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Opened 3 years ago
Closed 2 years ago
#8866 closed defect (fixed)
Dead PositionRestraintMgr (and other problems)
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Linux-5.19.0-38-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF 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/20-9-FINAL-Outliers-Refinement.cxs
Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
pixel 1.16, shown at level 0.261, 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
Log from Wed Apr 12 06:33:04 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/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
Log from Tue Apr 11 17:31:47 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/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
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 cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde cisflip #1.2/h:76
Performing cis<\-->trans flip for 1 residues
> isolde cisflip #1.2/h:76
Performing cis<\-->trans 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 cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde cisflip #1.2/h:92
Performing cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans 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 cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans 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 cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans 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 cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans 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
[had to delete part of log to fit within ticket limits]
> 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"
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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
[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
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"
[Repeated 2 time(s)]
> 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"
[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
> 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
[Repeated 2 time(s)]
> 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"
[Repeated 1 time(s)]
> 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
[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 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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
[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 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"
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> view #1/u:101
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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
[Repeated 2 time(s)]
> 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
[Repeated 2 time(s)]
> isolde sim pause
> isolde sim resume
> select clear
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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.
[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 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"
[Repeated 1 time(s)]
> 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
[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
> 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"
[Repeated 1 time(s)]
> 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
[Repeated 2 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
> 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"
[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/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
[Repeated 2 time(s)]
> 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"
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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
[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
> 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
[Repeated 2 time(s)]
> 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"
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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"
[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 1 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"
> 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
[Repeated 1 time(s)]
> 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
[Repeated 3 time(s)]
> 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"
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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"
[Repeated 1 time(s)]
> 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
——— End of log from Tue Apr 11 17:31:47 2023 ———
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
[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 #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"
[Repeated 1 time(s)]
> 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"
[Repeated 1 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)]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
——— End of log from Wed Apr 12 06:33:04 2023 ———
opened ChimeraX session
> view #1/h|/P
> stotlight #1 radius 20
Unknown command: clipper stotlight #1 radius 20
> view #1/h|/P
> select #1/h|/P
6565 atoms, 6613 bonds, 402 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,P
6565 atoms, 6613 bonds, 402 residues, 1 model selected
> hide
Must specify one map, got 2
Must specify one map, got 0
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #1.3 models
> show #1.3 models
> show #1
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> clipper isolate sel maskRadius 12.0 focus false
> hide
> select #1/h,P
6565 atoms, 6613 bonds, 402 residues, 1 model selected
Must specify one map, got 2
> clipper isolate sel maskRadius 4.0 focus false
> alphafold match #1/P|/h:68-220 trim false
ChimeraX AlphaFold sequence search currently only searches v2 of the AlphaFold
sequence database, covering the original release of 40 reference genomes. To
search the complete database, go to https://www.ebi.ac.uk/Tools/sss/fasta/ in
your web browserand tick (only) "AlphaFold DB" under "Structures" in the first
window. Due to the size of the database, expect that to take a while.
Fetching compressed AlphaFold Q4DSU0 from
https://alphafold.ebi.ac.uk/files/AF-Q4DSU0-F1-model_v2.cif
Fetching compressed AlphaFold Q4DY30 from
https://alphafold.ebi.ac.uk/files/AF-Q4DY30-F1-model_v2.cif
2 AlphaFold models found using sequence similarity searches: Q4DSU0 (chain P),
Q4DY30 (chain h)
AlphaFold chains matching 5opt-concatenated-Map-Mut8-40S-noCter.pdb
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
P | Q4DSU0_TRYCC | Q4DSU0 | 3.65 | 250 | 249 | 100
h | Q4DY30_TRYCC | Q4DY30 | 14.20 | 249 | 153 | 100
Opened 2 AlphaFold models
> hide #2.2 models
> hide #2.1 models
> hide #!2 models
> show #!2 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #2.1 models
> show #!2 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.1 models
> clipper isolate sel maskRadius 12.0 focus false
> clipper isolate sel maskRadius 20.0 focus false
> show #2.2 models
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/Productive-Annealing/By-alpha-fold-
> restrainings/21-af-0-20-9-state-PLUS-alphaFoldStructures-S6-ksrp.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> clipper isolate sel maskRadius 4.0 focus false
> clipper isolate sel maskRadius 7.0 focus false
> clipper isolate sel maskRadius 15.0 focus false
> matchmaker #2.1 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5opt-concatenated-Map-Mut8-40S-noCter.pdb, chain P (#1.2) with
AlphaFold Q4DSU0_TRYCC chain P, chain P (#2.1), sequence alignment score =
1205.5
RMSD between 176 pruned atom pairs is 0.941 angstroms; (across all 249 pairs:
3.653)
> color #2.1 bychain
> color #2.1 byhetero
> color modify #2.1 hue + 50
ISOLDE: attempting to load PAE matrix for model #2.1 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.
