95
105 residues renumbered
> changechains #2/Ip J6
Chain IDs of 105 residues changed
Renumering chain LtaP04.0630.mRNA-B
['3', '29']
> select #2/KW
289 atoms, 295 bonds, 35 residues, 1 model selected
0
118
>118
> renumber #2/KW start 118
35 residues renumbered
['3', '33']
> select #2/I6
315 atoms, 327 bonds, 36 residues, 1 model selected
152
159
>7
> renumber #2/I6 start 159
36 residues renumbered
> changechains #2/I6 KW
Chain IDs of 36 residues changed
Renumering chain LtaP05.0500.mRNA
['1', '5']
> select #2/CS
32 atoms, 32 bonds, 5 residues, 1 model selected
0
25
>25
> renumber #2/CS start 25
5 residues renumbered
['1', '8']
> select #2/L8
73 atoms, 74 bonds, 8 residues, 1 model selected
29
30
>1
> renumber #2/L8 start 30
8 residues renumbered
> changechains #2/L8 CS
Chain IDs of 8 residues changed
['5', '25']
> select #2/d
292 atoms, 300 bonds, 31 residues, 1 model selected
37
45
>8
> renumber #2/d start 45
31 residues renumbered
> changechains #2/d CS
Chain IDs of 31 residues changed
['1', '4']
> select #2/Km
28 atoms, 27 bonds, 4 residues, 1 model selected
75
76
>1
> renumber #2/Km start 76
4 residues renumbered
> changechains #2/Km CS
Chain IDs of 4 residues changed
['9', '30']
> select #2/LK
336 atoms, 342 bonds, 41 residues, 1 model selected
79
80
>1
> renumber #2/LK start 80
41 residues renumbered
> changechains #2/LK CS
Chain IDs of 41 residues changed
Renumering chain LtaP05.1110.mRNA
['1', '16']
> select #2/NM
131 atoms, 133 bonds, 16 residues, 1 model selected
0
82
>82
> renumber #2/NM start 82
16 residues renumbered
['1', '1']
> select #2/Fk
4 atoms, 3 bonds, 1 residue, 1 model selected
97
98
>1
> renumber #2/Fk start 98
1 residues renumbered
> changechains #2/Fk NM
Chain IDs of 1 residues changed
['4', '36']
> select #2/JM
298 atoms, 307 bonds, 36 residues, 1 model selected
98
99
>1
> renumber #2/JM start 99
36 residues renumbered
> changechains #2/JM NM
Chain IDs of 36 residues changed
['1', '1']
> select #2/AV
9 atoms, 8 bonds, 1 residue, 1 model selected
134
135
>1
> renumber #2/AV start 135
1 residues renumbered
> changechains #2/AV NM
Chain IDs of 1 residues changed
['1', '3']
> select #2/K2
27 atoms, 27 bonds, 3 residues, 1 model selected
135
136
>1
> renumber #2/K2 start 136
3 residues renumbered
> changechains #2/K2 NM
Chain IDs of 3 residues changed
['1', '6']
> select #2/Jh
49 atoms, 50 bonds, 6 residues, 1 model selected
138
139
>1
> renumber #2/Jh start 139
6 residues renumbered
> changechains #2/Jh NM
Chain IDs of 6 residues changed
Renumering chain LtaP25.1190.mRNA-A
['2', '80']
> select #2/LY
677 atoms, 700 bonds, 80 residues, 1 model selected
0
182
>182
> renumber #2/LY start 182
80 residues renumbered
> delete #2/Ld:63
> renumber #2/Ld:64-9999999 start 63
16 residues renumbered
> bond #2/Ld:62@C #2/Ld:63@N reasonable false
Created 1 bond
['1', '77']
> select #2/Ld
648 atoms, 672 bonds, 78 residues, 1 model selected
261
262
>1
> renumber #2/Ld start 262
78 residues renumbered
> changechains #2/Ld LY
Chain IDs of 78 residues changed
['1', '6']
> select #2/b
50 atoms, 51 bonds, 6 residues, 1 model selected
339
340
>1
> renumber #2/b start 340
6 residues renumbered
> changechains #2/b LY
Chain IDs of 6 residues changed
Renumering chain LtaP25.1190.mRNA-B
['309', '337']
> select #2/LW
2870 atoms, 2963 bonds, 344 residues, 1 model selected
0
-51
>-51
> delete #2/LW:52
> delete #2/LW:51
> delete #2/LW:50
> delete #2/LW:49
> delete #2/LW:48
> delete #2/LW:47
> delete #2/LW:46
> delete #2/LW:45
> delete #2/LW:44
> delete #2/LW:43
> delete #2/LW:42
> delete #2/LW:41
> delete #2/LW:40
> delete #2/LW:39
> delete #2/LW:38
> delete #2/LW:37
> delete #2/LW:36
> delete #2/LW:35
> delete #2/LW:34
> delete #2/LW:33
> delete #2/LW:32
> delete #2/LW:31
> delete #2/LW:30
> delete #2/LW:29
> delete #2/LW:28
> delete #2/LW:27
> delete #2/LW:26
> delete #2/LW:25
> delete #2/LW:24
> delete #2/LW:23
> delete #2/LW:22
> delete #2/LW:21
> delete #2/LW:20
> delete #2/LW:19
> delete #2/LW:18
> delete #2/LW:17
> delete #2/LW:16
> delete #2/LW:15
> delete #2/LW:14
> delete #2/LW:13
> delete #2/LW:12
> delete #2/LW:11
> delete #2/LW:10
> delete #2/LW:9
> delete #2/LW:8
> delete #2/LW:7
> delete #2/LW:6
> delete #2/LW:5
> delete #2/LW:4
> delete #2/LW:3
> delete #2/LW:2
> delete #2/LW:1
> renumber #2/LW start 1
292 residues renumbered
['4', '22']
> select #2/Mi
327 atoms, 341 bonds, 38 residues, 1 model selected
292
293
>1
> renumber #2/Mi start 293
38 residues renumbered
> changechains #2/Mi LW
Chain IDs of 38 residues changed
Renumering chain LtaP09.0030.mRNA-A
['6', '62']
> select #2/JN
537 atoms, 559 bonds, 64 residues, 1 model selected
0
2
>2
> renumber #2/JN start 2
64 residues renumbered
['1', '9']
> select #2/Ia
84 atoms, 86 bonds, 9 residues, 1 model selected
65
65
>0
> delete #2/Ia:1
> renumber #2/Ia start 66
8 residues renumbered
> changechains #2/Ia JN
Chain IDs of 8 residues changed
['1', '5']
> select #2/I
39 atoms, 40 bonds, 5 residues, 1 model selected
73
75
>2
> renumber #2/I start 75
5 residues renumbered
> changechains #2/I JN
Chain IDs of 5 residues changed
['1', '27']
> select #2/Iz
227 atoms, 232 bonds, 29 residues, 1 model selected
79
80
>1
> renumber #2/Iz start 80
29 residues renumbered
> changechains #2/Iz JN
Chain IDs of 29 residues changed
Renumering chain LtaP09.0030.mRNA-B
['1', '16']
> select #2/MG
223 atoms, 228 bonds, 26 residues, 1 model selected
0
56
>56
> renumber #2/MG start 56
26 residues renumbered
Renumering chain LtaP16.0500.mRNA
['2', '20']
> select #2/L3
182 atoms, 182 bonds, 22 residues, 1 model selected
0
52
>52
> renumber #2/L3 start 52
22 residues renumbered
['1', '1']
> select #2/Ad
8 atoms, 7 bonds, 1 residue, 1 model selected
73
74
>1
> renumber #2/Ad start 74
1 residues renumbered
> changechains #2/Ad L3
Chain IDs of 1 residues changed
['1', '1']
> select #2/A9
9 atoms, 8 bonds, 1 residue, 1 model selected
74
75
>1
> renumber #2/A9 start 75
1 residues renumbered
> changechains #2/A9 L3
Chain IDs of 1 residues changed
['1', '1']
> select #2/Aq
8 atoms, 7 bonds, 1 residue, 1 model selected
75
76
>1
> renumber #2/Aq start 76
1 residues renumbered
> changechains #2/Aq L3
Chain IDs of 1 residues changed
['1', '7']
> select #2/Kk
60 atoms, 60 bonds, 7 residues, 1 model selected
76
78
>2
> renumber #2/Kk start 78
7 residues renumbered
> changechains #2/Kk L3
Chain IDs of 7 residues changed
['2', '8']
> select #2/Jc
195 atoms, 196 bonds, 24 residues, 1 model selected
84
94
>10
> renumber #2/Jc start 94
24 residues renumbered
> changechains #2/Jc L3
Chain IDs of 24 residues changed
['1', '13']
> select #2/MS
111 atoms, 113 bonds, 13 residues, 1 model selected
117
198
>81
> renumber #2/MS start 198
13 residues renumbered
> changechains #2/MS L3
Chain IDs of 13 residues changed
['1', '10']
> select #2/W
77 atoms, 76 bonds, 10 residues, 1 model selected
210
213
>3
> renumber #2/W start 213
10 residues renumbered
> changechains #2/W L3
Chain IDs of 10 residues changed
['1', '6']
> select #2/Kx
44 atoms, 43 bonds, 6 residues, 1 model selected
222
222
>0
> delete #2/Kx:1
> renumber #2/Kx start 223
5 residues renumbered
> changechains #2/Kx L3
Chain IDs of 5 residues changed
['1', '11']
> select #2/X
89 atoms, 89 bonds, 11 residues, 1 model selected
227
228
>1
> renumber #2/X start 228
11 residues renumbered
> changechains #2/X L3
Chain IDs of 11 residues changed
['1', '26']
> select #2/I7
214 atoms, 218 bonds, 26 residues, 1 model selected
238
240
>2
> renumber #2/I7 start 240
26 residues renumbered
> changechains #2/I7 L3
Chain IDs of 26 residues changed
