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Opened 3 years ago
Last modified 3 years ago
#8823 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Eric Pettersen, Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.19.0-38-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007f7c20e1bb80 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 838 in rapid_access_shown
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 860 in showEvent
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 551 in __init__
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 237 in build
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 691 in init
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open 20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-KSRP.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.264, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0965, step 1, values float32
Log from Mon Mar 27 09:38:45 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open 18-KSRP-no-C-ter-Step1-SevententhSubsteps-POST-FIRST-SIM-ANN-KSRP.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.106, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0965, step 1, values float32
Log from Fri Mar 24 14:43:56 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open 12-KSRP-no-C-ter-Step1-twelventhSubsteps-
> simulatedAnnealingIn-u37-o55-region.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.166, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0727, step 1, values float32
Log from Fri Mar 17 17:24:40 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/11-KSRP-no-C-ter-Step1-EleventhSubsteps.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.166, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0727, step 1, values float32
Restoring stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
Log from Thu Mar 9 08:50:34 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open 9-KSRP-no-C-ter-Step1-NinthSubsteps.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.166, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0727, step 1, values float32
Log from Wed Mar 8 06:50:37 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open 8-KSRP-no-C-ter-Step1-EightenthSubsteps.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.166, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0727, step 1, values float32
Log from Mon Mar 6 10:45:08 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open 4-KSRP-no-C-ter-Step1-FourthSubsteps.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.166, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0727, step 1, values float32
Log from Thu Mar 2 07:30:34 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open 3-KSRP-no-C-ter-Step1-ThirdSubsteps.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.166, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0727, step 1, values float32
Log from Wed Mar 1 11:53:58 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 5opt-concatenated-Map-Mut8-40S-noCter.pdb
Chain information for 5opt-concatenated-Map-Mut8-40S-noCter.pdb #1
---
Chain | Description
E | No description available
L | No description available
M | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
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
r | No description available
t | No description available
u | No description available
> hide
> riboon
Unknown command: riboon
> ribbon
> set bgColor
Missing "bgColor" keyword's argument
> set bgColor white
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> Mut8_40S-concatenated-5opt.mrc
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #2, grid size 400,400,400, pixel
1.16, shown at level 0.131, step 2, values float32
> clipper associate #2 toModel #1
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.436, step 1, values float32
Chain information for 5opt-concatenated-Map-Mut8-40S-noCter.pdb
---
Chain | Description
1.2/E | No description available
1.2/L | No description available
1.2/M | No description available
1.2/O | No description available
1.2/P | No description available
1.2/Q | No description available
1.2/R | No description available
1.2/S | No description available
1.2/T | No description available
1.2/U | No description available
1.2/V | No description available
1.2/W | No description available
1.2/X | No description available
1.2/Y | No description available
1.2/Z | No description available
1.2/a | No description available
1.2/b | No description available
1.2/c | No description available
1.2/d | No description available
1.2/e | No description available
1.2/f | No description available
1.2/g | No description available
1.2/h | No description available
1.2/i | No description available
1.2/j | No description available
1.2/k | No description available
1.2/l | No description available
1.2/m | No description available
1.2/n | No description available
1.2/o | No description available
1.2/p | No description available
1.2/q | No description available
1.2/r | No description available
1.2/t | No description available
1.2/u | No description available
> view #1/h:210-220
> volume gaussian #1 bfactor 150
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #2, grid size
400,400,400, pixel 1.16, shown at step 1, values float32
> clipper associate #2 toModel #1
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at step 1, values float32
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 475 residues in model #1.2 to IUPAC-IUB
standards.
