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Opened 3 years ago
Closed 3 years ago
#8880 closed defect (duplicate)
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
[deleted to fit within tickets limits]
clipper spotlight #1 radius 20
> view #1/h|/P|/E:61-87,121-247,298-307,790-841
> select #1/h|/P|/E:61-87,121-247,298-307,790-841
17799 atoms, 18434 bonds, 1138 residues, 3 models selected
> hide #3 models
> clipper isolate sel maskRadius 4.0 focus false
> select clear
> view #1/h|/P|/E:61-87,121-247,298-307,790-84|/X|/L|/Z|/Y
> select #1/h|/P|/E:61-87,121-247,298-307,790-84|/X|/L|/Z|/Y
40642 atoms, 41455 bonds, 1 pseudobond, 3398 residues, 8 models selected
> clipper isolate sel maskRadius 4.0 focus false
> select #1/h|/P|/E:61-87,121-247,298-307,790-84
16134 atoms, 16641 bonds, 1086 residues, 3 models selected
> clipper isolate sel maskRadius 4.0 focus false
> clipper isolate sel maskRadius 12.0 focus false
> clipper isolate sel maskRadius 15.0 focus false
> isolde sim start sel
ISOLDE: started sim
> view #1/h
> ui tool show "Ramachandran Plot"
> hide ~@CA
> show @CA,P,C2,C4'
> isolde sim pause
> isolde sim resume
> isolde adjust distances #1 displayThreshold 0.5
> view #1/240-249
No objects specified.
> view #1/P:240-249
> show ~HC
> isolde release distances #1
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> select ~@CA,C,O,N
171603 atoms, 152750 bonds, 4 pseudobonds, 17929 residues, 58 models selected
> isolde release torsions sel
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> ui tool show "Ramachandran Plot"
> isolde sim resume
> ui tool show "Ramachandran Plot"
> isolde sim pause
> select clear
> isolde sim resume
> isolde release torsions #1
> ui tool show "Ramachandran Plot"
> hide ~@CA
> show ~HC
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 27 residues in model #1.2 to IUPAC-IUB
standards.
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/Sim-Low-Fidelity-AlphaFold-Rest-Protocol/11-KSRPwt-
> LowFidelitysim-AlphaFoldProtocol-chainsP-h-Neighborhood.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/Sim-Low-Fidelity-AlphaFold-Rest-Protocol/11-KSRPwt-
> LowFidelitysim-AlphaFoldProtocol-chainsP-h-Neighborhood.pdb models #1
> relModel #1.2
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
> byRafael-19-04-2023/Sim-Low-Fidelity-AlphaFold-Rest-Protocol/11-KSRPwt-
> LowFidelitysim-AlphaFoldProtocol-chainsP-h-Neighborhood.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.
> view
> select #1/X|/L|/Z|/Y
21698 atoms, 21944 bonds, 1 pseudobond, 1966 residues, 6 models selected
> select #1/X|/L|/Y
15243 atoms, 15421 bonds, 1349 residues, 4 models selected
> select #1/X|/Y
6728 atoms, 6801 bonds, 545 residues, 3 models selected
> select #1/X|/Y|/Q
13675 atoms, 13847 bonds, 1167 residues, 4 models selected
> select #1/X|/Y|/Q|/R
18461 atoms, 18696 bonds, 1610 residues, 5 models selected
> select #1/X|/Y|/Q|/R|/c
20520 atoms, 20781 bonds, 1802 residues, 6 models selected
> select #1/X|/Q|/R|/c
16257 atoms, 16471 bonds, 1405 residues, 5 models selected
> select #1/X|/Q|/R|/c|/b
22147 atoms, 22450 bonds, 1949 residues, 6 models selected
> select #1/X|/Q|/R|/c|/b|/S
24738 atoms, 25078 bonds, 2203 residues, 7 models selected
> select #1/X|/Q|/R|/c|/b|/S
24738 atoms, 25078 bonds, 2203 residues, 7 models selected
> clipper isolate sel maskRadius 15.0 focus false
> select #1/X|/Q|/R|/c|/b|/S|/E:529-562
25818 atoms, 26240 bonds, 2237 residues, 7 models selected
> select #1/X|/Q|/R|/c|/b|/S|/E:529-562,937-958
26505 atoms, 26976 bonds, 2259 residues, 7 models selected
> select #1/X|/Q|/R|/c|/b|/S|/E:529-562,937-958,981-1187
28424 atoms, 29040 bonds, 2 pseudobonds, 2319 residues, 8 models selected
> select #1/X|/Q|/R|/c|/b|/S|/E:529-562,937-958,981-1187,707-750
29822 atoms, 30543 bonds, 2 pseudobonds, 2363 residues, 8 models selected
> select #1/X|/Q|/R|/c|/b|/S|/E:529-562,927-970,981-1187,707-750
30526 atoms, 31302 bonds, 2 pseudobonds, 2385 residues, 8 models selected