['1', '12']
> select #2/Ib
146 atoms, 149 bonds, 18 residues, 1 model selected
265
266
>1
> renumber #2/Ib start 266
18 residues renumbered
> changechains #2/Ib L3
Chain IDs of 18 residues changed
['1', '2']
> select #2/AD
13 atoms, 12 bonds, 2 residues, 1 model selected
283
312
>29
> renumber #2/AD start 312
2 residues renumbered
> changechains #2/AD L3
Chain IDs of 2 residues changed
['1', '12']
> select #2/KV
90 atoms, 92 bonds, 12 residues, 1 model selected
313
314
>1
> renumber #2/KV start 314
12 residues renumbered
> changechains #2/KV L3
Chain IDs of 12 residues changed
Renumering chain LtaP30.2840.mRNA
['1', '2']
> select #2/M
14 atoms, 13 bonds, 2 residues, 1 model selected
0
2
>2
> renumber #2/M start 2
2 residues renumbered
['1', '1']
> select #2/A5
7 atoms, 6 bonds, 1 residue, 1 model selected
3
4
>1
> renumber #2/A5 start 4
1 residues renumbered
> changechains #2/A5 M
Chain IDs of 1 residues changed
['1', '1']
> select #2/7
7 atoms, 6 bonds, 1 residue, 1 model selected
4
5
>1
> renumber #2/7 start 5
1 residues renumbered
> changechains #2/7 M
Chain IDs of 1 residues changed
> renumber #2/JH:48-9999999 start 49
13 residues renumbered
> ~bond #2/JH:47@C #2/JH:49@N
['1', '59']
> select #2/JH
496 atoms, 508 bonds, 1 pseudobond, 60 residues, 2 models selected
5
6
>1
> renumber #2/JH start 6
60 residues renumbered
> changechains #2/JH M
Chain IDs of 60 residues changed
['1', '4']
> select #2/l
32 atoms, 32 bonds, 4 residues, 1 model selected
66
66
>0
> delete #2/l:1
> renumber #2/l start 67
3 residues renumbered
> changechains #2/l M
Chain IDs of 3 residues changed
['1', '2']
> select #2/BF
15 atoms, 14 bonds, 2 residues, 1 model selected
69
70
>1
> renumber #2/BF start 70
2 residues renumbered
> changechains #2/BF M
Chain IDs of 2 residues changed
['2', '30']
> select #2/NV
238 atoms, 244 bonds, 30 residues, 1 model selected
71
74
>3
> renumber #2/NV start 74
30 residues renumbered
> changechains #2/NV M
Chain IDs of 30 residues changed
Renumering chain LtaP34.3980.mRNA
['1', '20']
> select #2/J4
191 atoms, 202 bonds, 20 residues, 1 model selected
0
4
>4
> renumber #2/J4 start 4
20 residues renumbered
['1', '2']
> select #2/A4
12 atoms, 11 bonds, 2 residues, 1 model selected
23
24
>1
> renumber #2/A4 start 24
2 residues renumbered
> changechains #2/A4 J4
Chain IDs of 2 residues changed
['1', '11']
> select #2/LA
92 atoms, 97 bonds, 11 residues, 1 model selected
25
26
>1
> renumber #2/LA start 26
11 residues renumbered
> changechains #2/LA J4
Chain IDs of 11 residues changed
['1', '2']
> select #2/EA
12 atoms, 11 bonds, 2 residues, 1 model selected
36
40
>4
> renumber #2/EA start 40
2 residues renumbered
> changechains #2/EA J4
Chain IDs of 2 residues changed
['1', '6']
> select #2/Md
48 atoms, 47 bonds, 6 residues, 1 model selected
41
42
>1
> renumber #2/Md start 42
6 residues renumbered
> changechains #2/Md J4
Chain IDs of 6 residues changed
['1', '8']
> select #2/J2
60 atoms, 61 bonds, 8 residues, 1 model selected
47
52
>5
> renumber #2/J2 start 52
8 residues renumbered
> changechains #2/J2 J4
Chain IDs of 8 residues changed
['1', '2']
> select #2/Ah
20 atoms, 20 bonds, 2 residues, 1 model selected
59
60
>1
> renumber #2/Ah start 60
2 residues renumbered
> changechains #2/Ah J4
Chain IDs of 2 residues changed
['19', '23']
> select #2/KK
325 atoms, 333 bonds, 41 residues, 1 model selected
61
62
>1
> renumber #2/KK start 62
41 residues renumbered
> changechains #2/KK J4
Chain IDs of 41 residues changed
Renumering chain LtaP33.1260.mRNA
['5', '68']
> select #2/LR
558 atoms, 564 bonds, 71 residues, 1 model selected
0
78
>78
> renumber #2/LR start 78
71 residues renumbered
Renumering chain LtaP27.2160.mRNA
['2', '112']
> select #2/Jx
964 atoms, 986 bonds, 114 residues, 1 model selected
0
11
>11
> renumber #2/Jx start 11
114 residues renumbered
Renumering chain LtaP05.0800.mRNA
['2', '29']
> select #2/Jw
250 atoms, 257 bonds, 29 residues, 1 model selected
0
21
>21
> renumber #2/Jw start 21
29 residues renumbered
> delete #2/Jt:54
> renumber #2/Jt:55-9999999 start 54
34 residues renumbered
> bond #2/Jt:53@C #2/Jt:54@N reasonable false
Created 1 bond
['1', '87']
> select #2/Jt
745 atoms, 777 bonds, 87 residues, 1 model selected
49
50
>1
> renumber #2/Jt start 50
87 residues renumbered
> changechains #2/Jt Jw
Chain IDs of 87 residues changed
['1', '8']
> select #2/M9
65 atoms, 66 bonds, 8 residues, 1 model selected
136
137
>1
> renumber #2/M9 start 137
8 residues renumbered
> changechains #2/M9 Jw
Chain IDs of 8 residues changed
Renumering chain LtaP23.0450.mRNA
['1', '2']
> select #2/Ar
16 atoms, 16 bonds, 2 residues, 1 model selected
0
23
>23
> renumber #2/Ar start 23
2 residues renumbered
['1', '9']
> select #2/Ie
71 atoms, 74 bonds, 9 residues, 1 model selected
24
25
>1
> renumber #2/Ie start 25
9 residues renumbered
> changechains #2/Ie Ar
Chain IDs of 9 residues changed
['1', '3']
> select #2/Ig
29 atoms, 29 bonds, 3 residues, 1 model selected
33
34
>1
> renumber #2/Ig start 34
3 residues renumbered
> changechains #2/Ig Ar
Chain IDs of 3 residues changed
['4', '80']
> select #2/Ih
715 atoms, 734 bonds, 82 residues, 1 model selected
36
37
>1
> renumber #2/Ih start 37
82 residues renumbered
> changechains #2/Ih Ar
Chain IDs of 82 residues changed
Renumering chain AAA31882.1
['2', '25']
> select #2/Mw
202 atoms, 205 bonds, 25 residues, 1 model selected
0
1
>1
> renumber #2/Mw start 1
0 residues renumbered
['1', '2']
> select #2/DT
13 atoms, 12 bonds, 2 residues, 1 model selected
25
26
>1
> renumber #2/DT start 26
2 residues renumbered
> changechains #2/DT Mw
Chain IDs of 2 residues changed
['1', '2']
> select #2/CP
12 atoms, 11 bonds, 2 residues, 1 model selected
27
28
>1
> renumber #2/CP start 28
2 residues renumbered
> changechains #2/CP Mw
Chain IDs of 2 residues changed
['1', '10']
> select #2/Kg
91 atoms, 91 bonds, 10 residues, 1 model selected
29
30
>1
> renumber #2/Kg start 30
10 residues renumbered
> changechains #2/Kg Mw
Chain IDs of 10 residues changed
['1', '33']
> select #2/Mv
284 atoms, 293 bonds, 33 residues, 1 model selected
39
41
>2
> renumber #2/Mv start 41
33 residues renumbered
> changechains #2/Mv Mw
Chain IDs of 33 residues changed
['1', '24']
> select #2/MX
209 atoms, 215 bonds, 24 residues, 1 model selected
73
79
>6
> renumber #2/MX start 79
24 residues renumbered
> changechains #2/MX Mw
Chain IDs of 24 residues changed
['1', '27']
> select #2/G
232 atoms, 236 bonds, 27 residues, 1 model selected
102
136
>34
> renumber #2/G start 136
27 residues renumbered
> changechains #2/G Mw
Chain IDs of 27 residues changed
['1', '49']
> select #2/Lm
415 atoms, 426 bonds, 49 residues, 1 model selected
162
161
>-1
> delete #2/Lm:2
> delete #2/Lm:1
> renumber #2/Lm start 163
47 residues renumbered
> changechains #2/Lm Mw
Chain IDs of 47 residues changed
Renumering chain LtaP25.2210.mRNA
> delete #2/Lb:16
> renumber #2/Lb:17-9999999 start 16
9 residues renumbered
> bond #2/Lb:15@C #2/Lb:16@N reasonable false
Created 1 bond
['2', '24']
> select #2/Lb
175 atoms, 178 bonds, 24 residues, 1 model selected
0
18
>18
> renumber #2/Lb start 18
24 residues renumbered
['1', '24']
> select #2/I5
193 atoms, 201 bonds, 24 residues, 1 model selected
41
44
>3
> renumber #2/I5 start 44
24 residues renumbered
> changechains #2/I5 Lb
Chain IDs of 24 residues changed
['1', '4']
> select #2/KP
28 atoms, 30 bonds, 4 residues, 1 model selected
67
68
>1
> renumber #2/KP start 68
4 residues renumbered
> changechains #2/KP Lb
Chain IDs of 4 residues changed
['1', '2']
> select #2/Ew