> select clear
> addh
Summary of feedback from adding hydrogens to 5opt-concatenated-Map-
Mut8-40S-noCter.pdb #1.2
---
notes | No usable SEQRES records for 5opt-concatenated-Map-Mut8-40S-noCter.pdb
(#1.2) chain E; guessing termini instead
No usable SEQRES records for 5opt-concatenated-Map-Mut8-40S-noCter.pdb (#1.2)
chain L; guessing termini instead
No usable SEQRES records for 5opt-concatenated-Map-Mut8-40S-noCter.pdb (#1.2)
chain M; guessing termini instead
No usable SEQRES records for 5opt-concatenated-Map-Mut8-40S-noCter.pdb (#1.2)
chain O; guessing termini instead
No usable SEQRES records for 5opt-concatenated-Map-Mut8-40S-noCter.pdb (#1.2)
chain P; guessing termini instead
30 messages similar to the above omitted
Chain-initial residues that are actual N termini: /L THR 2, /M THR 2, /O MET
1, /P MET 1, /Q VAL 3, /R VAL 2, /S ASP 5, /T MET 1, /U ASP 45, /V PHE 9, /W
GLU 22, /X HIS 11, /Y GLN 4, /Z GLY 2, /a ALA 41, /b MET 1, /c SER 7, /d LYS
37, /e THR 2, /f VAL 4, /g ILE 4, /h ASN 68, /i ALA 21, /j PRO 86, /k LYS 58,
/l GLN 15, /m LYS 6, /n LYS 7, /o ILE 12, /p TYR 5, /q ARG 20, /r LYS 10, /t
GLU 16, /u GLU 8
Chain-initial residues that are not actual N termini: /Z ASP 157
Chain-final residues that are actual C termini: /M ASN 143, /O ARG 190, /Q ARG
202, /S HIS 86, /U ARG 112, /a VAL 110, /c GLY 66, /e TYR 130, /i ARG 141, /q
ARG 57, /r ARG 149
Chain-final residues that are not actual C termini: /L ALA 259, /P LYS 249, /R
GLU 142, /T VAL 104, /V ARG 143, /W PRO 238, /X VAL 158, /Y GLY 126, /Z LEU
216, /Z HIS 116, /b GLY 164, /d LYS 259, /f PRO 210, /g LYS 86, /h ARG 220, /j
ALA 149, /k VAL 175, /l ILE 113, /m THR 205, /n LYS 99, /o ILE 151, /p VAL
314, /t ILE 134, /u ALA 127
6846 hydrogen bonds
Adding 'H' to /Z ASP 157
/L ALA 259 is not terminus, removing H atom from 'C'
/P LYS 249 is not terminus, removing H atom from 'C'
/R GLU 142 is not terminus, removing H atom from 'C'
/T VAL 104 is not terminus, removing H atom from 'C'
/V ARG 143 is not terminus, removing H atom from 'C'
18 messages similar to the above omitted
62353 hydrogens added
> isolde restrain ligands #1
> ui tool show "Ramachandran Plot"
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> ui tool show "Ramachandran Plot"
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 11 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde cisflip #1.2/U:83
Performing cistrans flip for 1 residues
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/U:83
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 2 time(s)]
> style #1/U:107|/U:110 spheres
Expected a keyword
> style #1/U:107|/U:110 sphere
Changed 39 atom styles
> style #1/U:107|/U:110|/T:48 sphere
Changed 51 atom styles
> style #1/U:107|/U:110|/T:48 stick
Changed 51 atom styles
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/U:83
24 atoms, 23 bonds, 1 residue, 1 model selected
> view #1/U:83
> select #1/U:83
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/U:83
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde cisflip #1.2/c:52
Performing cistrans flip for 1 residues
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-no-C-
> ter-Step1d1-firstSubsteps.csx.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-no-C-
> ter-Step1d1-firstSubsteps.pdb
> isolde cisflip #1.2/f:6
Performing cistrans flip for 1 residues
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde cisflip #1.2/h:76
Performing cistrans flip for 1 residues
ISOLDE: started sim
> isolde cisflip #1.2/h:76
Performing cistrans flip for 1 residues
> isolde cisflip #1.2/h:76
Performing cistrans flip for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde cisflip #1.2/h:90
Performing cistrans flip for 1 residues
ISOLDE: started sim
> isolde cisflip #1.2/h:92
Performing cistrans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
3 models selected
> select clear
3 models selected
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde cisflip #1.2/h:150
Performing cistrans flip for 1 residues
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde cisflip #1.2/h:205
Performing cistrans flip for 1 residues
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 6 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde cisflip #1.2/i:140
Performing cistrans flip for 1 residues
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde cisflip #1.2/k:142
Performing cistrans flip for 1 residues
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/2-KSRP-no-
> C-ter-Step1d1-SecondSubsteps.csx.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/2-KSRP-no-
> C-ter-Step1d1-SecondSubsteps.csx.pdb
> select #1/k:141-142
29 atoms, 29 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde cisflip #1.2/m:144
Performing cistrans flip for 1 residues
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 5 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 2 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde cisflip #1.2/r:136
Performing cistrans flip for 1 residues
ISOLDE: started sim
> select clear
[Repeated 4 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
[Repeated 2 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/3-KSRP-no-
> C-ter-Step1-ThirdSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
——— End of log from Wed Mar 1 11:53:58 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
> isolde restrain ligands #1
> select clear
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde cisflip #1.2/t:134
Performing cistrans flip for 1 residues
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Peptide bond must be mobile in the simulation!