> clipper isolate sel maskRadius 15.0 focus false
> clipper isolate sel maskRadius 4.0 focus false
> select #1/X|/Q|/R|/c|/b|/S|/E:529-562,927-970,981-1187,707-750,2243-2277
31646 atoms, 32510 bonds, 2 pseudobonds, 2420 residues, 8 models selected
> select #1/X|/Q|/R|/c|/b|/S|/E:529-562,927-970,981-1187,707-750,2205-2277
32869 atoms, 33830 bonds, 2 pseudobonds, 2458 residues, 8 models selected
> select #1/X|/Q|/R|/c|/b|/S|/E:529-562,927-970,981-1187,707-750,243-2277
80548 atoms, 85289 bonds, 4 pseudobonds, 3942 residues, 8 models selected
> select #1/X|/Q|/R|/c|/b|/S|/E:529-562,927-970,981-1187,707-750,2243-2277
31646 atoms, 32510 bonds, 2 pseudobonds, 2420 residues, 8 models selected
> select
> #1/X|/Q|/R|/c|/b|/S|/E:529-562,927-970,981-1187,707-750,2243-2277,2175-2205
32636 atoms, 33576 bonds, 2 pseudobonds, 2451 residues, 8 models selected
> clipper isolate sel maskRadius 4.0 focus false
"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.
> isolde restrain distances
> "#1.2/L","#1.2/M","#1.2/O","#1.2/P","#1.2/Q","#1.2/R","#1.2/S","#1.2/T","#1.2/U","#1.2/V","#1.2/W","#1.2/X","#1.2/Y","#1.2/Z","#1.2/a","#1.2/b","#1.2/c","#1.2/d","#1.2/e","#1.2/f","#1.2/g","#1.2/h","#1.2/i","#1.2/j","#1.2/k","#1.2/l","#1.2/m","#1.2/n","#1.2/o","#1.2/p","#1.2/q","#1.2/r","#1.2/t","#1.2/u"
> templateAtoms
> "#3/L","#3/M","#3/O","#3/P","#3/Q","#3/R","#3/S","#3/T","#3/U","#3/V","#3/W","#3/X","#3/Y","#3/Z","#3/a","#3/b","#3/c","#3/d","#3/e","#3/f","#3/g","#3/h","#3/i","#3/j","#3/k","#3/l","#3/m","#3/n","#3/o","#3/p","#3/q","#3/r","#3/t","#3/u"
> perChain true adjustForConfidence false useCoordinateAlignment false kappa
> 4.40 fallOff 2.50 groupName "Reference Distance Restraints"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/L templateResidues #3/L adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/M templateResidues #3/M adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/O templateResidues #3/O adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/P templateResidues #3/P adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/Q templateResidues #3/Q adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/R templateResidues #3/R adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/S templateResidues #3/S adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/T templateResidues #3/T adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/U templateResidues #3/U adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/V templateResidues #3/V adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/W templateResidues #3/W adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/X templateResidues #3/X adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/Y templateResidues #3/Y adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/Z templateResidues #3/Z adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/a templateResidues #3/a adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/b templateResidues #3/b adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/c templateResidues #3/c adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/d templateResidues #3/d adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/e templateResidues #3/e adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/f templateResidues #3/f adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/g templateResidues #3/g adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/h templateResidues #3/h adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/i templateResidues #3/i adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/j templateResidues #3/j adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/k templateResidues #3/k adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/l templateResidues #3/l adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/m templateResidues #3/m adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/n templateResidues #3/n adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/o templateResidues #3/o adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/p templateResidues #3/p adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/q templateResidues #3/q adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/r templateResidues #3/r adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/t templateResidues #3/t adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/u templateResidues #3/u adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain distances