15 atoms, 14 bonds, 2 residues, 1 model selected
71
72
>1
> renumber #2/Ew start 72
2 residues renumbered
> changechains #2/Ew Lb
Chain IDs of 2 residues changed
['1', '4']
> select #2/Cb
34 atoms, 34 bonds, 4 residues, 1 model selected
73
76
>3
> renumber #2/Cb start 76
4 residues renumbered
> changechains #2/Cb Lb
Chain IDs of 4 residues changed
['1', '14']
> select #2/LD
123 atoms, 128 bonds, 14 residues, 1 model selected
79
80
>1
> renumber #2/LD start 80
14 residues renumbered
> changechains #2/LD Lb
Chain IDs of 14 residues changed
['2', '37']
> select #2/Mc
338 atoms, 348 bonds, 39 residues, 1 model selected
93
94
>1
> renumber #2/Mc start 94
39 residues renumbered
> changechains #2/Mc Lb
Chain IDs of 39 residues changed
Renumering chain LtaP26.1720.mRNA
['1', '2']
> select #2/AG
25 atoms, 27 bonds, 2 residues, 1 model selected
0
18
>18
> renumber #2/AG start 18
2 residues renumbered
['1', '2']
> select #2/Ap
13 atoms, 12 bonds, 2 residues, 1 model selected
19
20
>1
> renumber #2/Ap start 20
2 residues renumbered
> changechains #2/Ap AG
Chain IDs of 2 residues changed
['1', '175']
> select #2/L7
1428 atoms, 1458 bonds, 175 residues, 1 model selected
21
22
>1
> renumber #2/L7 start 22
175 residues renumbered
> changechains #2/L7 AG
Chain IDs of 175 residues changed
Renumering chain LtaP36.0470.mRNA
['5', '199']
> select #2/KI
1693 atoms, 1753 bonds, 200 residues, 1 model selected
0
26
>26
> renumber #2/KI start 26
200 residues renumbered
Renumering chain LtaP25.1690.mRNA
['1', '36']
> select #2/Ii
314 atoms, 325 bonds, 37 residues, 1 model selected
0
3
>3
> renumber #2/Ii start 3
37 residues renumbered
> renumber #2/LP:21-9999999 start 22
11 residues renumbered
> ~bond #2/LP:20@C #2/LP:22@N
['4', '29']
> select #2/LP
256 atoms, 263 bonds, 1 pseudobond, 31 residues, 2 models selected
39
47
>8
> renumber #2/LP start 47
31 residues renumbered
> changechains #2/LP Ii
Chain IDs of 31 residues changed
['1', '18']
> select #2/L
146 atoms, 146 bonds, 18 residues, 1 model selected
78
98
>20
> renumber #2/L start 98
18 residues renumbered
> changechains #2/L Ii
Chain IDs of 18 residues changed
Renumering chain LtaP14.1460.mRNA
> delete #2/Ke:13
> renumber #2/Ke:14-9999999 start 13
51 residues renumbered
> bond #2/Ke:12@C #2/Ke:13@N reasonable false
Created 1 bond
['12', '63']
> select #2/Ke
490 atoms, 498 bonds, 63 residues, 1 model selected
0
44
>44
> renumber #2/Ke start 44
63 residues renumbered
['1', '30']
> select #2/TA
243 atoms, 252 bonds, 30 residues, 1 model selected
106
109
>3
> renumber #2/TA start 109
30 residues renumbered
> changechains #2/TA Ke
Chain IDs of 30 residues changed
Renumering chain LtaP34.1060.mRNA
['1', '7']
> select #2/Mh
63 atoms, 65 bonds, 7 residues, 1 model selected
0
38
>38
> renumber #2/Mh start 38
7 residues renumbered
['1', '50']
> select #2/o
470 atoms, 489 bonds, 52 residues, 1 model selected
44
45
>1
> renumber #2/o start 45
52 residues renumbered
> changechains #2/o Mh
Chain IDs of 52 residues changed
Renumering chain LtaP12.0690.mRNA
> delete #2/LO:101
> delete #2/LO:103
> delete #2/LO:272
> delete #2/LO:274
> renumber #2/LO:102-9999999 start 101
205 residues renumbered
> bond #2/LO:100@C #2/LO:101@N reasonable false
Created 1 bond
> renumber #2/LO:103-9999999 start 102
204 residues renumbered
> bond #2/LO:101@C #2/LO:102@N reasonable false
Created 1 bond
> renumber #2/LO:271-9999999 start 270
36 residues renumbered
> bond #2/LO:269@C #2/LO:270@N reasonable false
Created 1 bond
> renumber #2/LO:272-9999999 start 271
35 residues renumbered
> bond #2/LO:270@C #2/LO:271@N reasonable false
Created 1 bond
> renumber #2/LO:96-9999999 start 97
210 residues renumbered
> ~bond #2/LO:95@C #2/LO:97@N
['1', '303']
> select #2/LO
2517 atoms, 2567 bonds, 1 pseudobond, 305 residues, 2 models selected
0
37
>37
> renumber #2/LO start 37
305 residues renumbered
Renumering chain LtaP24.1430.mRNA
['1', '8']
> select #2/Mq
62 atoms, 63 bonds, 8 residues, 1 model selected
0
34
>34
> renumber #2/Mq start 34
8 residues renumbered
['1', '4']
> select #2/MA
28 atoms, 28 bonds, 4 residues, 1 model selected
41
42
>1
> renumber #2/MA start 42
4 residues renumbered
> changechains #2/MA Mq
Chain IDs of 4 residues changed
['1', '44']
> select #2/I1
395 atoms, 411 bonds, 45 residues, 1 model selected
45
46
>1
> renumber #2/I1 start 46
45 residues renumbered
> changechains #2/I1 Mq
Chain IDs of 45 residues changed
Renumering chain LtaP04.1180.mRNA
['1', '43']
> select #2/TB
353 atoms, 357 bonds, 43 residues, 1 model selected
0
18
>18
> renumber #2/TB start 18
43 residues renumbered
['1', '2']
> select #2/At
14 atoms, 13 bonds, 2 residues, 1 model selected
60
61
>1
> renumber #2/At start 61
2 residues renumbered
> changechains #2/At TB
Chain IDs of 2 residues changed
['1', '16']
> select #2/L4
114 atoms, 117 bonds, 16 residues, 1 model selected
62
63
>1
> renumber #2/L4 start 63
16 residues renumbered
> changechains #2/L4 TB
Chain IDs of 16 residues changed
['1', '3']
> select #2/FA
22 atoms, 23 bonds, 3 residues, 1 model selected
78
79
>1
> renumber #2/FA start 79
3 residues renumbered
> changechains #2/FA TB
Chain IDs of 3 residues changed
Renumering chain LtaP08.0840.mRNA
> delete #2/Ml:54
> renumber #2/Ml:55-9999999 start 54
13 residues renumbered
> bond #2/Ml:53@C #2/Ml:54@N reasonable false
Created 1 bond
['2', '65']
> select #2/Ml
543 atoms, 554 bonds, 66 residues, 1 model selected
0
230
>230
> renumber #2/Ml start 230
66 residues renumbered
['1', '5']
> select #2/ND
40 atoms, 41 bonds, 5 residues, 1 model selected
295
296
>1
> renumber #2/ND start 296
5 residues renumbered
> changechains #2/ND Ml
Chain IDs of 5 residues changed
Renumering chain LdBPK_301100.1ReplacementOfLtaP30.1150.mRNA
['18', '97']
> select #2/Mg
851 atoms, 877 bonds, 100 residues, 1 model selected
0
36
>36
> renumber #2/Mg start 36
100 residues renumbered
['1', '10']
> select #2/Lh
88 atoms, 91 bonds, 10 residues, 1 model selected
135
135
>0
> delete #2/Lh:1
> renumber #2/Lh start 136
9 residues renumbered
> changechains #2/Lh Mg
Chain IDs of 9 residues changed
['12', '92']
> select #2/Kw
815 atoms, 834 bonds, 94 residues, 1 model selected
144
144
>0
> delete #2/Kw:1
> renumber #2/Kw start 145
93 residues renumbered
> changechains #2/Kw Mg
Chain IDs of 93 residues changed
['1', '13']
> select #2/Kh
94 atoms, 95 bonds, 13 residues, 1 model selected
237
236
>-1
> delete #2/Kh:2
> delete #2/Kh:1
> renumber #2/Kh start 238
11 residues renumbered
> changechains #2/Kh Mg
Chain IDs of 11 residues changed
['1', '1']
> select #2/DC
11 atoms, 10 bonds, 1 residue, 1 model selected
248
249
>1
> renumber #2/DC start 249
1 residues renumbered
> changechains #2/DC Mg
Chain IDs of 1 residues changed
['1', '1']
> select #2/ES
8 atoms, 7 bonds, 1 residue, 1 model selected
249
250
>1
> renumber #2/ES start 250
1 residues renumbered
> changechains #2/ES Mg
Chain IDs of 1 residues changed
Renumering chain LtaP32.0010.mRNA
> delete #2/LG:14
> renumber #2/LG:15-9999999 start 14
65 residues renumbered
> bond #2/LG:13@C #2/LG:14@N reasonable false
Created 1 bond
['1', '78']
> select #2/LG
683 atoms, 700 bonds, 78 residues, 1 model selected
0
20
>20
> renumber #2/LG start 20
78 residues renumbered
['1', '5']
> select #2/Ll
38 atoms, 37 bonds, 5 residues, 1 model selected
97
98
>1
> renumber #2/Ll start 98
5 residues renumbered
> changechains #2/Ll LG
Chain IDs of 5 residues changed
['1', '21']
> select #2/Ij
186 atoms, 190 bonds, 21 residues, 1 model selected
102
103
>1
> renumber #2/Ij start 103
21 residues renumbered
