![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 18 months ago
#8877 closed defect (fixed)
ResidueStepper referencing dead 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-5.19.0-40-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 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.cxs
restore_snapshot for "NXmapHandler" returned None
restore_snapshot for "FastVolumeSurface" returned None
restore_snapshot for "MDFFMgr" returned None
Opened 40S-wt-concat.mrc gaussian as #1.1.1.2, grid size 400,400,400, pixel
1.16, shown at level 0.292, step 1, values float32
Log from Wed Apr 19 16:46:00 2023UCSF ChimeraX version: 1.6rc202304150037
(2023-04-15)
© 2016-2023 Regents of the University of California. All rights reserved.
> open C:/Users/Rafa/OneDrive2/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-
> refinement/40S-wt-refinement/9-40S-KSRP-wt-Second-steps.cxs
Opened 40S-wt-concat.mrc as #1.1.1.1, grid size 400,400,400, pixel 1.16, shown
at level 0.578, step 1, values float32
Opened 40S-wt-concat.mrc gaussian as #3, grid size 400,400,400, pixel 1.16,
shown at level 0.3, step 1, values float32
Restoring stepper: 40S-wt-concat.pdb
Log from Wed Apr 19 10:10:38 2023UCSF ChimeraX version: 1.6rc202304150037
(2023-04-15)
© 2016-2023 Regents of the University of California. All rights reserved.
> open C:\Users\Rafa\OneDrive2\OneDrive\Documentos\ubuntuStorage\krsp\5OPT-
> refinement\40S-wt-refinement\8-40S-KSRP-wt-Second-steps.cxs format session
Opened 40S-wt-concat.mrc as #1.1.1.1, grid size 400,400,400, pixel 1.16, shown
at level 0.578, step 1, values float32
Opened 40S-wt-concat.mrc gaussian as #1.1.1.2, grid size 400,400,400, pixel
1.16, shown at level 0.329, step 1, values float32
Restoring stepper: 40S-wt-concat.pdb
Log from Mon Apr 17 16:03:12 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
> refinement/4-40S-KSRP-wt-Second-steps.cxs
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time
Opened 40S-wt-concat.mrc as #1.1.1.1, grid size 400,400,400, pixel 1.16, shown
at level 0.537, step 1, values float32
Opened 40S-wt-concat.mrc gaussian as #1.1.1.2, grid size 400,400,400, pixel
1.16, shown at level 0.259, step 1, values float32
Restoring stepper: 40S-wt-concat.pdb
Log from Wed Apr 12 18:13:39 2023UCSF ChimeraX version: 1.6rc202304050652
(2023-04-05)
© 2016-2023 Regents of the University of California. All rights reserved.
> open D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
> refinement/2-40S-KSRP-wt-Second-steps.cxs
Opened 40S-wt-concat.mrc as #1.1.1.1, grid size 400,400,400, pixel 1.16, shown
at level 0.537, step 1, values float32
Opened 40S-wt-concat.mrc gaussian as #1.1.1.2, grid size 400,400,400, pixel
1.16, shown at level 0.402, step 1, values float32
Restoring stepper: 40S-wt-concat.pdb
Log from Wed Apr 12 10:10:43 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 40S-wt-concat.pdb
40S-wt-concat.pdb title:
Structure of KSRP In context of trypanosoma cruzi 40S [more info...]