> alphafold pae #2.1 uniprotId Q4DSU0 plot false
Fetching compressed AlphaFold PAE Q4DSU0 from
https://alphafold.ebi.ac.uk/files/AF-Q4DSU0-F1-predicted_aligned_error_v3.json
> combine #2
> hide #2.2 models
> hide #2.1 models
> hide #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> matchmaker #3 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5opt-concatenated-Map-Mut8-40S-noCter.pdb, chain P (#1.2) with
combination, chain P (#3), sequence alignment score = 1205.5
RMSD between 176 pruned atom pairs is 0.941 angstroms; (across all 249 pairs:
3.653)
> color #3 bychain
> color #3 byhetero
> color modify #3 hue + 50
> hide #3 models
> show #3 models
> hide #3 models
> isolde restrain torsions #1/P templateResidues #3/P adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 50 residues in
model #3 to IUPAC-IUB standards.
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> isolde restrain distances #1/P templateAtoms #3/P adjustForConfidence true
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 38 residues in
model #3 to IUPAC-IUB standards.
RMSD between 249 pruned atom pairs is 1.914 angstroms; (across all 249 pairs:
1.914)
> select #1/P,h
6565 atoms, 6613 bonds, 402 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> show #!2 models
> hide #!2 models
> show #!2 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #3 models
> hide #3 models
> show #2.2 models
> hide #2.2 models
> select add #1.1
6565 atoms, 6613 bonds, 402 residues, 9 models selected
> hide #!1.1 models
> show #!1.1 models
> show #3 models
> hide #3 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #!1 models
> show #!1 models
> select add #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> select add #1.2
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #1 ~HC
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show ~HC
> select #1/P,h
6565 atoms, 6613 bonds, 402 residues, 1 model selected
> clipper isolate sel maskRadius 15.0 focus false
> select clear
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select #1/P,h
6565 atoms, 6613 bonds, 402 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> show #2.2 models
> hide #2.2 models
> show #3 models
> hide #3 models
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 9 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> select #1/P,h|/E:797-814
7127 atoms, 7215 bonds, 420 residues, 1 model selected
> clipper isolate sel maskRadius 15.0 focus false
> isolde sim start sel
ISOLDE: started sim
> show #3 models
> isolde sim pause
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/Productive-Annealing/By-alpha-fold-restrainings/test.pdb
> models #1 relModel #1.2
> close]
Unknown command: close]
> close
> isolde sim stop discardTo 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/openmm/openmm_interface.py", line 1038, in
_sim_end_cb
self._pr_sim_end_cb()
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1095, in
_pr_sim_end_cb
restraints =
self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 2382, in get_restraints
return self._get_restraints(atoms)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 2335, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 2335, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
See log for complete Python traceback.
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)
AttributeError: 'NoneType' object has no attribute 'id_string'
Error processing trigger "sim terminated":
AttributeError: 'NoneType' object has no attribute 'id_string'
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)
See log for complete Python traceback.
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 12Gi 4.7Gi 155Mi 14Gi 18Gi
Swap: 2.0Gi 1.0Mi 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
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Dead PositionRestraintMgr (and other problems) |
comment:2 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed since ISOLDE 1.5: prior to that version, closing a model with an active simulation running would cause an almighty mess. In current versions everything should recover gracefully.
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Reported by Leonardo Lima