> changechains #2/Ij LG
Chain IDs of 21 residues changed
Renumering chain LtaP27.0660.mRNA
['1', '18']
> select #2/MC
153 atoms, 156 bonds, 18 residues, 1 model selected
0
37
>37
> renumber #2/MC start 37
18 residues renumbered
['1', '3']
> select #2/s
32 atoms, 33 bonds, 3 residues, 1 model selected
54
55
>1
> renumber #2/s start 55
3 residues renumbered
> changechains #2/s MC
Chain IDs of 3 residues changed
['1', '1']
> select #2/DB
9 atoms, 8 bonds, 1 residue, 1 model selected
57
59
>2
> renumber #2/DB start 59
1 residues renumbered
> changechains #2/DB MC
Chain IDs of 1 residues changed
['1', '8']
> select #2/Lv
76 atoms, 76 bonds, 8 residues, 1 model selected
59
60
>1
> renumber #2/Lv start 60
8 residues renumbered
> changechains #2/Lv MC
Chain IDs of 8 residues changed
['1', '21']
> select #2/LV
157 atoms, 159 bonds, 21 residues, 1 model selected
67
68
>1
> renumber #2/LV start 68
21 residues renumbered
> changechains #2/LV MC
Chain IDs of 21 residues changed
['1', '8']
> select #2/i
69 atoms, 68 bonds, 8 residues, 1 model selected
88
92
>4
> renumber #2/i start 92
8 residues renumbered
> changechains #2/i MC
Chain IDs of 8 residues changed
> renumber #2/IZ:18-9999999 start 19
12 residues renumbered
> ~bond #2/IZ:17@C #2/IZ:19@N
['3', '26']
> select #2/IZ
246 atoms, 250 bonds, 1 pseudobond, 29 residues, 2 models selected
99
135
>36
> renumber #2/IZ start 135
29 residues renumbered
> changechains #2/IZ MC
Chain IDs of 29 residues changed
['1', '10']
> select #2/Li
77 atoms, 77 bonds, 10 residues, 1 model selected
164
163
>-1
> delete #2/Li:2
> delete #2/Li:1
> renumber #2/Li start 165
8 residues renumbered
> changechains #2/Li MC
Chain IDs of 8 residues changed
['1', '7']
> select #2/NH
47 atoms, 46 bonds, 7 residues, 1 model selected
172
175
>3
> renumber #2/NH start 175
7 residues renumbered
> changechains #2/NH MC
Chain IDs of 7 residues changed
Renumering chain AAA31877.1
['2', '278']
> select #2/Np
2425 atoms, 2510 bonds, 284 residues, 1 model selected
0
0
>0
> delete #2/Np:1
> renumber #2/Np start 1
283 residues renumbered
Renumering chain LtaP22.1610.mRNA
['2', '15']
> select #2/I2
137 atoms, 142 bonds, 16 residues, 1 model selected
0
84
>84
> renumber #2/I2 start 84
16 residues renumbered
['1', '29']
> select #2/JR
246 atoms, 253 bonds, 29 residues, 1 model selected
99
99
>0
> delete #2/JR:1
> renumber #2/JR start 100
28 residues renumbered
> changechains #2/JR I2
Chain IDs of 28 residues changed
> runscript
> /Users/rafaelrocha/GitHub/KRSPs/modelangeloScripts/bondFragmentsFillGapsMutateForMultipleChains.py
> combine #2 close false name mutadedModel
> select #2/Ks
1351 atoms, 1400 bonds, 153 residues, 1 model selected
> bond #2/Ks:117@C #2/Ks:118@N reasonable false
Created 0 bonds
> bond #2/Ks:118@C #2/Ks:119@N reasonable false
Created 0 bonds
> bond #2/Ks:119@C #2/Ks:120@N reasonable false
Created 0 bonds
> bond #2/Ks:120@C #2/Ks:121@N reasonable false
Created 0 bonds
> bond #2/Ks:121@C #2/Ks:122@N reasonable false
Created 0 bonds
> bond #2/Ks:122@C #2/Ks:123@N reasonable false
Created 0 bonds
> bond #2/Ks:123@C #2/Ks:124@N reasonable false
Created 0 bonds
> bond #2/Ks:124@C #2/Ks:125@N reasonable false
Created 0 bonds
> bond #2/Ks:125@C #2/Ks:126@N reasonable false
Created 0 bonds
> bond #2/Ks:126@C #2/Ks:127@N reasonable false
Created 0 bonds
> bond #2/Ks:127@C #2/Ks:128@N reasonable false
Created 0 bonds
> bond #2/Ks:128@C #2/Ks:129@N reasonable false
Created 0 bonds
> bond #2/Ks:129@C #2/Ks:130@N reasonable false
Created 0 bonds
> bond #2/Ks:130@C #2/Ks:131@N reasonable false
Created 0 bonds
> bond #2/Ks:131@C #2/Ks:132@N reasonable false
Created 0 bonds
> bond #2/Ks:132@C #2/Ks:133@N reasonable false
Created 0 bonds
> bond #2/Ks:133@C #2/Ks:134@N reasonable false
Created 0 bonds
> bond #2/Ks:134@C #2/Ks:135@N reasonable false
Created 0 bonds
> bond #2/Ks:135@C #2/Ks:136@N reasonable false
Created 0 bonds
> bond #2/Ks:136@C #2/Ks:137@N reasonable false
Created 0 bonds
> bond #2/Ks:137@C #2/Ks:138@N reasonable false
Created 0 bonds
> bond #2/Ks:138@C #2/Ks:139@N reasonable false
Created 0 bonds
> bond #2/Ks:139@C #2/Ks:140@N reasonable false
Created 0 bonds
> bond #2/Ks:140@C #2/Ks:141@N reasonable false
Created 0 bonds
> bond #2/Ks:141@C #2/Ks:142@N reasonable false
Created 0 bonds
> bond #2/Ks:142@C #2/Ks:143@N reasonable false
Created 0 bonds
> bond #2/Ks:143@C #2/Ks:144@N reasonable false
Created 0 bonds
> bond #2/Ks:144@C #2/Ks:145@N reasonable false
Created 0 bonds
> bond #2/Ks:145@C #2/Ks:146@N reasonable false
Created 0 bonds
> bond #2/Ks:146@C #2/Ks:147@N reasonable false
Created 0 bonds
> bond #2/Ks:147@C #2/Ks:148@N reasonable false
Created 0 bonds
> bond #2/Ks:148@C #2/Ks:149@N reasonable false
Created 0 bonds
> bond #2/Ks:149@C #2/Ks:150@N reasonable false
Created 0 bonds
> bond #2/Ks:150@C #2/Ks:151@N reasonable false
Created 0 bonds
> bond #2/Ks:151@C #2/Ks:152@N reasonable false
Created 0 bonds
> bond #2/Ks:152@C #2/Ks:153@N reasonable false
Created 0 bonds
> bond #2/Ks:153@C #2/Ks:154@N reasonable false
Created 0 bonds
> bond #2/Ks:154@C #2/Ks:155@N reasonable false
Created 0 bonds
> bond #2/Ks:155@C #2/Ks:156@N reasonable false
Created 0 bonds
> bond #2/Ks:95@C #2/Ks:96@N reasonable false
Created 0 bonds
> bond #2/Ks:96@C #2/Ks:97@N reasonable false
Created 0 bonds
> bond #2/Ks:97@C #2/Ks:98@N reasonable false
Created 0 bonds
> bond #2/Ks:98@C #2/Ks:99@N reasonable false
Created 0 bonds
> bond #2/Ks:99@C #2/Ks:100@N reasonable false
Created 0 bonds
> bond #2/Ks:100@C #2/Ks:101@N reasonable false
Created 0 bonds
> bond #2/Ks:101@C #2/Ks:102@N reasonable false
Created 0 bonds
> bond #2/Ks:102@C #2/Ks:103@N reasonable false
Created 0 bonds
> bond #2/Ks:103@C #2/Ks:104@N reasonable false
Created 0 bonds
> bond #2/Ks:104@C #2/Ks:105@N reasonable false
Created 0 bonds
> bond #2/Ks:105@C #2/Ks:106@N reasonable false
Created 0 bonds
> bond #2/Ks:106@C #2/Ks:107@N reasonable false
Created 0 bonds
> bond #2/Ks:107@C #2/Ks:108@N reasonable false
Created 0 bonds
> bond #2/Ks:108@C #2/Ks:109@N reasonable false
Created 0 bonds
> bond #2/Ks:109@C #2/Ks:110@N reasonable false
Created 0 bonds
> bond #2/Ks:110@C #2/Ks:111@N reasonable false
Created 0 bonds
> bond #2/Ks:111@C #2/Ks:112@N reasonable false
Created 0 bonds
> bond #2/Ks:112@C #2/Ks:113@N reasonable false
Created 0 bonds
> bond #2/Ks:113@C #2/Ks:114@N reasonable false
Created 0 bonds
> bond #2/Ks:114@C #2/Ks:115@N reasonable false
Created 0 bonds
> bond #2/Ks:115@C #2/Ks:116@N reasonable false
Created 0 bonds
> bond #2/Ks:116@C #2/Ks:117@N reasonable false
Created 1 bond
> bond #2/Ks:4@C #2/Ks:5@N reasonable false
Created 0 bonds
> bond #2/Ks:5@C #2/Ks:6@N reasonable false
Created 0 bonds
> bond #2/Ks:6@C #2/Ks:7@N reasonable false
Created 0 bonds
> bond #2/Ks:7@C #2/Ks:8@N reasonable false
Created 0 bonds
> bond #2/Ks:8@C #2/Ks:9@N reasonable false
Created 0 bonds
> bond #2/Ks:9@C #2/Ks:10@N reasonable false
Created 0 bonds
> bond #2/Ks:10@C #2/Ks:11@N reasonable false
Created 0 bonds
> bond #2/Ks:11@C #2/Ks:12@N reasonable false
Created 0 bonds
> bond #2/Ks:12@C #2/Ks:13@N reasonable false
Created 0 bonds
> bond #2/Ks:13@C #2/Ks:14@N reasonable false
Created 0 bonds
> bond #2/Ks:14@C #2/Ks:15@N reasonable false
Created 0 bonds
> bond #2/Ks:15@C #2/Ks:16@N reasonable false
Created 0 bonds
> bond #2/Ks:16@C #2/Ks:17@N reasonable false
Created 0 bonds
> bond #2/Ks:17@C #2/Ks:18@N reasonable false
Created 0 bonds
> bond #2/Ks:18@C #2/Ks:19@N reasonable false
Created 0 bonds
> bond #2/Ks:19@C #2/Ks:20@N reasonable false