Chain information for 40S-wt-concat.pdb #1
---
Chain | Description | UniProt
E | 18S RRNA |
L | 40S ribosomal protein S4 | Q4D5P4_TRYCC
M | 40S ribosomal protein S23, putative | Q4DTQ1_TRYCC
O | 40S ribosomal protein S5, putative | Q4E0Q3_TRYCC
P | 40S ribosomal protein S6 | Q4DSU0_TRYCC
Q | ribosomal protein S7, putative | Q4CUC7_TRYCC
R | 40S ribosomal protein S13, putative | Q4DC38_TRYCC
S | 40S ribosomal protein S27, putative | Q4DN73_TRYCC
T | 40S ribosomal protein S26 | Q4CYE4_TRYCC
U | 40S ribosomal protein S33, putative | Q4D7C8_TRYCC
V | 40S ribosomal protein S14, putative | Q4D6I5_TRYCC
W | 40S ribosomal protein S3A-2 | RS3A2_TRYCC
X | 40S ribosomal protein S11, putative | Q4D0U7_TRYCC
Y | 40S ribosomal protein S24 | Q4DW38_TRYCC
Z | 40S ribosomal protein S8 | Q4DU83_TRYCC
a | ribosomal protein S25, putative | Q4DTX6_TRYCC
b | 40S ribosomal protein S9, putative | Q4D4S1_TRYCC
c | 40S ribosomal protein S30 | Q4DA48_TRYCC
d | 40S ribosomal protein S2, putative | Q4DIZ9_TRYCC
e | 40S ribosomal protein S15A, putative | Q4E0N6_TRYCC
f | 40S ribosomal protein sa | Q4CQ63_TRYCC
g | 40S ribosomal protein S21, putative | Q4E3M0_TRYCC
h | RNA-binding protein, putative | Q4DY32_TRYCC
i | 40S ribosomal protein S12 | Q4CSL1_TRYCC
j | ubiquitin/ribosomal protein S27A, putative | Q4D1T6_TRYCC
k | 40S ribosomal protein S17, putative | Q4DK40_TRYCC
l | ribosomal protein S20, putative | Q4D6H7_TRYCC
m | 40S ribosomal protein S3, putative | Q4DMK9_TRYCC
n | 40S ribosomal protein S10, putative | Q4E088_TRYCC
o | ribosomal protein S19, putative | Q4DJY1_TRYCC
p | activated protein kinase C receptor, putative | Q4DTN2_TRYCC
q | ribosomal protein S29, putative | Q4CXR4_TRYCC
r | 40S ribosomal protein S16, putative | Q4DEK4_TRYCC
t | 40S ribosomal protein S15, putative | Q4DGZ5_TRYCC
u | 40S ribosomal protein S18, putative | Q4E093_TRYCC
> hide
> ribbon
> set bgColor white
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/40S-wt-concat.mrc
Opened 40S-wt-concat.mrc as #2, grid size 400,400,400, pixel 1.16, shown at
level 0.185, step 2, values float32
> isolde start
> set selectionWidth 4
> clipper associate #2 toModel #1
Opened 40S-wt-concat.mrc as #1.1.1.1, grid size 400,400,400, pixel 1.16, shown
at level 0.537, step 1, values float32
40S-wt-concat.pdb title:
Structure of KSRP In context of trypanosoma cruzi 40S [more info...]
Chain information for 40S-wt-concat.pdb
---
Chain | Description | UniProt
1.2/E | 18S RRNA |
1.2/L | 40S ribosomal protein S4 | Q4D5P4_TRYCC
1.2/M | 40S ribosomal protein S23, putative | Q4DTQ1_TRYCC
1.2/O | 40S ribosomal protein S5, putative | Q4E0Q3_TRYCC
1.2/P | 40S ribosomal protein S6 | Q4DSU0_TRYCC
1.2/Q | ribosomal protein S7, putative | Q4CUC7_TRYCC
1.2/R | 40S ribosomal protein S13, putative | Q4DC38_TRYCC
1.2/S | 40S ribosomal protein S27, putative | Q4DN73_TRYCC
1.2/T | 40S ribosomal protein S26 | Q4CYE4_TRYCC
1.2/U | 40S ribosomal protein S33, putative | Q4D7C8_TRYCC
1.2/V | 40S ribosomal protein S14, putative | Q4D6I5_TRYCC
1.2/W | 40S ribosomal protein S3A-2 | RS3A2_TRYCC
1.2/X | 40S ribosomal protein S11, putative | Q4D0U7_TRYCC
1.2/Y | 40S ribosomal protein S24 | Q4DW38_TRYCC
1.2/Z | 40S ribosomal protein S8 | Q4DU83_TRYCC
1.2/a | ribosomal protein S25, putative | Q4DTX6_TRYCC
1.2/b | 40S ribosomal protein S9, putative | Q4D4S1_TRYCC
1.2/c | 40S ribosomal protein S30 | Q4DA48_TRYCC
1.2/d | 40S ribosomal protein S2, putative | Q4DIZ9_TRYCC
1.2/e | 40S ribosomal protein S15A, putative | Q4E0N6_TRYCC
1.2/f | 40S ribosomal protein sa | Q4CQ63_TRYCC
1.2/g | 40S ribosomal protein S21, putative | Q4E3M0_TRYCC
1.2/h | RNA-binding protein, putative | Q4DY32_TRYCC
1.2/i | 40S ribosomal protein S12 | Q4CSL1_TRYCC
1.2/j | ubiquitin/ribosomal protein S27A, putative | Q4D1T6_TRYCC
1.2/k | 40S ribosomal protein S17, putative | Q4DK40_TRYCC
1.2/l | ribosomal protein S20, putative | Q4D6H7_TRYCC
1.2/m | 40S ribosomal protein S3, putative | Q4DMK9_TRYCC
1.2/n | 40S ribosomal protein S10, putative | Q4E088_TRYCC
1.2/o | ribosomal protein S19, putative | Q4DJY1_TRYCC
1.2/p | activated protein kinase C receptor, putative | Q4DTN2_TRYCC
1.2/q | ribosomal protein S29, putative | Q4CXR4_TRYCC
1.2/r | 40S ribosomal protein S16, putative | Q4DEK4_TRYCC
1.2/t | 40S ribosomal protein S15, putative | Q4DGZ5_TRYCC
1.2/u | 40S ribosomal protein S18, putative | Q4E093_TRYCC
> volume gaussian #1 bfactor 150
Opened 40S-wt-concat.mrc gaussian as #2, grid size 400,400,400, pixel 1.16,
shown at step 1, values float32
> clipper associate #2 toModel #1
Opened 40S-wt-concat.mrc gaussian as #1.1.1.2, grid size 400,400,400, pixel
1.16, shown at step 1, values float32
> select #1/h|/P|/Z
4745 atoms, 4813 bonds, 1 pseudobond, 597 residues, 2 models selected
> view #1/h|/P|/Z
> select clear
> addh
Summary of feedback from adding hydrogens to 40S-wt-concat.pdb #1.2
---
notes | No usable SEQRES records for 40S-wt-concat.pdb (#1.2) chain E;
guessing termini instead
No usable SEQRES records for 40S-wt-concat.pdb (#1.2) chain L; guessing
termini instead
No usable SEQRES records for 40S-wt-concat.pdb (#1.2) chain M; guessing
termini instead
No usable SEQRES records for 40S-wt-concat.pdb (#1.2) chain O; guessing
termini instead
