![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8835 closed defect (duplicate)
AdaptiveDihedralRestraintMgr creation for closed structure
| 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 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
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
[deleted to fit within ticket limits]
> 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
> isolde start
> set selectionWidth 4
> view #1/P:240-249
> select up
144426 atoms, 150208 bonds, 6905 residues, 3 models selected
> select #1
144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 21 models selected
> ui tool show "Ramachandran Plot"
> select
> #1/P:240-249|/E:790-841|/E:247-291|/E:934-961|/E:182-203|/E:225-239|/E:124-126
5435 atoms, 5837 bonds, 175 residues, 1 model selected
> select #1/P:240-249|
Expected an objects specifier or a keyword
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> select #1/P:239-249
185 atoms, 185 bonds, 11 residues, 1 model selected
> select #1/P:220-249
503 atoms, 505 bonds, 30 residues, 1 model selected
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/21-b-1-FisrtStep-S6-C-ter-Sim-Annealing-Middle-of-
> FirstSnap.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/21-b-1-FisrtStep-S6-C-ter-Sim-Annealing-Middle-of-
> FirstSnap.pdb
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim pause
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/22-prod1-FirstSnapsh-ProdAnnealing.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
> mut8-no-C-ter/22-prod1-FirstSnapsh-ProdAnnealing.cxs
Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb
> close
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/ui/restraints_tab/position.py", line 118, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
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/ui/restraints_tab/distance.py", line 150, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
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/ui/restraints_tab/secondary_structure.py", line 79,
in _selection_changed_cb
sel = self.isolde.selected_atoms.unique_residues
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
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/ui/restraints_tab/register_shift.py", line 105, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/Yaser-
> deltaKSRP/5opt-noKSRP.pdb
Chain information for 5opt-noKSRP.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
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
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/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb
self._expanded_cb()
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb
tm = self.torsion_restraint_mgr
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr
return AdaptiveDihedralRestraintMgr(model)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__
super().__init__(model, c_pointer=c_pointer,
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__
super().__init__(display_name, model, c_pointer)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
AttributeError: 'AtomicStructure' object has no attribute 'session'
Error processing trigger "add models":
AttributeError: 'AtomicStructure' object has no attribute 'session'
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x7fb55dee2040>
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1187, in __del__
if not self.was_deleted:
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'
> hide
> ribbon
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/Yaser-
> deltaKSRP/Linfantum-deltKSRP-40S-ETA-BODY-focused-3,14A-Resampled.mrc
Opened Linfantum-deltKSRP-40S-ETA-BODY-focused-3,14A-Resampled.mrc as #2, grid
size 400,400,400, pixel 1.16, shown at level 0.108, step 2, values float32
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/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb
self._expanded_cb()
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb
tm = self.torsion_restraint_mgr
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr
return AdaptiveDihedralRestraintMgr(model)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__
super().__init__(model, c_pointer=c_pointer,
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__
super().__init__(display_name, model, c_pointer)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
AttributeError: 'AtomicStructure' object has no attribute 'session'
Error processing trigger "add models":
AttributeError: 'AtomicStructure' object has no attribute 'session'
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x7fb55dee2040>
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1187, in __del__
if not self.was_deleted:
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'
> hide #!1 models
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/40S-wt-concat.mrc
Opened 40S-wt-concat.mrc as #3, grid size 400,400,400, pixel 1.16, shown at
level 0.185, step 2, values float32
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/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb
self._expanded_cb()
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb
tm = self.torsion_restraint_mgr
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr
return AdaptiveDihedralRestraintMgr(model)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__
super().__init__(model, c_pointer=c_pointer,
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__
super().__init__(display_name, model, c_pointer)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
AttributeError: 'AtomicStructure' object has no attribute 'session'
Error processing trigger "add models":
AttributeError: 'AtomicStructure' object has no attribute 'session'
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x7fb55dee2040>
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1187, in __del__
if not self.was_deleted:
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'
> surface dust #2 size 11.6
> surface dust #3 size 11.6
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
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/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb
self._expanded_cb()
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb
tm = self.torsion_restraint_mgr
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr
return AdaptiveDihedralRestraintMgr(model)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__
super().__init__(model, c_pointer=c_pointer,
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__
super().__init__(display_name, model, c_pointer)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
AttributeError: 'AtomicStructure' object has no attribute 'session'
Error processing trigger "add models":
AttributeError: 'AtomicStructure' object has no attribute 'session'
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x7fb55dee2040>
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1187, in __del__
if not self.was_deleted:
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'
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/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb
self._expanded_cb()
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb
tm = self.torsion_restraint_mgr
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr
return AdaptiveDihedralRestraintMgr(model)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__
super().__init__(model, c_pointer=c_pointer,
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__
super().__init__(display_name, model, c_pointer)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
AttributeError: 'AtomicStructure' object has no attribute 'session'
Error processing trigger "add models":
AttributeError: 'AtomicStructure' object has no attribute 'session'
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x7fb55dee2040>
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1187, in __del__
if not self.was_deleted:
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'
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 7.6Gi 10Gi 78Mi 13Gi 23Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK104GL [Quadro K4200] [10de:11b4] (rev a1)
Subsystem: NVIDIA Corporation GK104GL [Quadro K4200] [10de:1096]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.18.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.4
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
distro: 1.6.0
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
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 → AdaptiveDihedralRestraintMgr creation for closed structure |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Reported by Leonardo Lima