Created 0 bonds
> bond #2/Ks:20@C #2/Ks:21@N reasonable false
Created 0 bonds
> bond #2/Ks:21@C #2/Ks:22@N reasonable false
Created 0 bonds
> bond #2/Ks:22@C #2/Ks:23@N reasonable false
Created 0 bonds
> bond #2/Ks:23@C #2/Ks:24@N reasonable false
Created 0 bonds
> bond #2/Ks:24@C #2/Ks:25@N reasonable false
Created 0 bonds
> bond #2/Ks:25@C #2/Ks:26@N reasonable false
Created 0 bonds
> bond #2/Ks:26@C #2/Ks:27@N reasonable false
Created 0 bonds
> bond #2/Ks:27@C #2/Ks:28@N reasonable false
Created 0 bonds
> bond #2/Ks:28@C #2/Ks:29@N reasonable false
Created 0 bonds
> bond #2/Ks:29@C #2/Ks:30@N reasonable false
Created 0 bonds
> bond #2/Ks:30@C #2/Ks:31@N reasonable false
Created 0 bonds
> bond #2/Ks:31@C #2/Ks:32@N reasonable false
Created 0 bonds
> bond #2/Ks:32@C #2/Ks:33@N reasonable false
Created 0 bonds
> bond #2/Ks:33@C #2/Ks:34@N reasonable false
Created 0 bonds
> bond #2/Ks:34@C #2/Ks:35@N reasonable false
Created 0 bonds
> bond #2/Ks:35@C #2/Ks:36@N reasonable false
Created 0 bonds
> bond #2/Ks:36@C #2/Ks:37@N reasonable false
Created 0 bonds
> bond #2/Ks:37@C #2/Ks:38@N reasonable false
Created 0 bonds
> bond #2/Ks:38@C #2/Ks:39@N reasonable false
Created 0 bonds
> bond #2/Ks:39@C #2/Ks:40@N reasonable false
Created 0 bonds
> bond #2/Ks:40@C #2/Ks:41@N reasonable false
Created 0 bonds
> bond #2/Ks:41@C #2/Ks:42@N reasonable false
Created 0 bonds
> bond #2/Ks:42@C #2/Ks:43@N reasonable false
Created 0 bonds
> bond #2/Ks:43@C #2/Ks:44@N reasonable false
Created 0 bonds
> bond #2/Ks:44@C #2/Ks:45@N reasonable false
Created 0 bonds
> bond #2/Ks:45@C #2/Ks:46@N reasonable false
Created 0 bonds
> bond #2/Ks:46@C #2/Ks:47@N reasonable false
Created 0 bonds
> bond #2/Ks:47@C #2/Ks:48@N reasonable false
Created 0 bonds
> bond #2/Ks:48@C #2/Ks:49@N reasonable false
Created 0 bonds
> bond #2/Ks:49@C #2/Ks:50@N reasonable false
Created 0 bonds
> bond #2/Ks:50@C #2/Ks:51@N reasonable false
Created 0 bonds
> bond #2/Ks:51@C #2/Ks:52@N reasonable false
Created 0 bonds
> bond #2/Ks:52@C #2/Ks:53@N reasonable false
Created 0 bonds
> bond #2/Ks:53@C #2/Ks:54@N reasonable false
Created 0 bonds
> bond #2/Ks:54@C #2/Ks:55@N reasonable false
Created 0 bonds
> bond #2/Ks:55@C #2/Ks:56@N reasonable false
Created 0 bonds
> bond #2/Ks:56@C #2/Ks:57@N reasonable false
Created 0 bonds
> bond #2/Ks:57@C #2/Ks:58@N reasonable false
Created 0 bonds
> bond #2/Ks:58@C #2/Ks:59@N reasonable false
Created 0 bonds
> bond #2/Ks:59@C #2/Ks:60@N reasonable false
Created 0 bonds
> bond #2/Ks:60@C #2/Ks:61@N reasonable false
Created 0 bonds
> bond #2/Ks:61@C #2/Ks:62@N reasonable false
Created 0 bonds
> bond #2/Ks:62@C #2/Ks:63@N reasonable false
Created 0 bonds
> bond #2/Ks:63@C #2/Ks:64@N reasonable false
Created 0 bonds
> bond #2/Ks:64@C #2/Ks:65@N reasonable false
Created 0 bonds
> bond #2/Ks:65@C #2/Ks:66@N reasonable false
Created 0 bonds
> bond #2/Ks:66@C #2/Ks:67@N reasonable false
Created 0 bonds
> bond #2/Ks:67@C #2/Ks:68@N reasonable false
Created 0 bonds
> bond #2/Ks:68@C #2/Ks:69@N reasonable false
Created 0 bonds
> bond #2/Ks:69@C #2/Ks:70@N reasonable false
Created 0 bonds
> bond #2/Ks:70@C #2/Ks:71@N reasonable false
Created 0 bonds
> bond #2/Ks:71@C #2/Ks:72@N reasonable false
Created 0 bonds
> bond #2/Ks:72@C #2/Ks:73@N reasonable false
Created 0 bonds
> bond #2/Ks:73@C #2/Ks:74@N reasonable false
Created 0 bonds
> bond #2/Ks:74@C #2/Ks:75@N reasonable false
Created 0 bonds
> bond #2/Ks:75@C #2/Ks:76@N reasonable false
Created 0 bonds
> bond #2/Ks:76@C #2/Ks:77@N reasonable false
Created 0 bonds
> bond #2/Ks:77@C #2/Ks:78@N reasonable false
Created 0 bonds
> bond #2/Ks:78@C #2/Ks:79@N reasonable false
Created 0 bonds
> bond #2/Ks:79@C #2/Ks:80@N reasonable false
Created 0 bonds
> bond #2/Ks:80@C #2/Ks:81@N reasonable false
Created 0 bonds
> bond #2/Ks:81@C #2/Ks:82@N reasonable false
Created 0 bonds
> bond #2/Ks:82@C #2/Ks:83@N reasonable false
Created 0 bonds
> bond #2/Ks:83@C #2/Ks:84@N reasonable false
Created 0 bonds
> bond #2/Ks:84@C #2/Ks:85@N reasonable false
Created 0 bonds
> bond #2/Ks:85@C #2/Ks:86@N reasonable false
Created 0 bonds
> bond #2/Ks:86@C #2/Ks:87@N reasonable false
Created 0 bonds
> bond #2/Ks:87@C #2/Ks:88@N reasonable false
Created 0 bonds
> bond #2/Ks:88@C #2/Ks:89@N reasonable false
Created 0 bonds
> bond #2/Ks:89@C #2/Ks:90@N reasonable false
Created 0 bonds
> bond #2/Ks:90@C #2/Ks:91@N reasonable false
Created 0 bonds
> bond #2/Ks:91@C #2/Ks:92@N reasonable false
Created 0 bonds
> bond #2/Ks:92@C #2/Ks:93@N reasonable false
Created 0 bonds
> bond #2/Ks:93@C #2/Ks:94@N reasonable false
Created 0 bonds
> bond #2/Ks:94@C #2/Ks:95@N reasonable false
Created 1 bond
> swapaa #2/Ks:4 GLU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks LYS 4: phi none, psi -39.6 trans
Applying GLU rotamer (chi angles: -66.2 82.2 1.9) to renamedAndRenumberedModel
#2/Ks GLU 4
> swapaa #2/Ks:5 ASP
Using Dunbrack library
renamedAndRenumberedModel #2/Ks LYS 5: phi -64.5, psi -29.4 trans
Applying ASP rotamer (chi angles: -71.8 -39.9) to renamedAndRenumberedModel
#2/Ks ASP 5
> swapaa #2/Ks:6 HIS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks PHE 6: phi -37.8, psi -11.2 trans
Applying HIS rotamer (chi angles: 66.6 -77.3) to renamedAndRenumberedModel
#2/Ks HIS 6
> swapaa #2/Ks:8 LYS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ARG 8: phi -114.1, psi 1.2 trans
Applying LYS rotamer (chi angles: 66.8 178.5 72.8 65.2) to
renamedAndRenumberedModel #2/Ks LYS 8
> swapaa #2/Ks:10 LYS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ARG 10: phi -100.9, psi 129.2 trans
Applying LYS rotamer (chi angles: -65.2 -178.8 -179.6 179.5) to
renamedAndRenumberedModel #2/Ks LYS 10
> swapaa #2/Ks:11 VAL
Using Dunbrack library
renamedAndRenumberedModel #2/Ks PRO 11: phi -63.4, psi 135.2 trans
Applying VAL rotamer (chi angles: 66.7) to renamedAndRenumberedModel #2/Ks VAL
11
> swapaa #2/Ks:13 ARG
Using Dunbrack library
renamedAndRenumberedModel #2/Ks TRP 13: phi -93.9, psi -11.2 trans
Applying ARG rotamer (chi angles: 178.6 65.7 -178.2 83.3) to
renamedAndRenumberedModel #2/Ks ARG 13
> swapaa #2/Ks:14 GLU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks PRO 14: phi -73.0, psi -7.0 trans
Applying GLU rotamer (chi angles: -63.3 81.4 62.0) to
renamedAndRenumberedModel #2/Ks GLU 14
> swapaa #2/Ks:15 GLU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ASN 15: phi -105.7, psi -18.3 trans
Applying GLU rotamer (chi angles: 67.4 -177.6 -64.9) to
renamedAndRenumberedModel #2/Ks GLU 15
> swapaa #2/Ks:21 HIS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks PHE 21: phi -119.4, psi 135.2 trans
Applying HIS rotamer (chi angles: -63.2 -110.4) to renamedAndRenumberedModel
#2/Ks HIS 21
> swapaa #2/Ks:23 ASN
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ASP 23: phi -120.4, psi 29.7 trans
Applying ASN rotamer (chi angles: -161.8 7.9) to renamedAndRenumberedModel
#2/Ks ASN 23
> swapaa #2/Ks:27 ASP
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ASN 27: phi -112.1, psi 122.6 trans
Applying ASP rotamer (chi angles: 63.1 -13.1) to renamedAndRenumberedModel
#2/Ks ASP 27
> swapaa #2/Ks:29 ARG
Using Dunbrack library
renamedAndRenumberedModel #2/Ks TRP 29: phi -82.2, psi -3.4 trans
Applying ARG rotamer (chi angles: 68.0 173.9 65.4 89.7) to
renamedAndRenumberedModel #2/Ks ARG 29
> swapaa #2/Ks:31 CYS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ILE 31: phi -67.8, psi -37.6 trans
Applying CYS rotamer (chi angles: 64.4) to renamedAndRenumberedModel #2/Ks CYS
31
> swapaa #2/Ks:32 GLY