No usable SEQRES records for 40S-wt-concat.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 LYS 240, /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
6858 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
62524 hydrogens added
> isolde restrain ligands #1
> select #1/h|/P|/Z
9805 atoms, 9873 bonds, 1 pseudobond, 597 residues, 2 models selected
> isolde sim start sel
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 480 residues in model #1.2 to IUPAC-IUB
standards.
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
> ui tool show "Ramachandran Plot"
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/h|/P|/Z
9805 atoms, 9873 bonds, 1 pseudobond, 597 residues, 2 models selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 18 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/b|/e
> select #1/b|/e
4848 atoms, 4895 bonds, 293 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 11 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/R|/M
> select #1/R|/M
4660 atoms, 4702 bonds, 283 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/a|/W
> select #1/a|/W
4801 atoms, 4835 bonds, 287 residues, 1 model selected
> isolde sim start sel
ISOLDE: stopped sim
> select #1/a|/W
4801 atoms, 4835 bonds, 287 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/O|/p|/t
9761 atoms, 9858 bonds, 619 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 17 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/n|/i
3496 atoms, 3528 bonds, 214 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 12 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/E:1851-1867
544 atoms, 585 bonds, 17 residues, 1 model selected
> select #1/E:1848-1867
635 atoms, 682 bonds, 20 residues, 1 model selected
> select #1/E:1848-1870
737 atoms, 793 bonds, 23 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/40S-wt-concat-REF.pdb
40S-wt-concat-REF.pdb title:
Structure of KSRP In context of trypanosoma cruzi 40S [more info...]
Chain information for 40S-wt-concat-REF.pdb #2
---
Chain | Description | UniProt
E | 18S RRNA |
L | 40S ribosomal protein S4 | Q4D5P4_TRYCC
M | 40S ribosomal protein S23, putative | Q4DTQ1_TRYCC
O | 40S ribosomal protein S5, putative | Q4E0Q3_TRYCC
P | 40S ribosomal protein S6 | Q4DSU0_TRYCC
Q | ribosomal protein S7, putative | Q4CUC7_TRYCC
R | 40S ribosomal protein S13, putative | Q4DC38_TRYCC
S | 40S ribosomal protein S27, putative | Q4DN73_TRYCC
T | 40S ribosomal protein S26 | Q4CYE4_TRYCC
U | 40S ribosomal protein S33, putative | Q4D7C8_TRYCC
V | 40S ribosomal protein S14, putative | Q4D6I5_TRYCC
W | 40S ribosomal protein S3A-2 | RS3A2_TRYCC
X | 40S ribosomal protein S11, putative | Q4D0U7_TRYCC
Y | 40S ribosomal protein S24 | Q4DW38_TRYCC
Z | 40S ribosomal protein S8 | Q4DU83_TRYCC
a | ribosomal protein S25, putative | Q4DTX6_TRYCC
b | 40S ribosomal protein S9, putative | Q4D4S1_TRYCC
c | 40S ribosomal protein S30 | Q4DA48_TRYCC
d | 40S ribosomal protein S2, putative | Q4DIZ9_TRYCC
e | 40S ribosomal protein S15A, putative | Q4E0N6_TRYCC
f | 40S ribosomal protein sa | Q4CQ63_TRYCC
g | 40S ribosomal protein S21, putative | Q4E3M0_TRYCC
h | RNA-binding protein, putative | Q4DY32_TRYCC
i | 40S ribosomal protein S12 | Q4CSL1_TRYCC
j | ubiquitin/ribosomal protein S27A, putative | Q4D1T6_TRYCC
k | 40S ribosomal protein S17, putative | Q4DK40_TRYCC
l | ribosomal protein S20, putative | Q4D6H7_TRYCC
m | 40S ribosomal protein S3, putative | Q4DMK9_TRYCC
n | 40S ribosomal protein S10, putative | Q4E088_TRYCC
o | ribosomal protein S19, putative | Q4DJY1_TRYCC
p | activated protein kinase C receptor, putative | Q4DTN2_TRYCC
q | ribosomal protein S29, putative | Q4CXR4_TRYCC
r | 40S ribosomal protein S16, putative | Q4DEK4_TRYCC
t | 40S ribosomal protein S15, putative | Q4DGZ5_TRYCC
u | 40S ribosomal protein S18, putative | Q4E093_TRYCC
> hide #!2 models
> isolde restrain distances #1/E:1830-1850 templateAtoms #2/E:1830-1850
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 480 residues in
model #2 to IUPAC-IUB standards.
RMSD between 10 pruned atom pairs is 1.566 angstroms; (across all 10 pairs:
1.566)
> show #!2 models
> hide #!2 models
> isolde restrain distances #1/E:1832-1846 templateAtoms #2/E:1832-1846
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]RMSD between 4 pruned atom pairs is 1.814 angstroms;
(across all 4 pairs: 1.814)
> select #1/E:1848-1870
737 atoms, 793 bonds, 23 residues, 1 model selected
> select #1/E:1832-1846
125 atoms, 132 bonds, 1 pseudobond, 4 residues, 2 models selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/E:1832-1870
893 atoms, 959 bonds, 1 pseudobond, 28 residues, 2 models selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> select #1
144755 atoms, 150537 bonds, 5 pseudobonds, 6925 residues, 22 models selected
> select #1/E:1832-1850
247 atoms, 262 bonds, 1 pseudobond, 8 residues, 2 models selected
> isolde sim resume
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> remove distances #1/E:1832-1846 templateAtoms #2/E:1832-1846
Unknown command: isolde remove distances #1/E:1832-1846 templateAtoms
#2/E:1832-1846
> isolde release distances #1/E:1832-1846 templateAtoms #2/E:1832-1846
Expected a keyword
> isolde release distances #1/E:1832-1846
> isolde restrain distances #1/E:1832-1846