> select clear
[Repeated 3 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
[Repeated 5 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 10 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 5 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/4-KSRP-no-C-ter-Step1-FourthSubsteps.pdb
> isolde restrain torsions #1/O:147-152
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select clear
> isolde sim resume
> isolde release torsions #1/O:152
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde release torsions #1/O:151
> select clear
[Repeated 4 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> select clear
> isolde release torsions #1/O:147-150
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/4-KSRP-no-C-ter-Step1-FourthSubsteps.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/4-KSRP-no-C-ter-Step1-FourthSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
——— End of log from Thu Mar 2 07:30:34 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
> select clear
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 3 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: stopped sim
Fetching CCD CTN from http://ligand-expo.rcsb.org/reports/C/CTN/CTN.cif
Fetching CCD DCZ from http://ligand-expo.rcsb.org/reports/D/DCZ/DCZ.cif
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/-KSRP-no-C-ter-Step1-FourthSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/5-KSRP-no-C-ter-Step1-FifthSubsteps.pdb
[Repeated 1 time(s)]
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/5-KSRP-no-C-ter-Step1-FifthSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> isolde sim start sel
Simulation already running!
> isolde sim resume
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/Q:40-46
132 atoms, 133 bonds, 7 residues, 1 model selected
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 2 time(s)]
> select #1/Q:37
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/Q:37
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/Q:43-44
33 atoms, 33 bonds, 2 residues, 1 model selected
> isolde sim pause
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/Q:42
17 atoms, 16 bonds, 1 residue, 1 model selected
> isolde sim resume
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> select #1/Q:42
17 atoms, 16 bonds, 1 residue, 1 model selected
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
[Repeated 1 time(s)]
> isolde cisflip sel
Performing cistrans flip for 1 residues
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/6-KSRP-no-C-ter-Step1-SixthSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/6-KSRP-no-C-ter-Step1-SixthSubsteps.pdb
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 4 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 7 time(s)]
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 4 time(s)]
> isolde sim pause
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/o:60
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Peptide bond must be mobile in the simulation!
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 4 time(s)]
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/a:47
16 atoms, 15 bonds, 1 residue, 1 model selected
> view #1/a:47
> view #1/o:63
[Repeated 1 time(s)]
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/7-KSRP-no-C-ter-Step1-SeventhSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/7-KSRP-no-C-ter-Step1-SeventhSubsteps.pdb
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Peptide bond must be mobile in the simulation!
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/p:43
24 atoms, 25 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> view sel
> select clear
> isolde sim start sel
Simulation already running!
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/p:43
24 atoms, 25 bonds, 1 residue, 1 model selected
> view #1/p:43
> select #1/p:43
24 atoms, 25 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/p:111
> select #1/p:111
12 atoms, 11 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> view sele
Expected an objects specifier or a view name or a keyword
> view sel
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 6 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/p:64
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/8-KSRP-no-C-ter-Step1-EightenthSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
——— End of log from Mon Mar 6 10:45:08 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
> select clear
> view #1/p:118
> view #1/p:161
> select #1/p:161
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/p:158-161|/p:167-171
150 atoms, 150 bonds, 9 residues, 1 model selected
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/p:158-161|/p:167-171
150 atoms, 150 bonds, 9 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1/p:158-161|/p:167-171
150 atoms, 150 bonds, 9 residues, 1 model selected
> select #1/p:158-171
223 atoms, 225 bonds, 14 residues, 1 model selected
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 5 time(s)]
> show target m
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde start
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/9-KSRP-no-C-ter-Step1-NinthSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
——— End of log from Wed Mar 8 06:50:37 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> style #1/r:116|/r:112 sphere
Changed 41 atom styles
> style #1/r:116|/r:112|/r:113 sphere
Changed 53 atom styles
> select clear
> style #1/r:116|/r:112|/r:113 stick
Changed 53 atom styles
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/r:121
> select #1/r:121
21 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 2 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/r:121
> select #1/r:121
21 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select #1/O:9
20 atoms, 20 bonds, 1 residue, 1 model selected
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1>O8-13
Expected an objects specifier or a keyword
> select #1/O:8-13
110 atoms, 112 bonds, 6 residues, 1 model selected
> select #1/O:10-11
36 atoms, 35 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/r:58-64|/O:1-15
358 atoms, 361 bonds, 22 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Unable to flip peptide bond after 50 rounds. Giving up.
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> view sel
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> select #1/r:58-64|/O:1-15
358 atoms, 361 bonds, 22 residues, 1 model selected
> select #1/r:42
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/r:42
> select #1/r:42
16 atoms, 15 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/r:58-64|/O:1-15
> select #1/r:58-64|/O:1-15
358 atoms, 361 bonds, 22 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/O:10
> select#1/O:10
Unknown command: select#1/O:10
> select #1/O:10
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/O:10
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/O:10
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
[Repeated 6 time(s)]
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/u:8-9
34 atoms, 33 bonds, 2 residues, 1 model selected
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/u:60-65|/u:8-12
180 atoms, 180 bonds, 11 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/10-KSRP-no-C-ter-Step1-tenthSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/10-KSRP-no-C-ter-Step1-tenthSubsteps.pdb
> select #1/u:47-54
123 atoms, 122 bonds, 8 residues, 1 model selected
> select clear
> select #1/u:57-67
162 atoms, 161 bonds, 11 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select #1/u:57-67
162 atoms, 161 bonds, 11 residues, 1 model selected
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/u:57-67
162 atoms, 161 bonds, 11 residues, 1 model selected
> select #1/u:57-71
223 atoms, 222 bonds, 15 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim start sel
Simulation already running!