Using Dunbrack library
Swapping renamedAndRenumberedModel #2/Ks SER 32 to GLY
> swapaa #2/Ks:36 LYS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks GLN 36: phi -107.3, psi 27.2 trans
Applying LYS rotamer (chi angles: -62.4 -64.3 -71.6 -176.1) to
renamedAndRenumberedModel #2/Ks LYS 36
> swapaa #2/Ks:38 LYS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ARG 38: phi -61.5, psi -34.2 trans
Applying LYS rotamer (chi angles: -76.9 86.2 96.3 -92.7) to
renamedAndRenumberedModel #2/Ks LYS 38
> swapaa #2/Ks:49 HIS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks TYR 49: phi -60.2, psi -39.2 trans
Applying HIS rotamer (chi angles: -177.8 70.7) to renamedAndRenumberedModel
#2/Ks HIS 49
> swapaa #2/Ks:51 ILE
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ASN 51: phi -70.5, psi -44.7 trans
Applying ILE rotamer (chi angles: -67.0 169.0) to renamedAndRenumberedModel
#2/Ks ILE 51
> swapaa #2/Ks:54 TRP
Using Dunbrack library
renamedAndRenumberedModel #2/Ks TYR 54: phi -78.9, psi -111.6 trans
Applying TRP rotamer (chi angles: -68.5 75.9) to renamedAndRenumberedModel
#2/Ks TRP 54
> swapaa #2/Ks:59 SER
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ALA 59: phi -71.7, psi -20.6 trans
Applying SER rotamer (chi angles: 68.0) to renamedAndRenumberedModel #2/Ks SER
59
> swapaa #2/Ks:60 MET
Using Dunbrack library
renamedAndRenumberedModel #2/Ks GLU 60: phi -57.0, psi -40.0 trans
Applying MET rotamer (chi angles: -179.6 -178.9 71.4) to
renamedAndRenumberedModel #2/Ks MET 60
> swapaa #2/Ks:63 LYS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ARG 63: phi -64.6, psi -41.6 trans
Applying LYS rotamer (chi angles: -176.8 176.7 78.9 -74.4) to
renamedAndRenumberedModel #2/Ks LYS 63
> swapaa #2/Ks:66 TRP
Using Dunbrack library
renamedAndRenumberedModel #2/Ks TYR 66: phi -61.3, psi -49.1 trans
Applying TRP rotamer (chi angles: 179.4 85.5) to renamedAndRenumberedModel
#2/Ks TRP 66
> swapaa #2/Ks:71 MET
Using Dunbrack library
renamedAndRenumberedModel #2/Ks LYS 71: phi -102.4, psi -39.1 trans
Applying MET rotamer (chi angles: -66.7 176.8 70.6) to
renamedAndRenumberedModel #2/Ks MET 71
> swapaa #2/Ks:74 GLU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks LYS 74: phi -70.7, psi -34.5 trans
Applying GLU rotamer (chi angles: -65.3 82.2 1.8) to renamedAndRenumberedModel
#2/Ks GLU 74
> swapaa #2/Ks:75 THR
Using Dunbrack library
renamedAndRenumberedModel #2/Ks VAL 75: phi -68.2, psi -36.5 trans
Applying THR rotamer (chi angles: -60.5) to renamedAndRenumberedModel #2/Ks
THR 75
> swapaa #2/Ks:81 GLU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ASN 81: phi -69.4, psi -28.9 trans
Applying GLU rotamer (chi angles: -68.1 -62.2 -46.6) to
renamedAndRenumberedModel #2/Ks GLU 81
> swapaa #2/Ks:85 ALA
Using Dunbrack library
Swapping renamedAndRenumberedModel #2/Ks SER 85 to ALA
> swapaa #2/Ks:86 LEU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks GLN 86: phi -68.3, psi -36.5 trans
Applying LEU rotamer (chi angles: -68.3 173.0) to renamedAndRenumberedModel
#2/Ks LEU 86
> swapaa #2/Ks:88 HIS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks PHE 88: phi -64.1, psi -21.0 trans
Applying HIS rotamer (chi angles: -70.1 -68.5) to renamedAndRenumberedModel
#2/Ks HIS 88
> swapaa #2/Ks:89 PHE
Using Dunbrack library
renamedAndRenumberedModel #2/Ks TYR 89: phi -112.7, psi 26.0 trans
Applying PHE rotamer (chi angles: -63.5 101.9) to renamedAndRenumberedModel
#2/Ks PHE 89
> swapaa #2/Ks:90 ASP
Using Dunbrack library
renamedAndRenumberedModel #2/Ks THR 90: phi -63.9, psi -27.6 trans
Applying ASP rotamer (chi angles: -171.5 -61.2) to renamedAndRenumberedModel
#2/Ks ASP 90
> swapaa #2/Ks:91 HIS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks PHE 91: phi -67.0, psi -37.9 trans
Applying HIS rotamer (chi angles: -70.4 -67.5) to renamedAndRenumberedModel
#2/Ks HIS 91
> swapaa #2/Ks:92 THR
Using Dunbrack library
renamedAndRenumberedModel #2/Ks VAL 92: phi -77.9, psi -37.6 trans
Applying THR rotamer (chi angles: 59.2) to renamedAndRenumberedModel #2/Ks THR
92
> swapaa #2/Ks:94 LEU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks GLN 94: phi -70.6, psi -89.8 trans
Applying LEU rotamer (chi angles: -179.8 62.1) to renamedAndRenumberedModel
#2/Ks LEU 94
> swapaa #2/Ks:95 TYR
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ARG 95: phi -146.6, psi 168.2 trans
Applying TYR rotamer (chi angles: 65.0 70.8) to renamedAndRenumberedModel
#2/Ks TYR 95
> swapaa #2/Ks:97 VAL
Using Dunbrack library
renamedAndRenumberedModel #2/Ks LEU 97: phi -90.8, psi 152.7 trans
Applying VAL rotamer (chi angles: -61.5) to renamedAndRenumberedModel #2/Ks
VAL 97
> swapaa #2/Ks:101 LYS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks GLU 101: phi -80.8, psi -43.8 trans
Applying LYS rotamer (chi angles: -176.8 175.1 78.9 -74.4) to
renamedAndRenumberedModel #2/Ks LYS 101
> swapaa #2/Ks:102 GLU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ASP 102: phi -96.8, psi 20.0 trans
Applying GLU rotamer (chi angles: -63.7 -179.0 54.9) to
renamedAndRenumberedModel #2/Ks GLU 102
> swapaa #2/Ks:103 PHE
Using Dunbrack library
renamedAndRenumberedModel #2/Ks TYR 103: phi -89.5, psi 90.1 trans
Applying PHE rotamer (chi angles: -172.0 76.2) to renamedAndRenumberedModel
#2/Ks PHE 103
> swapaa #2/Ks:104 GLU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks VAL 104: phi -72.3, psi 146.5 trans
Applying GLU rotamer (chi angles: -64.3 85.3 -8.7) to
renamedAndRenumberedModel #2/Ks GLU 104
> swapaa #2/Ks:107 TYR
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ARG 107: phi -92.5, psi 75.5 trans
Applying TYR rotamer (chi angles: 63.9 33.5) to renamedAndRenumberedModel
#2/Ks TYR 107
> swapaa #2/Ks:108 GLN
Using Dunbrack library
renamedAndRenumberedModel #2/Ks THR 108: phi -68.1, psi 135.6 trans
Applying GLN rotamer (chi angles: 62.8 84.2 86.5) to renamedAndRenumberedModel
#2/Ks GLN 108
> swapaa #2/Ks:111 LYS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ARG 111: phi -62.5, psi 138.3 trans
Applying LYS rotamer (chi angles: -67.4 -178.7 -179.6 179.2) to
renamedAndRenumberedModel #2/Ks LYS 111
> swapaa #2/Ks:113 ASN
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ARG 113: phi -108.4, psi -26.8 trans
Applying ASN rotamer (chi angles: -65.8 138.0) to renamedAndRenumberedModel
#2/Ks ASN 113
> swapaa #2/Ks:115 LYS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ILE 115: phi -70.9, psi 159.0 trans
Applying LYS rotamer (chi angles: 65.1 87.7 74.0 79.6) to
renamedAndRenumberedModel #2/Ks LYS 115
> swapaa #2/Ks:119 GLU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks PRO 119: phi -73.4, psi -37.3 trans
Applying GLU rotamer (chi angles: -66.4 80.3 36.8) to
renamedAndRenumberedModel #2/Ks GLU 119
> swapaa #2/Ks:125 ASP
Using Dunbrack library
renamedAndRenumberedModel #2/Ks GLY 125: phi 58.3, psi 41.2 trans
Applying ASP rotamer (chi angles: -64.2 -34.2) to renamedAndRenumberedModel
#2/Ks ASP 125
> swapaa #2/Ks:129 LEU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ARG 129: phi -71.6, psi -109.9 trans
Applying LEU rotamer (chi angles: -179.8 62.5) to renamedAndRenumberedModel
#2/Ks LEU 129
> swapaa #2/Ks:135 ALA
Using Dunbrack library
Swapping renamedAndRenumberedModel #2/Ks GLY 135 to ALA
> swapaa #2/Ks:139 GLU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ASP 139: phi -91.5, psi -32.9 trans
Applying GLU rotamer (chi angles: -170.7 -83.6 62.5) to
renamedAndRenumberedModel #2/Ks GLU 139
> swapaa #2/Ks:143 ILE
Using Dunbrack library
renamedAndRenumberedModel #2/Ks ASN 143: phi -71.4, psi -14.5 trans