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde release distances #1/E:1832-1846
> isolde restrain distances #1/E:1830-1870
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde release distances #1/E:1830-1870
> select #1
144755 atoms, 150537 bonds, 5 pseudobonds, 6925 residues, 22 models selected
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/1-40S-KSRP-wt-first-steps.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/1-40S-KSRP-wt-first-steps.cxs
> select clear
> isolde cisflip #1.2/r:136
Performing cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde sim stop
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
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde cisflip #1.2/U:83
Performing cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/2-40S-KSRP-wt-Second-steps.cxs
Taking snapshot of stepper: 40S-wt-concat.pdb
——— End of log from Wed Apr 12 10:10:43 2023 ———
opened ChimeraX session
> ui tool show "Volume Viewer"
> volume #1.1.1.2 level 0.4059
> volume #1.1.1.2 level 0.2592
> volume #1.1.1.2 color black
> isolde start
> set selectionWidth 4
> ui tool show "Ramachandran Plot"
> isolde cisflip #1.2/Q:137
Performing cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde cisflip #1.2/f:6
Performing cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
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 sim stop
Sim termination reason: None
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 cisflip #1.2/k:142
Performing cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
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 cisflip #1.2/m:144
Performing cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
Sim termination reason: None
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
Sim termination reason: None
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 sim stop
Sim termination reason: None
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/h:90
Performing cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
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 cisflip #1.2/h:92
Performing cis<\-->trans flip for 1 residues
> isolde sim stop
Sim termination reason: None
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/h:150
Performing cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
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
> isolde cisflip #1.2/h:222
Performing cis<\-->trans flip for 1 residues
> isolde cisflip #1.2/h:223
Performing cis<\-->trans flip for 1 residues
> isolde sim stop
Sim termination reason: None
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/h:205
Performing cis<\-->trans flip for 1 residues
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
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 D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
> refinement/3-40S-KSRP-wt-Second-steps.cxs
Taking snapshot of stepper: 40S-wt-concat.pdb
> save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
> refinement/3-40S-KSRP-wt-Second-steps.pdb models #1
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
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
Sim termination reason: None
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
Sim termination reason: None
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
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
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 cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
Sim termination reason: None
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
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/Q:137
> isolde sim start sel
ISOLDE: started sim
> view #1/Q:137
> view #1/Q:137|/Q:181
> selct #1/Q:137|/Q:181
Unknown command: selct #1/Q:137|/Q:181
> select #1/Q:137|/Q:181
41 atoms, 39 bonds, 3 residues, 2 models selected
> select #1/Q:137|/Q:181
41 atoms, 39 bonds, 3 residues, 2 models selected
> select clear
> select #1/Q:137|/Q:181
41 atoms, 39 bonds, 3 residues, 2 models selected
> isolde sim stop
Sim termination reason: None
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 cisflip sel
Performing cis<\-->trans flip for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> style #1/Q:81|/Q:137 spheres
Expected a keyword
> style #1/Q:81|/Q:137 sphere
Changed 45 atom styles
> style #1/Q:81|/Q:137 stick
Changed 45 atom styles
> isolde sim stop
Sim termination reason: None
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
Sim termination reason: None
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 D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
> refinement/4-40S-KSRP-wt-Second-steps.cxs
Taking snapshot of stepper: 40S-wt-concat.pdb
——— End of log from Wed Apr 12 18:13:39 2023 ———
opened ChimeraX session
> ui tool show "Volume Viewer"
> isolde start
> set selectionWidth 4
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.2 level 0.3144
> volume #1.1.1.2
> 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 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 pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> 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 sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop 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 pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim pause
