Opened 3 years ago

Closed 3 years ago

#8834 closed defect (fixed)

AdaptiveDihedralRestraintMgr creation for closed structure

Reported by: leofrancalima@… 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 pett) 

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  

> 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

[deleted to fit within ticket limits]

> 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  

> 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'  




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       7.5Gi        10Gi        72Mi        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 pett, 3 years ago

Component: Unassigned → Third Party
Description: modified (diff)
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → AdaptiveDihedralRestraintMgr creation for closed structure

Reported by Leonardo Lima

comment:2 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

It used to be that closing the working model with an active simulation running (even if paused) would cause all sorts of nastiness like this. That's fixed in 1.5 onwards.

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