Applying ILE rotamer (chi angles: -67.4 168.7) to renamedAndRenumberedModel
#2/Ks ILE 143
> swapaa #2/Ks:145 HIS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks TYR 145: phi -64.8, psi -40.8 trans
Applying HIS rotamer (chi angles: -177.8 -18.8) to renamedAndRenumberedModel
#2/Ks HIS 145
> swapaa #2/Ks:146 ASP
Using Dunbrack library
renamedAndRenumberedModel #2/Ks GLU 146: phi -71.1, psi -32.2 trans
Applying ASP rotamer (chi angles: -71.2 -15.9) to renamedAndRenumberedModel
#2/Ks ASP 146
> swapaa #2/Ks:147 MET
Using Dunbrack library
renamedAndRenumberedModel #2/Ks LEU 147: phi -76.1, psi -35.1 trans
Applying MET rotamer (chi angles: -67.5 176.5 70.8) to
renamedAndRenumberedModel #2/Ks MET 147
> swapaa #2/Ks:148 PHE
Using Dunbrack library
renamedAndRenumberedModel #2/Ks TYR 148: phi -98.8, psi -32.3 trans
Applying PHE rotamer (chi angles: -66.6 102.8) to renamedAndRenumberedModel
#2/Ks PHE 148
> swapaa #2/Ks:149 VAL
Using Dunbrack library
renamedAndRenumberedModel #2/Ks THR 149: phi -96.8, psi -31.3 trans
Applying VAL rotamer (chi angles: 174.9) to renamedAndRenumberedModel #2/Ks
VAL 149
> swapaa #2/Ks:150 LEU
Using Dunbrack library
renamedAndRenumberedModel #2/Ks LYS 150: phi -90.7, psi -23.4 trans
Applying LEU rotamer (chi angles: -62.6 176.2) to renamedAndRenumberedModel
#2/Ks LEU 150
> swapaa #2/Ks:152 LYS
Using Dunbrack library
renamedAndRenumberedModel #2/Ks GLN 152: phi -89.2, psi 125.7 trans
Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to
renamedAndRenumberedModel #2/Ks LYS 152
> swapaa #2/Ks:155 VAL
Using Dunbrack library
renamedAndRenumberedModel #2/Ks LYS 155: phi -62.5, psi -58.3 trans
Applying VAL rotamer (chi angles: 171.9) to renamedAndRenumberedModel #2/Ks
VAL 155
> swapaa #2/Ks:156 ALA
Using Dunbrack library
Swapping renamedAndRenumberedModel #2/Ks VAL 156 to ALA
> hide sel atoms
> show sel cartoons
> select all
249012 atoms, 253392 bonds, 12 pseudobonds, 30014 residues, 5 models selected
> hide sel atoms
> show sel cartoons
> select clear
> hide #!3 models
> hide #!2 models
> hide #1 models
> show #!2 models
> select ~/Ks
245514 atoms, 249766 bonds, 12 pseudobonds, 29617 residues, 5 models selected
> hide sel & #!2 cartoons
> show #!3 models
> hide #!2 models
> show #1 models
> hide #1 models
> hide sel & #!3 cartoons
> show #1 models
> hide #1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> select /Ks
3498 atoms, 3626 bonds, 397 residues, 3 models selected
> show sel & #!3 atoms
> style sel & #!3 stick
Changed 1351 atom styles
> select clear
> select /Ks
3498 atoms, 3626 bonds, 397 residues, 3 models selected
> hide sel & #!3 cartoons
> bond #2/Ks:94@C #2/Ks:95@N reasonable false
Created 0 bonds
> color sel & #!3 byhetero
> bond #2/Ks:94@C #2/Ks:95@N reasonable false
Created 0 bonds
> show #!2 models
> hide #!2 models
> select mutadedModel
Expected an objects specifier or a keyword
> select #mutadedModel
Expected an objects specifier or a keyword
> select #mutadedModel
Expected an objects specifier or a keyword
> select mutadedModel
Expected an objects specifier or a keyword
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 11, in
models = models.all_models(session)
^^^^^^^^^^^^^^^^^
AttributeError: module 'chimerax.core.models' has no attribute 'all_models'
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 11, in
models = models.model.all_models(session)
^^^^^^^^^^^^
AttributeError: module 'chimerax.core.models' has no attribute 'model'
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 11, in
modelsasd = models.all_models(session)
^^^^^^^^^^^^^^^^^
AttributeError: module 'chimerax.core.models' has no attribute 'all_models'
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 11, in
modelsasd = models(session)
^^^^^^^^^^^^^^^
TypeError: 'module' object is not callable
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> ui tool show Log
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 11, in
modelsasd = models.Model.all_models(session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 326, in all_models
for d in self.child_drawings():
^^^^^^^^^^^^^^^^^^^
AttributeError: 'Session' object has no attribute 'child_drawings'
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 11, in
modelsasd = models.Model.all_models()
^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: Model.all_models() missing 1 required positional argument: 'self'
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> select all
249012 atoms, 253392 bonds, 12 pseudobonds, 30014 residues, 5 models selected
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 11, in
modelsasd = models.Model.all_models(session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/rafaelrocha/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 326, in all_models
for d in self.child_drawings():
^^^^^^^^^^^^^^^^^^^
AttributeError: 'Session' object has no attribute 'child_drawings'
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> select all
249012 atoms, 253392 bonds, 12 pseudobonds, 30014 residues, 5 models selected
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 11, in
modelsasd = models.Models.all_models(session)
^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: type object 'Models' has no attribute 'all_models'
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> select all
249012 atoms, 253392 bonds, 12 pseudobonds, 30014 residues, 5 models selected
mutadedModel
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> select all
249012 atoms, 253392 bonds, 12 pseudobonds, 30014 residues, 5 models selected
None
> select clear
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
None
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
mutadedModel
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
[]
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 11, in
modelsasd = models.Model('mutadedModel',session).id_string()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'str' object is not callable
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
mutadedModel
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
None
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
None
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 14, in
for i in objt:
TypeError: 'AllObjects' object is not iterable
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
Traceback (most recent call last):
File "/Users/rafaelrocha/GitHub/KRSPs/teste.py", line 13, in
objt = session.models.all_models()
^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'Models' object has no attribute 'all_models'
Error opening python file /Users/rafaelrocha/GitHub/KRSPs/teste.py
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
[,
,
,
,
]
> runscript /Users/rafaelrocha/GitHub/KRSPs/teste.py
[,
,
,
,
]
cryosparc_P43_J436_002_volume_map_sharp_NOSEQFixed.cif #1
renamedAndRenumberedModel #2
missing structure #2.1
mutadedModel #3
missing structure #3.1
> close #3
> show #1 models
> close #2
> runscript
> /Users/rafaelrocha/GitHub/KRSPs/modelangeloScripts/renameAndRenumberChainsChimeraX.py
> #1 alignmentsModCorrected.txt
['4', '91']
['4', '91']
['1', '23']
['1', '23']
['1', '33']
['1', '33']
['3', '12']
['3', '12']
['1', '84']
['1', '84']
['3', '6']
['3', '6']
['3', '93']
['3', '93']
['5', '38']
['5', '38']
['1', '38']
['1', '38']
['3', '101']
['3', '101']
['2', '12']
['2', '12']
['1', '13']
['1', '13']
['1', '45']
['1', '45']
['1', '9']
['1', '9']
['11']
['1', '1']
['2', '17']
['2', '17']
['1', '3']
['1', '3']
['1', '59']
['1', '59']
['1', '34']
['1', '34']
['4', '57']
['4', '57']
['12']