> isolde sim resume
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim 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 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 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
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Peptide bond must be mobile in the simulation!
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> 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 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
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> 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 clear
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde 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 sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> 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 discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide 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 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 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 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 sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide 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 sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Peptide bond must be mobile in the simulation!
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond 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
> save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
> refinement/5-40S-KSRP-wt-Second-steps.cxs
Taking snapshot of stepper: 40S-wt-concat.pdb
> save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
> refinement/5-40S-KSRP-wt-Second-steps.pdb models #1
> cd "D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
> refinement/New folder"
Current working directory is:
D:\Rafa\OneDrive\Documentos\ubuntuStorage\krsp\5OPT-refinement\40S-wt-
refinement\New folder
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> view #1/k:149
> select #1/k:149
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
[deleted to fit within ticket limits]
> 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
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui windowfill toggle
[Repeated 1 time(s)]
> select :B@10
Nothing selected
> select :I@52
Nothing selected
> view :B@10
No objects specified.
> view :B|10
Expected an objects specifier or a view name or a keyword
> view :B@10
No objects specified.
> view #B:10
Expected an objects specifier or a view name or a keyword
> view #1/I:10
No objects specified.
> view #1/I:52
No objects specified.
> select #1/I:52
Nothing selected
> select #1/o:52
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/o:60
24 atoms, 23 bonds, 1 residue, 1 model selected
> view #1/o:60
> view #1/l:52
> select #1/l:52
24 atoms, 23 bonds, 1 residue, 1 model selected
> view #1/l:52
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/l:34
> select #1/l:34
14 atoms, 13 bonds, 1 residue, 1 model selected
> view #1/l:34,#1/l:52
Expected an objects specifier or a view name or a keyword
> select #1/l:34,#1/l:52
Expected an objects specifier or a keyword
> select #1/l:34,#1/l:52
Expected an objects specifier or a keyword
> select #1/l:34.52
Expected an objects specifier or a keyword
> select #1/l:34,#1/l:52
Expected an objects specifier or a keyword
> select #1/l:34,#1/l:52
Expected an objects specifier or a keyword
> select #1/l:34,#1/l:52
Expected an objects specifier or a keyword
> select #1/l:34,52
38 atoms, 36 bonds, 2 residues, 1 model selected
> view #1/l:34,52
> 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 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
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
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: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> 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 3 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Peptide bond must be mobile in the simulation!
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 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 sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: 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
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/m:137
16 atoms, 15 bonds, 1 residue, 1 model selected
> view #1/m:137
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/m:137,104
> select #1/m:137,104
35 atoms, 33 bonds, 2 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
> refinement/8-40S-KSRP-wt-Second-steps.cxs
Taking snapshot of stepper: 40S-wt-concat.pdb
——— End of log from Mon Apr 17 16:03:12 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
> volume gaussian #1 bfactor 150
Opened 40S-wt-concat.mrc gaussian as #3, grid size 400,400,400, pixel 1.16,
shown at step 1, values float32
Opened 40S-wt-concat.mrc gaussian as #4, grid size 400,400,400, pixel 1.16,
shown at step 1, values float32
> close #1.1.1.2
> close #4
> volume #3 level 0.3
> select #1/h
2780 atoms, 2803 bonds, 173 residues, 1 model selected
> view #1/h
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> 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.
