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Opened 8 months ago
Last modified 8 months ago
#17015 assigned defect
ISOLDE: 'AtomicStructure' object has no attribute '_c_pointer_ref'
| 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
The following bug report has been submitted:
Platform: macOS-14.7.3-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/uqnmodhi/Desktop/JEV/G4/RealSpaceRefine_27/bJEV4_0501-coot-0_real_space_refined_027_fixed_2.pdb
> format pdb
Chain information for bJEV4_0501-coot-0_real_space_refined_027_fixed_2.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
> close
> open /Volumes/4TB/Harrislab/Zmab20/20_sharp2_map13b_ZIKVm20.mrc format mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
> open /Volumes/4TB/Harrislab/Z_clone20_chainrename.pdb
Chain information for Z_clone20_chainrename.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
K | No description available
> select add #2
16211 atoms, 16566 bonds, 2121 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-318.74,0,1,0,-238.95,0,0,1,0
> view matrix models #2,1,0,0,-184.27,0,1,0,-147.01,0,0,1,-371.84
> view matrix models #2,1,0,0,-238.04,0,1,0,-259.57,0,0,1,-414.23
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.029534,-0.99916,-0.028524,554,-0.96074,0.036251,-0.27508,633.51,0.27589,0.01928,-0.961,593.44
> view matrix models
> #2,-0.042395,-0.91126,-0.40965,743.4,-0.62839,0.34309,-0.69815,630.92,0.77674,0.22782,-0.58717,107.89
> view matrix models
> #2,-0.98914,-0.11726,-0.088612,621.87,-0.064707,0.88876,-0.45378,67.015,0.13196,-0.44311,-0.8867,782.13
> view matrix models
> #2,0.58146,0.25862,-0.77137,265.48,0.049191,0.93522,0.35063,-454.3,0.81209,-0.24182,0.53107,-366.37
> volume #1 level 0.1403
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.58146,0.25862,-0.77137,246.58,0.049191,0.93522,0.35063,-460.71,0.81209,-0.24182,0.53107,-357.86
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99738,0.071741,-0.0090758,-278.03,-0.072308,0.99079,-0.11449,-169.24,0.00077858,0.11485,0.99338,-445.9
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99738,0.071741,-0.0090758,-251.06,-0.072308,0.99079,-0.11449,-162.81,0.00077858,0.11485,0.99338,-456.45
> ui tool show "Command Line Interface"
> fitmap #2 inMap #1
Fit molecule Z_clone20_chainrename.pdb (#2) to map
20_sharp2_map13b_ZIKVm20.mrc (#1) using 16211 atoms
average map value = 0.03279, steps = 132
shifted from previous position = 3.97
rotated from previous position = 3.8 degrees
atoms outside contour = 15413, contour level = 0.14027
Position of Z_clone20_chainrename.pdb (#2) relative to
20_sharp2_map13b_ZIKVm20.mrc (#1) coordinates:
Matrix rotation and translation
0.99591963 0.07866657 -0.04422301 -234.54403703
-0.08119425 0.99497373 -0.05860699 -191.57295489
0.03939032 0.06195850 0.99730113 -456.73004710
Axis 0.55563845 -0.38534062 -0.73673504
Axis point -1333.35017749 4889.95079354 0.00000000
Rotation angle (degrees) 6.22843667
Shift along axis 279.98818329
> view matrix models
> #2,0.99592,0.078667,-0.044223,-231.02,-0.081194,0.99497,-0.058607,-193.37,0.03939,0.061959,0.9973,-468.74
> fitmap #2 inMap #1
Fit molecule Z_clone20_chainrename.pdb (#2) to map
20_sharp2_map13b_ZIKVm20.mrc (#1) using 16211 atoms
average map value = 0.03434, steps = 84
shifted from previous position = 3.05
rotated from previous position = 3.04 degrees
atoms outside contour = 15121, contour level = 0.14027
Position of Z_clone20_chainrename.pdb (#2) relative to
20_sharp2_map13b_ZIKVm20.mrc (#1) coordinates:
Matrix rotation and translation
0.98983595 0.11913008 -0.07767131 -226.98089874
-0.12328713 0.99105408 -0.05110872 -182.42961655
0.07088788 0.06016512 0.99566815 -479.26242937
Axis 0.36445475 -0.48657533 -0.79398815
Axis point -177.01443394 3072.85156655 0.00000000
Rotation angle (degrees) 8.78099030
Shift along axis 386.57017203
> view matrix models
> #2,0.98984,0.11913,-0.077671,-247.02,-0.12329,0.99105,-0.051109,-190.94,0.070888,0.060165,0.99567,-468.7
> fitmap #2 inMap #1
Fit molecule Z_clone20_chainrename.pdb (#2) to map
20_sharp2_map13b_ZIKVm20.mrc (#1) using 16211 atoms
average map value = 0.03644, steps = 108
shifted from previous position = 2.06
rotated from previous position = 2.26 degrees
atoms outside contour = 14953, contour level = 0.14027
Position of Z_clone20_chainrename.pdb (#2) relative to