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 5 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Peptide bond must be mobile in the simulation!
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim start sel
No atoms selected!
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> select #1/u:57-71
223 atoms, 222 bonds, 15 residues, 1 model selected
> select #1/u:57-71
223 atoms, 222 bonds, 15 residues, 1 model selected
> select #1/u:57-67
162 atoms, 161 bonds, 11 residues, 1 model selected
> select clear
> select #1/u:25
24 atoms, 23 bonds, 1 residue, 1 model selected
> view #1/u:25
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 4 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> select #1/u:57-67
162 atoms, 161 bonds, 11 residues, 1 model selected
> select #1/u:28-42
245 atoms, 247 bonds, 15 residues, 1 model selected
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> style #1 ribbon
Expected a keyword
> select #1/u:57-67
162 atoms, 161 bonds, 11 residues, 1 model selected
> select #1/u:28-42
245 atoms, 247 bonds, 15 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select #1/u:28-42
245 atoms, 247 bonds, 15 residues, 1 model selected
> select #1/o:53-56
68 atoms, 67 bonds, 4 residues, 1 model selected
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/u:28-42|/o:53-56|/u:43-47
400 atoms, 402 bonds, 24 residues, 1 model selected
> select #1/u:28-42|/o:53-56|/u:43-47
400 atoms, 402 bonds, 24 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
[Repeated 1 time(s)]reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1
144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select clear
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/11-KSRP-no-C-ter-Step1-EleventhSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
——— End of log from Thu Mar 9 08:50:34 2023 ———
opened ChimeraX session
> select #1/u:28-42|/o:53-56|/u:43-47
400 atoms, 402 bonds, 24 residues, 1 model selected
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
ISOLDE: created disulfide bonds between the following residues:
T78-T81
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/u:28-42|/o:53-56|/u:43-47
400 atoms, 402 bonds, 24 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select #1/u:36-50
229 atoms, 230 bonds, 15 residues, 1 model selected
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/u:12
17 atoms, 17 bonds, 1 residue, 1 model selected
> view #1/u:12
> select #1/u:12
17 atoms, 17 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/o:55
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 5 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> view #1/o:55
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/o:55|/o:37
39 atoms, 37 bonds, 2 residues, 1 model selected
> select #1/o:55|/o:37
39 atoms, 37 bonds, 2 residues, 1 model selected
> select #1/o:37
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/u:37A/o:55
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/u:37/o:55
38 atoms, 36 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde sim pause
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select clear
[Repeated 2 time(s)]
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 4 time(s)]
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up.
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> view #1/u:37
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> ui tool show ISOLDE
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
[Repeated 3 time(s)]
> ui tool show "Ramachandran Plot"
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Unable to flip peptide bond after 50 rounds. Giving up.
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> hide #!1.2 models
> show #!1.2 models
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 3 time(s)]
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/12-KSRP-no-C-ter-Step1-twelventhSubsteps-
> simulatedAnnealingIn-u37-o55-region.csx.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
——— End of log from Fri Mar 17 17:24:40 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
> select clear
> view #1/o:55
> select #1/o:55
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/o:55
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:49
> select #1/u:49
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/u:49
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde sim pause
3 models selected
[Repeated 1 time(s)]
> view #1
> view #1/u:49
> view #1/P
> ui tool show "Ramachandran Plot"
> view #1/u:49
> isolde sim resume
> ui tool show "Ramachandran Plot"
[Repeated 2 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:63
> select #1/u:63
15 atoms, 14 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:49
> select #1/u:49
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:43
> select #1/u:43
21 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> view #1/u:43
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> ui tool show "Ramachandran Plot"
> select clear
> view #1/u:43
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/13-KSRP-no-C-ter-Step1-thirtenthSubsteps.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/13-KSRP-no-C-ter-Step1-thirtenthSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> view #1/u:42|u:55
Expected an objects specifier or a view name or a keyword
> view #1/u:42|/u:55
> select #1/u:42|/u:55
34 atoms, 32 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/u:42|/u:55
34 atoms, 32 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
Unable to flip peptide bond after 50 rounds. Giving up.