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
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
> isolde sim stop
Sim termination reason: None
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 sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/h
2780 atoms, 2803 bonds, 173 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P
4114 atoms, 4139 bonds, 249 residues, 1 model selected
> view #1/P
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
Sim termination reason: None
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/Z
2911 atoms, 2931 bonds, 1 pseudobond, 175 residues, 2 models selected
> view #1/Z
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/X
2465 atoms, 2491 bonds, 148 residues, 1 model selected
> view #1/X
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
Sim termination reason: None
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
> select #1/L
4183 atoms, 4218 bonds, 258 residues, 1 model selected
> view #1/L
> 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
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/Y
2057 atoms, 2072 bonds, 123 residues, 1 model selected
> view #1/Y
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save C:/Users/Rafa/OneDrive2/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-
> refinement/40S-wt-refinement/9-40S-KSRP-wt-Second-steps.cxs
Taking snapshot of stepper: 40S-wt-concat.pdb
——— End of log from Wed Apr 19 10:10:38 2023 ———
opened ChimeraX session
> isolde start
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> clipper associate #3 toModel #1
Opened 40S-wt-concat.mrc gaussian as #1.1.1.2, grid size 400,400,400, pixel
1.16, shown at step 1, values float32
> color #1.1.1.2 #004c4cff models
> volume #1.1.1.2 level 0.2598
> volume #1.1.1.2 level 0.5645
> select clear
> volume #1.1.1.2 color #002323
> volume #1.1.1.2 color #232323
> volume #1.1.1.2 color #545454
> view #1/h
> volume #1.1.1.2 level 0.2919
> save C:/Users/Rafa/OneDrive2/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-
> refinement/40S-wt-refinement/9-40S-KSRP-wt-Second-steps.cxs
Taking snapshot of stepper: 40S-wt-concat.pdb
——— End of log from Wed Apr 19 16:46:00 2023 ———
opened ChimeraX session
> hide #!1.2 models
> show #!1.2 models
> hide #1.3 models
> show #1.3 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1 models
> show #!1 models
> close
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
> byRafael-19-04-2023/9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb title:
Structure of KSRP In context of trypanosoma cruzi 40S [more info...]
Chain information for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb #1
---
Chain | Description | UniProt
E | 18S RRNA |
L | 40S ribosomal protein S4 | Q4D5P4_TRYCC
M | 40S ribosomal protein S23, putative | Q4DTQ1_TRYCC
O | 40S ribosomal protein S5, putative | Q4E0Q3_TRYCC
P | 40S ribosomal protein S6 | Q4DSU0_TRYCC
Q | ribosomal protein S7, putative | Q4CUC7_TRYCC
R | 40S ribosomal protein S13, putative | Q4DC38_TRYCC
S | 40S ribosomal protein S27, putative | Q4DN73_TRYCC
T | 40S ribosomal protein S26 | Q4CYE4_TRYCC
U | 40S ribosomal protein S33, putative | Q4D7C8_TRYCC
V | 40S ribosomal protein S14, putative | Q4D6I5_TRYCC
W | 40S ribosomal protein S3A-2 | RS3A2_TRYCC
X | 40S ribosomal protein S11, putative | Q4D0U7_TRYCC
Y | 40S ribosomal protein S24 | Q4DW38_TRYCC
Z | 40S ribosomal protein S8 | Q4DU83_TRYCC
a | ribosomal protein S25, putative | Q4DTX6_TRYCC
b | 40S ribosomal protein S9, putative | Q4D4S1_TRYCC
c | 40S ribosomal protein S30 | Q4DA48_TRYCC
d | 40S ribosomal protein S2, putative | Q4DIZ9_TRYCC
e | 40S ribosomal protein S15A, putative | Q4E0N6_TRYCC
f | 40S ribosomal protein sa | Q4CQ63_TRYCC
g | 40S ribosomal protein S21, putative | Q4E3M0_TRYCC
h | RNA-binding protein, putative | Q4DY32_TRYCC
i | 40S ribosomal protein S12 | Q4CSL1_TRYCC
j | ubiquitin/ribosomal protein S27A, putative | Q4D1T6_TRYCC
k | 40S ribosomal protein S17, putative | Q4DK40_TRYCC
l | ribosomal protein S20, putative | Q4D6H7_TRYCC
m | 40S ribosomal protein S3, putative | Q4DMK9_TRYCC
n | 40S ribosomal protein S10, putative | Q4E088_TRYCC
o | ribosomal protein S19, putative | Q4DJY1_TRYCC
p | activated protein kinase C receptor, putative | Q4DTN2_TRYCC
q | ribosomal protein S29, putative | Q4CXR4_TRYCC
r | 40S ribosomal protein S16, putative | Q4DEK4_TRYCC
t | 40S ribosomal protein S15, putative | Q4DGZ5_TRYCC
u | 40S ribosomal protein S18, putative | Q4E093_TRYCC
> hide
> ribbon
> open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/40S-wt-concat.mrc
Opened 40S-wt-concat.mrc as #2, grid size 400,400,400, pixel 1.16, shown at
level 0.185, step 2, values float32
> isolde start
> set selectionWidth 4
> clipper associate #2 toModel #1
Opened 40S-wt-concat.mrc as #1.1.1.1, grid size 400,400,400, pixel 1.16, shown
at level 0.542, step 1, values float32
9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb title:
Structure of KSRP In context of trypanosoma cruzi 40S [more info...]