20_sharp2_map13b_ZIKVm20.mrc (#1) coordinates:
Matrix rotation and translation
0.98925094 0.12297886 -0.07911245 -249.35439360
-0.12994027 0.98744143 -0.08986083 -164.24752281
0.06706793 0.09917480 0.99280726 -480.87317055
Axis 0.54327928 -0.42011535 -0.72687737
Axis point -660.07002633 3220.43263961 0.00000000
Rotation angle (degrees) 10.01910097
Shift along axis 283.06965458
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99622,-0.033778,0.08002,-283.39,0.032962,0.99939,0.011504,-289.36,-0.080359,-0.0088231,0.99673,-385.37
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99622,-0.033778,0.08002,-283.52,0.032962,0.99939,0.011504,-287.53,-0.080359,-0.0088231,0.99673,-397.25
> fitmap #2 inMap #1
Fit molecule Z_clone20_chainrename.pdb (#2) to map
20_sharp2_map13b_ZIKVm20.mrc (#1) using 16211 atoms
average map value = 0.2049, steps = 116
shifted from previous position = 4.93
rotated from previous position = 4.29 degrees
atoms outside contour = 7657, contour level = 0.14027
Position of Z_clone20_chainrename.pdb (#2) relative to
20_sharp2_map13b_ZIKVm20.mrc (#1) coordinates:
Matrix rotation and translation
0.99990624 -0.00121445 0.01363985 -254.99757408
0.00123258 0.99999837 -0.00132067 -266.60654673
-0.01363823 0.00133736 0.99990610 -429.37361125
Axis 0.09659838 0.99134259 0.08893044
Axis point -29461.45362900 0.00000000 16175.85758754
Rotation angle (degrees) 0.78830885
Shift along axis -327.11515919
> volume #1 level 0.125
> volume #1 step 1
> volume #1 level 0.1366
> volume #1 level 0.1459
> save /Volumes/4TB/Harrislab/Z_clone20_chainrename_corr.pdb
> save /Volumes/4TB/Harrislab/Z_clone20_chainrename_corr.pdb relModel #1
> close #2
> open /Volumes/4TB/Harrislab/Z_clone20_chainrename_corr.pdb
Chain information for Z_clone20_chainrename_corr.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
K | No description available
> select add #2
16211 atoms, 16566 bonds, 2121 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui tool show ISOLDE
> set selectionWidth 4
Populating font family aliases took 61 ms. Replace uses of missing font family
"Carlito" with one that exists to avoid this cost.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 88 residues in model #2 to IUPAC-IUB
standards.
Chain information for Z_clone20_chainrename_corr.pdb
---
Chain | Description
2.2/A | No description available
2.2/B | No description available
2.2/C | No description available
2.2/D | No description available
2.2/E | No description available
2.2/F | No description available
2.2/H | No description available
2.2/I | No description available
2.2/J | No description available
2.2/K | No description available
ISOLDE: created disulfide bonds between the following residues:
B180-B280; C300-C330; B2-B24; A174-A268; A285-A315; A81-A105; C183-C283;
B297-B326; B54-B113; B67-B97
> clipper associate #1 toModel #2
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> isolde sim start sel
ISOLDE: stopped sim
> addh #2.2
Summary of feedback from adding hydrogens to Z_clone20_chainrename_corr.pdb
#2.2
---
notes | Termini for Z_clone20_chainrename_corr.pdb (#2.2) chain A determined
from SEQRES records
Termini for Z_clone20_chainrename_corr.pdb (#2.2) chain B determined from
SEQRES records
Termini for Z_clone20_chainrename_corr.pdb (#2.2) chain C determined from
SEQRES records
Termini for Z_clone20_chainrename_corr.pdb (#2.2) chain D determined from
SEQRES records
Termini for Z_clone20_chainrename_corr.pdb (#2.2) chain E determined from
SEQRES records
5 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A ILE 1, /B ARG 1, /C ILE
1, /D THR 1, /E VAL 1, /F THR 1, /H LEU 1, /I ASP 1, /J GLN 1, /K ASP 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A VAL 477, /B ALA 483, /C ALA
492, /D SER 72, /E SER 74, /F SER 72, /H SER 119, /I ILE 106, /J SER 123, /K
LYS 103
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A VAL 477
Missing OXT added to C-terminal residue /B ALA 483
Missing OXT added to C-terminal residue /C ALA 492
Missing OXT added to C-terminal residue /D SER 72
Missing OXT added to C-terminal residue /E SER 74
5 messages similar to the above omitted
1460 hydrogen bonds
16017 hydrogens added
> isolde sim start sel
ISOLDE: started sim
> ~select
Nothing selected
> isolde sim stop
[Repeated 1 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...