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:43
> select #1/u:43
21 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:63
> select #1/u:63
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/u:63
15 atoms, 14 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> select #1/u:49
10 atoms, 9 bonds, 1 residue, 1 model selected
> view #1/u:49
> select #1/u:49
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/o:55
> select #1/o:55
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:12
> select #1/u:12
17 atoms, 17 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:28-42|/o:53-56|/u:43-47
> select #1/u:28-42|/o:53-56|/u:43-47
400 atoms, 402 bonds, 24 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
[Repeated 2 time(s)]
> isolde sim resume
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/u:35
22 atoms, 21 bonds, 1 residue, 1 model selected
> view #1/u:35
> select #1/u:35
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/u:35
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:25
> select #1/u:25
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:60-65|/u:8-12
> select #1/u:60-65|/u:8-12
180 atoms, 180 bonds, 11 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:12
> select sim start sel
Expected an objects specifier or a keyword
> view #1/u:12
> select #1/u:12
17 atoms, 17 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/4-KSRP-no-C-ter-Step1-FourtenthSubsteps-End1d1db.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/14-KSRP-no-C-ter-Step1-FourtenthSubsteps-End1d1db.pdb
> isolde cisflip #1.2/Q:137
Performing cistrans flip for 1 residues
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde cisflip sel
Performing cistrans flip for 1 residues
> isolde cisflip #1.2/Q:137
Performing cistrans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> view #1/Q:137
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FifttenthSubsteps.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FifttenthSubsteps.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> view #1/Q:137
> select #1/Q:137
14 atoms, 14 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/Q:181
19 atoms, 18 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/Q:137
> select #1/Q:137
14 atoms, 14 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde cisflip #1.2/O:156
Performing cistrans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/Q:137
[Repeated 1 time(s)]
> view #1/Q:156
> select #1/Q:156
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/O:156
14 atoms, 14 bonds, 1 residue, 1 model selected
> view #1/O:156
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde cisflip #1.2/Q:44
Performing cistrans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FivetenthSubsteps-Final-of-PART-1d1.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/16-KSRP-no-C-ter-Step1-FivetenthSubsteps-Final-of-PART-1d1.pdb
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
3 models selected
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> view #1/h:163
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> view #1/h:163
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde sim pause
> select #1/h:180|/h:184
28 atoms, 26 bonds, 2 residues, 1 model selected
> isolde sim start sel
Simulation already running!
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/17-KSRP-no-C-ter-Step1-SevententhSubstep.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/17-KSRP-no-C-ter-Step1-SevententhSubstep.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> isolde sim start sel
Simulation already running!
> isolde sim resume
> select clear
[Repeated 4 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select clear
> ui tool show "Ramachandran Plot"
> view #1/h:N183
No objects specified.
> view #1/h:183
> isolde sim pause
> isolde sim resume
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
[Repeated 1 time(s)]
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/h
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1/h:115-119
85 atoms, 84 bonds, 5 residues, 1 model selected
> select clear
> select #1/h:215-219
70 atoms, 69 bonds, 5 residues, 1 model selected
> select #1/h:152-155
61 atoms, 62 bonds, 4 residues, 1 model selected
> select #1/h:152-156
80 atoms, 81 bonds, 5 residues, 1 model selected
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> view #1/P:244
> view #1/h
> ui tool show "Ramachandran Plot"
3 models selected
[Repeated 2 time(s)]
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> select clear
3 models selected
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim resume
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Unable to flip peptide bond after 50 rounds. Giving up.
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 3 time(s)]
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
[Repeated 5 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> ui tool show "Ramachandran Plot"
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> ui tool show "Ramachandran Plot"
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 3 time(s)]
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
[Repeated 2 time(s)]Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 13 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
[Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select clear
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> style #1/h:84|/h:125 sphere
Changed 39 atom styles
> style #1/h:84|/h:125 stick
Changed 39 atom styles
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/18-KSRP-no-C-ter-Step1-SevententhSubsteps-POST-FIRST-SIM-ANN-
> KSRP.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
——— End of log from Fri Mar 24 14:43:56 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
> isolde restrain ligands #1
> select clear
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 2 time(s)]
> isolde sim pause
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/19a-Test-KSRP-Env-System-on-the-middle-of-
> overFittingTo-6Times-densityField.pdb
> isolde sim resume
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim pause
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/19b-Test-KSRP-Env-System-on-the-overFittingTo-6Times-
> densityFieldSmoth-NoSmoth.pdb
> isolde sim resume
> ui tool show "Ramachandran Plot"
[Repeated 4 time(s)]
> isolde sim pause
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/19c-Test-KSRP-Env-System-After-the-overFittingTo-6Times-And-
> ComeBack-to-Default.pdb
> isolde sim resume
> ui tool show "Ramachandran Plot"
[Repeated 3 time(s)]
> select clear
[Repeated 3 time(s)]
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 2 time(s)]
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
[Repeated 2 time(s)]
> ui tool show "Ramachandran Plot"
[Repeated 2 time(s)]
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
> KSRP.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
> KSRP.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
——— End of log from Mon Mar 27 09:38:45 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