> "#1.2/L","#1.2/M","#1.2/O","#1.2/P","#1.2/Q","#1.2/R","#1.2/S","#1.2/T","#1.2/U","#1.2/V","#1.2/W","#1.2/X","#1.2/Y","#1.2/Z","#1.2/a","#1.2/b","#1.2/c","#1.2/d","#1.2/e","#1.2/f","#1.2/g","#1.2/h","#1.2/i","#1.2/j","#1.2/k","#1.2/l","#1.2/m","#1.2/n","#1.2/o","#1.2/p","#1.2/q","#1.2/r","#1.2/t","#1.2/u"
> templateAtoms
> "#3/L","#3/M","#3/O","#3/P","#3/Q","#3/R","#3/S","#3/T","#3/U","#3/V","#3/W","#3/X","#3/Y","#3/Z","#3/a","#3/b","#3/c","#3/d","#3/e","#3/f","#3/g","#3/h","#3/i","#3/j","#3/k","#3/l","#3/m","#3/n","#3/o","#3/p","#3/q","#3/r","#3/t","#3/u"
> perChain true adjustForConfidence true useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> select
> #1/X|/Q|/R|/c|/b|/S|/E:529-562,927-970,981-1187,707-750,2243-2277,2175-2205
32636 atoms, 33576 bonds, 2 pseudobonds, 2451 residues, 8 models selected
> clipper isolate sel maskRadius 4.0 focus false
> 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/X|/Q|/R|/c|/b|/S|/E:529-2277
71333 atoms, 75338 bonds, 4 pseudobonds, 3656 residues, 8 models selected
> select
> #1/X|/Q|/R|/c|/b|/S|/E:529-562,927-970,981-1187,707-750,2243-2277,2175-2205
32636 atoms, 33576 bonds, 2 pseudobonds, 2451 residues, 8 models selected
> select
> #1/X|/Q|/R|/c|/b|/S|/M|/E:529-562,927-970,981-1187,707-750,2243-2277,2175-2205
37172 atoms, 38175 bonds, 2 pseudobonds, 2879 residues, 9 models selected
> clipper isolate sel maskRadius 4.0 focus false
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> hide ~@CA,P,C2,C4'
> isolde sim pause
> isolde adjust distances #1 displayThreshold 0.5
[Repeated 1 time(s)]
> isolde sim resume
> select clear
> isolde adjust distances #1 displayThreshold 0.5
> ui tool show "Ramachandran Plot"
> show ~HC
> isolde release distances #1
> isolde sim pause
> select #1~@CA,C,O,N
Expected an objects specifier or a keyword
> select #1/~@CA,C,O,N
Expected an objects specifier or a keyword
> select ~@CA,C,O,N
171603 atoms, 152750 bonds, 4 pseudobonds, 17929 residues, 58 models selected
> isolde release torsions sel
[Repeated 1 time(s)]
> isolde sim resume
> select clear
> ui tool show "Ramachandran Plot"
[Repeated 1 time(s)]
> view
> #1/X|/Q|/R|/c|/b|/S|/M|/E:529-562,927-970,981-1187,707-750,2243-2277,2175-2205
> hide ~@CA
> show ~HC
> isolde release torsions #1
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 42 residues in model #1.2 to IUPAC-IUB
standards.
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/Sim-Low-Fidelity-AlphaFold-Rest-Protocol/12-KSRPwt-
> LowFidelitysim-AlphaFoldProtocol-Second40Ssection-middleBody.pdb models #1
> relModel #1.2
> save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
> refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
> byRafael-19-04-2023/Sim-Low-Fidelity-AlphaFold-Rest-Protocol/12-KSRPwt-
> LowFidelitysim-AlphaFoldProtocol-Second40Ssection-middleBody.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 15Gi 8.8Gi 146Mi 7.1Gi 15Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK104GL [Quadro K4200] [10de:11b4] (rev a1)
Subsystem: NVIDIA Corporation GK104GL [Quadro K4200] [10de:1096]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.18.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.4
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
distro: 1.6.0
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ResidueStepper referencing dead structure |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Reported by Leonardo Lima