ISOLDE: Corrected atom nomenclature of 44 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select add #2.2
32238 atoms, 32603 bonds, 2121 residues, 11 models 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 20 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> select add #2.2
32238 atoms, 32603 bonds, 2121 residues, 11 models 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 8 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> close #2.2
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> open /Volumes/4TB/Harrislab/Z_clone20_chainrename_corr.pdb
Chain information for Z_clone20_chainrename_corr.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
K | No description available
> select #1/J
944 atoms, 965 bonds, 123 residues, 1 model selected
> select #1/J/K/I
2540 atoms, 2595 bonds, 332 residues, 1 model selected
> select #1/J/K/I/M
2540 atoms, 2595 bonds, 332 residues, 1 model selected
> select #1/J/K/I/H
3453 atoms, 3529 bonds, 451 residues, 1 model selected
> delete sel #1/J/K/I/H
Expected a keyword
> select del #1/J/K/I/H
Expected an objects specifier or a keyword
> delete sel #1/J/K/I/H
Expected a keyword
> delete #1/J/K/I/H
> select add #2.1
5 models selected
> select add #1
12758 atoms, 13037 bonds, 1670 residues, 6 models selected
> select subtract #1
5 models selected
> select add #1
12758 atoms, 13037 bonds, 1670 residues, 6 models selected
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 66 residues in model #1 to IUPAC-IUB
standards.
Chain information for Z_clone20_chainrename_corr.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
1.2/D | No description available
1.2/E | No description available
1.2/F | No description available
Deleting atomic symmetry model...
ISOLDE: created disulfide bonds between the following residues:
C183-C283; A285-A315; C300-C330; A174-A268; B2-B24; A81-A105; B180-B280;
B297-B326; B54-B113; B67-B97
> close #1
Deleting atomic symmetry model...
> close #2
Deleting atomic symmetry model...
> open /Volumes/4TB/Harrislab/Z_clone20_chainrename_corr.pdb
Chain information for Z_clone20_chainrename_corr.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
K | No description available
> delete #1/J/K/I/H
> save /Volumes/4TB/Harrislab/Z_clone20_chainrename_corr_justE.pdb relModel #1
> close
> open /Volumes/4TB/Harrislab/Z_clone20_chainrename_corr_justE.pdb format pdb
Chain information for Z_clone20_chainrename_corr_justE.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> open /Volumes/4TB/Harrislab/Zmab20/20_sharp2_map13b_ZIKVm20.mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
> select add #1
12758 atoms, 13037 bonds, 1670 residues, 1 model selected
> hide sel atoms
> show sel cartoons
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 66 residues in model #1 to IUPAC-IUB
standards.