['1', '2']
['11']
['1', '1']
['1', '4']
['1', '4']
['4', '10']
['4', '10']
['1', '39']
['1', '39']
['1', '127']
['1', '127']
['1', '4']
['1', '4']
['8', '304']
['8', '304']
['7', '17']
['7', '17']
['1', '68']
['1', '68']
['3', '92']
['3', '92']
['1', '25']
['1', '25']
['1', '47']
['1', '47']
['3', '53']
['3', '53']
['1', '11']
['1', '11']
['7', '43']
['7', '43']
['2', '11']
['2', '11']
['1', '7']
['1', '7']
['1', '8']
['1', '8']
['1', '3']
['1', '3']
['1', '20']
['1', '20']
['1', '16']
['1', '16']
['1', '26']
['1', '26']
['4', '35']
['4', '35']
['1', '4']
['1', '4']
['11']
['1', '1']
['12']
['1', '2']
['1', '3']
['1', '3']
['12']
['1', '2']
['11']
['1', '1']
['4', '59']
['4', '59']
['1', '17']
['1', '17']
['1', '11']
['1', '11']
['1', '6']
['1', '6']
['1', '8']
['1', '8']
['12']
['1', '2']
['1', '5']
['1', '5']
['1', '5']
['1', '5']
['1', '5']
['1', '5']
['1', '3']
['1', '3']
['1', '10']
['1', '10']
['1', '17']
['1', '17']
['1', '3']
['1', '3']
['1', '18']
['1', '18']
['1', '15']
['1', '15']
['1', '3']
['1', '3']
['1', '9']
['1', '9']
['3', '33']
['3', '33']
['1', '16']
['1', '16']
['1', '20']
['1', '20']
['1', '5']
['1', '5']
['11']
['1', '1']
['11']
['1', '1']
['11']
['1', '1']
['11']
['1', '1']
['1', '11']
['1', '11']
['4', '24']
['4', '24']
['1', '13']
['1', '13']
['12']
['1', '2']
['1', '4']
['1', '4']
['1', '6']
['1', '6']
['1', '12']
['1', '12']
['2', '46']
['2', '46']
['1', '25']
['1', '25']
['1', '64']
['1', '64']
['9', '13']
['9', '13']
['1', '43']
['1', '43']
['25', '72']
['25', '72']
['1', '6']
['1', '6']
['4', '41']
['4', '41']
['1', '159']
['1', '159']
['1', '24']
['1', '24']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['11']
['1', '1']
['1', '6']
['1', '6']
['1', '24']
['1', '24']
['1', '6']
['1', '6']
['11']
['1', '1']
['11']
['1', '1']
['11']
['1', '1']
['1', '19']
['1', '19']
['1', '21']
['1', '21']
['2', '12']
['2', '12']
['1', '12']
['1', '12']
['1', '128']
['1', '128']
['1', '44']
['1', '44']
['1', '48']
['1', '48']
['2', '32']
['2', '32']
['1', '13']
['1', '13']
['1', '14']
['1', '14']
['1', '6']
['1', '6']
['1', '4']
['1', '4']
['1', '3']
['1', '3']
['11']
['1', '1']
['11']
['1', '1']
['4', '21']
['4', '21']
['1', '46']
['1', '46']
['4', '24']
['4', '24']
['1', '3']
['1', '3']
['2', '16']
['2', '16']
['1', '4']
['1', '4']
['1', '49']
['1', '49']
['11']
['1', '1']
['11']
['1', '1']
['1', '6']
['1', '6']
['2', '92']
['2', '92']
['1', '3']
['1', '3']
['1', '5']
['1', '5']
['11']
['1', '1']
['1', '108']
['1', '108']
['2', '40']
['2', '40']
['1316']
['1', '3', '1', '6']
['1', '50']
['1', '50']
['1', '12']
['1', '12']
['3', '14']
['3', '14']
['1', '7']
['1', '7']
['1', '4']
['1', '4']
['1', '14']
['1', '14']
['1', '20']
['1', '20']
['2', '55']
['2', '55']
['8', '43']
['8', '43']
['7', '52']
['7', '52']
['1', '5']
['1', '5']
['3', '37']
['3', '37']
['2', '41']
['2', '41']
['1', '49']
['1', '49']
['2', '105']
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['3', '33']
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['5', '25']
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['309', '337']
['309', '337']
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['6', '62']
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['1', '27']
['1', '27']
['1', '16']
['1', '16']
['2', '20']
['2', '20']
['11']
['1', '1']
['11']
['1', '1']
['11']
['1', '1']
['1', '7']
['1', '7']
['2', '8']
['2', '8']
['1', '13']
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['1', '10']
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['1', '6']
['1', '11']
['1', '11']
['1', '26']
['1', '26']
['1', '12']
['1', '12']
['12']
['1', '2']
['1', '12']
['1', '12']
['12']
['1', '2']
['11']
['1', '1']
['11']
['1', '1']
['1', '60']
['1', '60']
['1', '4']
['1', '4']
['12']
['1', '2']
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['2', '30']
['1', '20']
['1', '20']
['12']
['1', '2']
['1', '11']
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['12']
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['1', '6']
['1', '6']
['1', '8']
['1', '8']
['12']
['1', '2']
['19', '23']
['19', '23']
['5', '68']
['5', '68']
['2', '112']
['2', '112']
['2', '29']
['2', '29']
['1', '88']
['1', '88']
['1', '8']
['1', '8']
['12']
['1', '2']
['1', '9']
['1', '9']
['1', '3']
['1', '3']
['4', '80']
['4', '80']
['2', '25']
['2', '25']
['12']
['1', '2']
['12']
['1', '2']
['1', '10']
['1', '10']
['1', '33']
['1', '33']
['1', '24']
['1', '24']
['1', '27']
['1', '27']
['1', '49']
['1', '49']
['2', '25']
['2', '25']
['1', '24']
['1', '24']
['1', '4']
['1', '4']
['12']
['1', '2']
['1', '4']
['1', '4']
['1', '14']
['1', '14']
['2', '37']
['2', '37']
['12']
['1', '2']
['12']
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['1', '175']
['5', '199']
['5', '199']
['1', '36']
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['4', '30']
['4', '30']
['1', '18']
['1', '18']
['12', '64']
['12', '64']
['1', '30']
['1', '30']
['1', '7']
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['1', '50']
['1', '308']
['1', '308']
['1', '8']
['1', '8']
['1', '4']
['1', '4']
['1', '44']
['1', '44']
['1', '43']
['1', '43']
['12']
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['11']
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['1', '21']
['1', '18']
['1', '18']
['1', '3']
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['11']
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['1', '21']
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['3', '27']
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['1', '10']
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['1', '7']
['2', '278']
['2', '278']
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['2', '15']
['1', '29']
['1', '29']
LtaP21.2040.mRNA-A
LtaP21.2040.mRNA-B
LtaP33.2260.mRNA-A
LtaP33.2260.mRNA-B
LtaP31.2040.mRNA
LtaP15.1010.mRNA
LtaP36.1760.mRNA-A
LtaP36.1760.mRNA-B
sp|P14544.1|COX1_LEITA-A
sp|P14544.1|COX1_LEITA-B
LtaP36.7290.mRNA-A
LtaP36.7290.mRNA-B
LtaP24.1770.mRNA
LtaP33.1170.mRNA-A
LtaP33.1170.mRNA-B
LtaP29.0960.mRNA
LtaP21.1790.mRNA
AAA31876.1-A
AAA31876.1-B
LtaP23.1700.mRNA
LtaP03.0910.mRNA
LtaP04.0630.mRNA-A
LtaP04.0630.mRNA-B
LtaP05.0500.mRNA
LtaP05.1110.mRNA
LtaP25.1190.mRNA-A
LtaP25.1190.mRNA-B
LtaP09.0030.mRNA-A
LtaP09.0030.mRNA-B
LtaP16.0500.mRNA
LtaP30.2840.mRNA
LtaP34.3980.mRNA
LtaP33.1260.mRNA
LtaP27.2160.mRNA
LtaP05.0800.mRNA
LtaP23.0450.mRNA
AAA31882.1
LtaP25.2210.mRNA
LtaP26.1720.mRNA
LtaP36.0470.mRNA
LtaP25.1690.mRNA
LtaP14.1460.mRNA
LtaP34.1060.mRNA
LtaP12.0690.mRNA
LtaP24.1430.mRNA
LtaP04.1180.mRNA
LtaP08.0840.mRNA
LdBPK_301100.1ReplacementOfLtaP30.1150.mRNA
LtaP32.0010.mRNA
LtaP27.0660.mRNA
AAA31877.1
LtaP22.1610.mRNA
> combine #1 close false name renamedAndRenumberedModel
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> set selectionWidth 4
Done loading forcefield
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
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: Mac15,6
Model Number: Z1AX002ENFN/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 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: 22 days, 3 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U3223QE:
Resolution: 6720 x 3780
UI Looks like: 3360 x 1890 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
ASUS VG278HE:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 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-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 (1)
comment:1 by , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
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