> select clear
> view #1/P:240-249
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/
Expected an objects specifier or a keyword
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/P:220-249
503 atoms, 505 bonds, 30 residues, 1 model selected
> select #1/P:220-249
503 atoms, 505 bonds, 30 residues, 1 model selected
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> select #1/P
4114 atoms, 4139 bonds, 249 residues, 1 model selected
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> select #1/P:236-249
221 atoms, 221 bonds, 14 residues, 1 model selected
> isolde sim resume
> isolde sim pause
> select #1/P:220-249
503 atoms, 505 bonds, 30 residues, 1 model selected
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> select clear
> select #1/P
4114 atoms, 4139 bonds, 249 residues, 1 model selected
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/22b-Second-Point-Previous-Sim-Ann-C-ter-ChainP.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/22b-Second-Point-Previous-Sim-Ann-C-ter-ChainP.pdb
> close
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
> KSRP.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.264, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0965, step 1, values float32
Restoring stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
opened ChimeraX session
> isolde start
> view #1/P:240-249
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> select clear
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/22c-third-Point-Previous-Sim-Ann-C-ter-ChainP.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/22c-third-Point-Previous-Sim-Ann-C-ter-ChainP.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> close
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
> KSRP.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.264, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0965, step 1, values float32
Restoring stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
opened ChimeraX session
> isolde start
> ui tool show "Ramachandran Plot"
> view #1/P:240-249
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/V:92
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/V:92
> select #1/V:92
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> style #1/i:72|/i:75 sphere
Changed 37 atom styles
> style #1/i:72|/i:75 stick
Changed 37 atom styles
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-continuingNew-FirstSteps-RefiningBEFORE-Annealing.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
> KSRP.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-continuingNew-FirstSteps-RefiningBEFORE-Annealing.pdb
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> view #1/d:155
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-1-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-1.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-1-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-1.pdb
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> view #1/q:29
> isolde sim pause
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> isolde sim resume
> isolde sim pause
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> style #1/q:34|/q:39 sphere
Changed 38 atom styles
> style #1/q:34|/q:39 stick
Changed 38 atom styles
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> style #1/q:34|/q:39|/q:32 sphere
Changed 57 atom styles
> style #1/q:34|/q:39|/q:32 stick
Changed 57 atom styles
> ui tool show "Ramachandran Plot"
> isolde sim resume
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> style #1/q:23-24 sphere
Changed 35 atom styles
> style #1/q:23-24 stick
Changed 35 atom styles
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-2-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-2.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-2-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-2.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> isolde sim resume
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> isolde sim pause
> view #1/q:24
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> style #1/i:23-24|/n:68 sphere
Changed 53 atom styles
> style #1/i:23-24|/n:68 stick]
Expected a keyword
> style #1/i:23-24|/n:68 stick
Changed 53 atom styles
> style #1/q:23-24|/n:68 sphere
Changed 59 atom styles
> style #1/q:23-24|/n:68 stick
Changed 59 atom styles
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/q:41
> select #1/q:41
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/q:41
> select #1/q:41
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> isolde sim resume
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/o:74-81|/o:12
140 atoms, 138 bonds, 9 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Multiple residues selected! Going to the first...
> view #1/o:74
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> view #1/o:74
> select clear
> ui tool show "Ramachandran Plot"
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> view #1/o:74
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> view #1/o:74
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/o:74
> view #1/o:74-81|/o:12
> select #1/o:74-81|/o:12
140 atoms, 138 bonds, 9 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/o:74
11 atoms, 10 bonds, 1 residue, 1 model selected
> view #1/o:74
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> view #1/l:33
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/l:33
> select #1/l:33
17 atoms, 16 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/l:33
> select #1/l:33
17 atoms, 16 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-3-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-3-afterStep1d2.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-3-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-3-afterStep1d2.pdb
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim pause
> select clear
> isolde sim resume
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/u:100-109
161 atoms, 160 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/u:115-116
43 atoms, 42 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> view #1/u:115-116
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/t:127-131
85 atoms, 85 bonds, 5 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/t:107-111
85 atoms, 85 bonds, 5 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
3 models selected
> select clear
> isolde sim resume
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-4-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-4.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-4-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-4.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/t:86
> select #1/t:86
17 atoms, 17 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/t:125
> select #1/t:125
15 atoms, 14 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/t:60-61
24 atoms, 24 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> view #1/t:55
> select #1/t:55
17 atoms, 17 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/t:47]
No objects specified.