Chain information for Z_clone20_chainrename_corr_justE.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
1.2/D | No description available
1.2/E | No description available
1.2/F | No description available
ISOLDE: created disulfide bonds between the following residues:
A285-A315; B180-B280; B67-B97; B2-B24; A81-A105; B54-B113; C300-C330;
A174-A268; B297-B326; C183-C283
> clipper associate #2 toModel #1
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> isolde sim start sel
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: stopped sim
> select add #1.2
12758 atoms, 13047 bonds, 1670 residues, 11 models selected
> isolde sim start sel
ISOLDE: stopped sim
> addh #1.2
Summary of feedback from adding hydrogens to
Z_clone20_chainrename_corr_justE.pdb #1.2
---
notes | Termini for Z_clone20_chainrename_corr_justE.pdb (#1.2) chain A
determined from SEQRES records
Termini for Z_clone20_chainrename_corr_justE.pdb (#1.2) chain B determined
from SEQRES records
Termini for Z_clone20_chainrename_corr_justE.pdb (#1.2) chain C determined
from SEQRES records
Termini for Z_clone20_chainrename_corr_justE.pdb (#1.2) chain D determined
from SEQRES records
Termini for Z_clone20_chainrename_corr_justE.pdb (#1.2) chain E determined
from SEQRES records
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A ILE 1, /B ARG 1, /C ILE
1, /D THR 1, /E VAL 1, /F THR 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A VAL 477, /B ALA 483, /C ALA
492, /D SER 72, /E SER 74, /F SER 72
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A VAL 477
Missing OXT added to C-terminal residue /B ALA 483
Missing OXT added to C-terminal residue /C ALA 492
Missing OXT added to C-terminal residue /D SER 72
Missing OXT added to C-terminal residue /E SER 74
1 messages similar to the above omitted
1133 hydrogen bonds
12710 hydrogens added
> 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 31 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1
25474 atoms, 25763 bonds, 1670 residues, 18 models 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 5 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.08363
> ~select
Nothing selected
> 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
> isolde pepflip sel
Flipping the peptide 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 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
> close #1
> open /Volumes/4TB/Harrislab/Zmab20/20_sharp2_map13b_ZIKVm20.mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
> open /Volumes/4TB/Harrislab/Z_clone20_chainrename_corr_justE.pdb
Chain information for Z_clone20_chainrename_corr_justE.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> volume #1 level 0.1439
> hide #2 models
> show #2 models
> select #2/B/A
7283 atoms, 7439 bonds, 960 residues, 1 model selected
> delete sel
> save /Volumes/4TB/Harrislab/ZIKA_E_A.pdb relModel #1
> select add #2
5475 atoms, 5598 bonds, 710 residues, 1 model selected
> hide sel atoms
> show sel cartoons
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 32 residues in model #2 to IUPAC-IUB
standards.
Chain information for Z_clone20_chainrename_corr_justE.pdb
---
Chain | Description
2.2/C | No description available
2.2/D | No description available
2.2/E | No description available
2.2/F | No description available
ISOLDE: created disulfide bonds between the following residues:
C300-C330; C183-C283
> clipper associate #1 toModel #2
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> isolde sim start sel
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: stopped sim
> addh #2.2
Summary of feedback from adding hydrogens to
Z_clone20_chainrename_corr_justE.pdb #2.2
---
notes | Termini for Z_clone20_chainrename_corr_justE.pdb (#2.2) chain C
determined from SEQRES records
Termini for Z_clone20_chainrename_corr_justE.pdb (#2.2) chain D determined
from SEQRES records
Termini for Z_clone20_chainrename_corr_justE.pdb (#2.2) chain E determined
from SEQRES records
Termini for Z_clone20_chainrename_corr_justE.pdb (#2.2) chain F determined
from SEQRES records
Chain-initial residues that are actual N termini: /C ILE 1, /D THR 1, /E VAL
1, /F THR 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /C ALA 492, /D SER 72, /E SER
74, /F SER 72
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /C ALA 492
Missing OXT added to C-terminal residue /D SER 72
Missing OXT added to C-terminal residue /E SER 74
Missing OXT added to C-terminal residue /F SER 72
498 hydrogen bonds
5506 hydrogens added
> 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 13 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ~select
Nothing 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 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
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> 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
> volume #2.1.1.1 level 0.158
Unable to flip peptide bond after 50 rounds. Giving up.