Chain information for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
---
Chain | Description | UniProt
1.2/E | 18S RRNA |
1.2/L | 40S ribosomal protein S4 | Q4D5P4_TRYCC
1.2/M | 40S ribosomal protein S23, putative | Q4DTQ1_TRYCC
1.2/O | 40S ribosomal protein S5, putative | Q4E0Q3_TRYCC
1.2/P | 40S ribosomal protein S6 | Q4DSU0_TRYCC
1.2/Q | ribosomal protein S7, putative | Q4CUC7_TRYCC
1.2/R | 40S ribosomal protein S13, putative | Q4DC38_TRYCC
1.2/S | 40S ribosomal protein S27, putative | Q4DN73_TRYCC
1.2/T | 40S ribosomal protein S26 | Q4CYE4_TRYCC
1.2/U | 40S ribosomal protein S33, putative | Q4D7C8_TRYCC
1.2/V | 40S ribosomal protein S14, putative | Q4D6I5_TRYCC
1.2/W | 40S ribosomal protein S3A-2 | RS3A2_TRYCC
1.2/X | 40S ribosomal protein S11, putative | Q4D0U7_TRYCC
1.2/Y | 40S ribosomal protein S24 | Q4DW38_TRYCC
1.2/Z | 40S ribosomal protein S8 | Q4DU83_TRYCC
1.2/a | ribosomal protein S25, putative | Q4DTX6_TRYCC
1.2/b | 40S ribosomal protein S9, putative | Q4D4S1_TRYCC
1.2/c | 40S ribosomal protein S30 | Q4DA48_TRYCC
1.2/d | 40S ribosomal protein S2, putative | Q4DIZ9_TRYCC
1.2/e | 40S ribosomal protein S15A, putative | Q4E0N6_TRYCC
1.2/f | 40S ribosomal protein sa | Q4CQ63_TRYCC
1.2/g | 40S ribosomal protein S21, putative | Q4E3M0_TRYCC
1.2/h | RNA-binding protein, putative | Q4DY32_TRYCC
1.2/i | 40S ribosomal protein S12 | Q4CSL1_TRYCC
1.2/j | ubiquitin/ribosomal protein S27A, putative | Q4D1T6_TRYCC
1.2/k | 40S ribosomal protein S17, putative | Q4DK40_TRYCC
1.2/l | ribosomal protein S20, putative | Q4D6H7_TRYCC
1.2/m | 40S ribosomal protein S3, putative | Q4DMK9_TRYCC
1.2/n | 40S ribosomal protein S10, putative | Q4E088_TRYCC
1.2/o | ribosomal protein S19, putative | Q4DJY1_TRYCC
1.2/p | activated protein kinase C receptor, putative | Q4DTN2_TRYCC
1.2/q | ribosomal protein S29, putative | Q4CXR4_TRYCC
1.2/r | 40S ribosomal protein S16, putative | Q4DEK4_TRYCC
1.2/t | 40S ribosomal protein S15, putative | Q4DGZ5_TRYCC
1.2/u | 40S ribosomal protein S18, putative | Q4E093_TRYCC
> view #1/P:240-249
> volume gaussian #1 bfactor 150
Opened 40S-wt-concat.mrc gaussian as #2, grid size 400,400,400, pixel 1.16,
shown at step 1, values float32
> clipper associate #2 toModel #1
Opened 40S-wt-concat.mrc gaussian as #1.1.1.2, grid size 400,400,400, pixel
1.16, shown at step 1, values float32
> addh
Summary of feedback from adding hydrogens to 9-40S-KSRP-wt-Second-steps-
FINALoutliersRaf.pdb #1.2
---
notes | No usable SEQRES records for 9-40S-KSRP-wt-Second-steps-
FINALoutliersRaf.pdb (#1.2) chain E; guessing termini instead
No usable SEQRES records for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
(#1.2) chain L; guessing termini instead
No usable SEQRES records for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
(#1.2) chain M; guessing termini instead
No usable SEQRES records for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
(#1.2) chain O; guessing termini instead
No usable SEQRES records for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.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 LYS 240, /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
7074 hydrogen bonds
/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
4 hydrogens added
> isolde restrain ligands #1
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:240-249
168 atoms, 168 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> 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
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:220-249
503 atoms, 505 bonds, 30 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: stopped sim
> select #1/P:220-249|/h
3283 atoms, 3308 bonds, 203 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/P:220-249|/h:231-239
653 atoms, 654 bonds, 39 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> select #1/P:220-249|/h
3283 atoms, 3308 bonds, 203 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/h:95-136
> select #1/h:95-136
685 atoms, 690 bonds, 42 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process
func(*args, **kwargs)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize
c.draw()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw
self.figure.draw(self.renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw
artists = self._get_draw_artists(renderer)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists
ax.apply_aspect()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
ValueError: 'box_aspect' and 'fig_aspect' must be positive
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde sim pause