> view #1/t:47
> select #1/t:47
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/t:125
> select #1/t:125
15 atoms, 14 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/t:125
15 atoms, 14 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/t:86
17 atoms, 17 bonds, 1 residue, 1 model selected
> view #1/t:86
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:87
> select #1/u:87
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/t:107-111
> select #1/t:107-111
85 atoms, 85 bonds, 5 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim pause
> view #1/t:100
> select #1/t:100
16 atoms, 15 bonds, 1 residue, 1 model selected
> isolde sim start sel
Simulation already running!
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/t:100
16 atoms, 15 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/t:100
16 atoms, 15 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/t:80|t:75
Expected an objects specifier or a keyword
> select #1/t:80|/t:75
36 atoms, 35 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/t:80
> select #1/t:80
14 atoms, 14 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/t:100
> select #1/t:100
16 atoms, 15 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/t:107-111
> select #1/t:107-111
85 atoms, 85 bonds, 5 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/t:127-131
> select #1/t:127-131
85 atoms, 85 bonds, 5 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:115-116
> select #1/u:115-116
43 atoms, 42 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/u:100-109
> select #1/u:100-109
161 atoms, 160 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> view #1/u:101
> select #1/u:101
11 atoms, 10 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-5-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-5.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-5-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-5.pdb
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-6-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-6-fixedNewTwistedBonds.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-6-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-6-fixedNewTwistedBonds.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> view #1/f:43
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/k:137
> select #1/k:137
17 atoms, 16 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/k:142
> select #1/k:142
15 atoms, 14 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/k:149
> select #1/k:149
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> isolde sim resume
> select clear
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/Z:116
> select #1/Z:116
17 atoms, 17 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/Z:69
> select #1/Z:69
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/W:111-113
61 atoms, 61 bonds, 3 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/W:119
24 atoms, 25 bonds, 1 residue, 1 model selected
> view #1/W:119
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/W:119
> select #1/W:119
24 atoms, 25 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> ui tool show "Ramachandran Plot"
> ui tool show "Build Structure"
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/f:9
22 atoms, 21 bonds, 1 residue, 1 model selected
> view #1/f:9
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/f:9
> select #1/f:9
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> view #1/O:69
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/f:9
> select #1/f:9
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/W:159
> select #1/W:159
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> select clear
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
> isolde sim pause
> select #1/n:91-94
55 atoms, 55 bonds, 4 residues, 1 model selected
> isolde sim start sel
Simulation already running!
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/n:91-94
55 atoms, 55 bonds, 4 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/n:88
20 atoms, 20 bonds, 1 residue, 1 model selected
> view #1/n:88
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> select #1/n:88|/i:40
36 atoms, 35 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> style #1/i:38-39|/n:86 sphere
Changed 60 atom styles
> style #1/i:38-39|/n:86|/i:36-40 sphere
Changed 109 atom styles
> style #1/i:38-39|/n:86|/i:36-40|n:88-90 sphere
Expected a keyword
> style #1/i:38-39|/n:86|/i:36-40|/n:88-90 sphere
Changed 162 atom styles
> style #1/i:38-39|/n:86|/i:36-40|/n:88-90 stick
Changed 162 atom styles
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/n:88
20 atoms, 20 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/m:140
> select #1/m:140
22 atoms, 21 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/m:178
10 atoms, 9 bonds, 1 residue, 1 model selected
> view #1/m:178
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde sim pause
> select #1/L:13|/L:16
39 atoms, 37 bonds, 2 residues, 1 model selected
> isolde sim start sel
Simulation already running!
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/L:13|/L:16
39 atoms, 37 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/L:13|/L:16
> select #1/L:13|/L:16
39 atoms, 37 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/L:21
> select #1/L:21
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> select #1/l:103|/l:107
35 atoms, 33 bonds, 2 residues, 1 model selected
> isolde sim start sel
Simulation already running!
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/l:103|/l:107
35 atoms, 33 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/l:103|/l:107|/l:97|/l:95|/m:41
87 atoms, 82 bonds, 5 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/l:91|/l:93
29 atoms, 28 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/l:91|/l:93
29 atoms, 28 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/R89
Nothing selected
> select #1/R:89
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/l:89
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim resume
> select clear
> select #1/l:88-87
Nothing selected
> isolde sim pause
> select #1/l:88-87
Nothing selected
> select #1/l:88-90
53 atoms, 52 bonds, 3 residues, 1 model selected
> isolde sim resume
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/l:103|/l:107|/l:97|/l:95|/m:41
> select #1/l:103|/l:107|/l:97|/l:95|/m:41
87 atoms, 82 bonds, 5 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/l:103|/l:107
35 atoms, 33 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/m:39
24 atoms, 23 bonds, 1 residue, 1 model selected
> view #1/m:39
> view #1/m:38
> select #1/m:38
17 atoms, 17 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/m:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> view #1/m:42
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-7-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-7-FinishedStep1d2dC.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-7-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-7-FinishedStep1d2dC.pdb
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/S:59-64
83 atoms, 82 bonds, 6 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/S:59-64
> view #1/S:53
> select #1/S:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> style #1/X:94|/E:395 sphere
Changed 56 atom styles
> style #1/X:94|/E:394-395 sphere
Changed 90 atom styles
> style #1/X:94|/E:394-395 sticks
Expected a keyword
> style #1/X:94|/E:394-395 stick
Changed 90 atom styles
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> view #1/h:102
> select #1/h:102
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/h:102
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/h:102
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim pause
> isolde sim resume
> select #1/h
2451 atoms, 2474 bonds, 153 residues, 1 model selected
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> style #1/j:119|/j:115 sphere
Changed 39 atom styles
> style #1/j:119|/j:115 stick
Changed 39 atom styles
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim pause
> view #1/u:55
> select #1/u:55
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/u:55
24 atoms, 23 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 1009, in _sim_end_cb
run(self.session, f'clipper spot #{self.selected_model.id_string}', log=False)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/cmd.py", line 109, in spotlight
sh = get_symmetry_handler(m, create=create, auto_add_to_session=True)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler
sh = _get_symmetry_handler(structure, create)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler
return SymmetryManager(structure.session, model=structure)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 594, in __init__
self.add_model(model, ignore_model_symmetry=ignore_model_symmetry,
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 649, in add_model
self.set_default_atom_display(mode=self._hydrogen_mode)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 922, in set_default_atom_display
atoms = model.atoms
AttributeError: 'NoneType' object has no attribute 'atoms'
Error processing trigger "sim terminated":
AttributeError: 'NoneType' object has no attribute 'atoms'
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 922, in set_default_atom_display
atoms = model.atoms
See log for complete Python traceback.
> ui tool show "Ramachandran Plot"
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-8-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-8.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-8-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-8.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> ui tool show "Ramachandran Plot"
> help help:quickstart
> close
Deleting atomic symmetry model...
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/1-KSRP-no-C-ter-Step1d1-firstSubsteps.csx.cxs
Deleting atomic symmetry model...
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.166, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.0727, step 1, values float32
Restoring stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
opened ChimeraX session
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
ISOLDE: created disulfide bonds between the following residues:
T78-T81
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> close
Deleting atomic symmetry model...
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-8-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
> step20-8.cxs
Deleting atomic symmetry model...
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.207, step 1, values float32
Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
400,400,400, pixel 1.16, shown at level 0.126, step 1, values float32
Restoring stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
opened ChimeraX session
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> view #1/P:140-149
> view #1/P:240-249
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Deleting atomic symmetry model...
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
Deleting atomic symmetry model...
> view #1/u:57-70
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim resume
Deleting atomic symmetry model...
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
Deleting atomic symmetry model...
> select clear
Deleting atomic symmetry model...
Deleting atomic symmetry model...
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> select clear
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> select clear
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> ui tool show "Ramachandran Plot"
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select clear
> select #1]
Expected an objects specifier or a keyword
> select #1]
Expected an objects specifier or a keyword
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> hide #!1.2 models
> show #!1.2 models
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> ui tool show "Ramachandran Plot"
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select clear
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> ui tool show "Ramachandran Plot"
> select clear
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> select #1/u:62-61
Nothing selected
> select #1/u:62-61
Nothing selected
> select #1/u:61-62
24 atoms, 23 bonds, 2 residues, 1 model selected
> select clear
> select #1/u:60-61
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #1/u:62
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select #1/u:62
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/u:57-70
207 atoms, 206 bonds, 14 residues, 1 model selected
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> select clear
Deleting atomic symmetry model...
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
Deleting atomic symmetry model...
> ui tool show "Ramachandran Plot"
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> ui tool show "Ramachandran Plot"
Deleting atomic symmetry model...
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/u:57
> view #1/u:70
> view #1/u:61
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-9-FINAL-Outliers-Refinement.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> ui tool show "Ramachandran Plot"
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/20-9-FINAL-Outliers-Refinement.pdb
> ui tool show "Ramachandran Plot"
> select clear
> close
Deleting atomic symmetry model...
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open KSRP-wt-40S-Body.mrc
Opened KSRP-wt-40S-Body.mrc as #1, grid size 400,400,400, pixel 1.16, shown at
level 0.128, step 2, values float32
OpenGL version: 3.3.0 NVIDIA 470.182.03
OpenGL renderer: Quadro K4200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 1.5Gi 26Gi 6.0Mi 3.0Gi 29Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK104GL [Quadro K4200] [10de:11b4] (rev a1)
Subsystem: NVIDIA Corporation GK104GL [Quadro K4200] [10de:1096]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.18.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.4
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
distro: 1.6.0
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
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