> isolde sim resume
> view h:135
Expected an objects specifier or a view name or a keyword
> view #1/h:135
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/h:95-136
685 atoms, 690 bonds, 42 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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/h:138-148
156 atoms, 159 bonds, 11 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
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
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> ui tool show "Ramachandran Plot"
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> ui tool show "Ramachandran Plot"
> view #1/h:138-148
[Repeated 1 time(s)]
> select #1/h:138-148
156 atoms, 159 bonds, 11 residues, 1 model selected
> select clear
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/h:93-136
> select #1/h:93-136
717 atoms, 722 bonds, 44 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim resume
> select clear
> ui tool show "Ramachandran Plot"
> select clear
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/h|/P:220-249
> select #1/h|/P:220-249
3283 atoms, 3308 bonds, 203 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> select #1/V:11-20
133 atoms, 132 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> select #1/V:21-26
96 atoms, 97 bonds, 6 residues, 1 model selected
> isolde sim start sel
Simulation already running!
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/V:21-26
96 atoms, 97 bonds, 6 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/V:11-20
> select #1/V:11-20
133 atoms, 132 bonds, 10 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
> byRafael-19-04-2023/10-FINAL-outlierRefinement-40S-KSRPwt.pdb
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
> byRafael-19-04-2023/10-FINAL-outlierRefinement-40S-KSRPwt.cxs
Taking snapshot of stepper: 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
Taking snapshot of stepper: 40S-wt-concat.pdb
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 3'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 3' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb'
ValueError: error processing: 'isolde residue stepper 3' -> -> '40S-wt-
concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
-> '40S-wt-concat.pdb'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 3'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 3' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb'
ValueError: error processing: 'isolde residue stepper 3' -> -> '40S-wt-
concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
-> '40S-wt-concat.pdb'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
> byRafael-19-04-2023/10-FINAL-outlierRefinement-40S-KSRPwt.cxs
Taking snapshot of stepper: 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
Taking snapshot of stepper: 40S-wt-concat.pdb
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 3'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 3' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb'
ValueError: error processing: 'isolde residue stepper 3' -> -> '40S-wt-
concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
-> '40S-wt-concat.pdb'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1389, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 208, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 3'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 3' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
concat.pdb'
ValueError: error processing: 'isolde residue stepper 3' -> -> '40S-wt-
concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
-> '40S-wt-concat.pdb'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 470.182.03
OpenGL renderer: Quadro K4200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 5.6Gi 20Gi 117Mi 5.6Gi 25Gi
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 (3)
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 → ResidueStepper referencing dead structure |
comment:2 by , 2 years ago
First thing I'd recommend is to *definitely* update your ChimeraX to 1.6.1 and ISOLDE to 1.6 - 1.4 is getting pretty ancient now. That being said, I'll do some digging into this - I think I may be doing something wrong in how the ResidueStepper is saved and restored across sessions, leading to accumulation of defunct copies of it after repeated save/restore cycles.
comment:3 by , 18 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Sorry it's taken such a long time, but this is now fixed. See #14894 if you're interested in the details.
Note:
See TracTickets
for help on using tickets.
Reported by Leonardo Lima