> volume #2.1.1.1 level 0.1311
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ~select
Nothing selected
> ui tool show "Ramachandran Plot"
[Repeated 2 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> volume #2.1.1.1 level 0.1097
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> volume #2.1.1.1 level 0.09252
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
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 pepflip sel
Flipping the peptide bond for 1 residues
> select clear
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> volume #2.1.1.1 level 0.1462
> 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 pepflip sel
Flipping the peptide bond 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: 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
> select clear
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide 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 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 pepflip sel
Flipping the peptide bond 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 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 sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.2216
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> volume #2.1.1.1 level 0.1805
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Volumes/4TB/Harrislab/Zika_A.pdb relModel #2.1.1.1.1
> close #2
> open /Volumes/4TB/Harrislab/Zmab20/20_sharp2_map13b_ZIKVm20.mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
> open /Volumes/4TB/Harrislab/ZIKA_A2.pdb
Chain information for ZIKA_A2.pdb #2
---
Chain | Description
C | No description available
F | No description available
> fitmap #2 inMap #1
Fit molecule ZIKA_A2.pdb (#2) to map 20_sharp2_map13b_ZIKVm20.mrc (#1) using
8585 atoms
average map value = 0.1536, steps = 28
shifted from previous position = 0.0176
rotated from previous position = 0.0348 degrees
atoms outside contour = 6194, contour level = 0.16857
Position of ZIKA_A2.pdb (#2) relative to 20_sharp2_map13b_ZIKVm20.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999991 0.00003958 -0.00042684 0.06614044
-0.00003976 0.99999991 -0.00043031 0.07569761
0.00042682 0.00043033 0.99999982 -0.08618567
Axis 0.70846858 -0.70271394 -0.06530995
Axis point 0.00000000 200.45931505 174.71503749
Rotation angle (degrees) 0.03480138
Shift along axis -0.00070656
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for ZIKA_A2.pdb
---
Chain | Description
2.2/C | No description available
2.2/F | No description available
> clipper associate #1 toModel #2
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> 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
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 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 pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Volumes/4TB/Harrislab/ZIKA_A3.pdb relModel #2.1.1.1
> fiew
Unknown command: fiew
> view
> select #2.2/F
1182 atoms, 1197 bonds, 72 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 clear
> 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 sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> close #2
> open /Volumes/4TB/Harrislab/Zmab20/20_sharp2_map13b_ZIKVm20.mrc format mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
> open /Volumes/4TB/Harrislab/ZIKA_A4.pdb
Chain information for ZIKA_A4.pdb #2
---
Chain | Description
C | No description available
F | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 22 residues in model #2 to IUPAC-IUB
standards.
Chain information for ZIKA_A4.pdb
---
Chain | Description
2.2/C | No description available
2.2/F | No description available
ISOLDE: created disulfide bonds between the following residues:
C300-C330; C183-C283
> clipper associate #1 toModel #2
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> view #2.2 :225
> isolde sim start sel
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: stopped sim
> addh #2.2
Summary of feedback from adding hydrogens to ZIKA_A4.pdb #2.2
---
notes | Termini for ZIKA_A4.pdb (#2.2) chain C determined from SEQRES records
Termini for ZIKA_A4.pdb (#2.2) chain F determined from SEQRES records
Chain-initial residues that are actual N termini: /C ILE 1, /F THR 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /C ALA 492, /F SER 72
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /C ALA 492
Missing OXT added to C-terminal residue /F SER 72
387 hydrogen bonds
4284 hydrogens added
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.1363
> isolde sim start sel
ISOLDE: started sim
> volume #2.1.1.1 level 0.05968
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.1012
> close #2
> open /Volumes/4TB/Harrislab/Zmab20/20_sharp2_map13b_ZIKVm20.mrc format mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
> open /Volumes/4TB/Harrislab/EM_5fold.pdb
Chain information for EM_5fold.pdb #2
---
Chain | Description
C | No description available
F | No description available
> ui mousemode right zoom
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 22 residues in model #2 to IUPAC-IUB
standards.
Chain information for EM_5fold.pdb
---
Chain | Description
2.2/C | No description available
2.2/F | No description available
ISOLDE: created disulfide bonds between the following residues:
C300-C330; C183-C283
> addh #2.2
Summary of feedback from adding hydrogens to EM_5fold.pdb #2.2
---
notes | Termini for EM_5fold.pdb (#2.2) chain C determined from SEQRES records
Termini for EM_5fold.pdb (#2.2) chain F determined from SEQRES records
Chain-initial residues that are actual N termini: /C ILE 1, /F THR 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /C ALA 492, /F SER 72
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /C ALA 492
Missing OXT added to C-terminal residue /F SER 72
387 hydrogen bonds
4284 hydrogens added
> isolde sim start sel
ISOLDE: started sim
> volume #1 level 0.2156
> clipper associate #1 toModel #2
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> volume #2.1.1.1 level 0.1445
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 14 residues in model #2.2 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 pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> volume #2.1.1.1 level 0.1279
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> volume #2.1.1.1 level 0.08225
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #2.2 :22ต
Expected an integer >= 1 or a keyword
> view #2.2 :229
> volume #2.1.1.1 level 0.1786
> view #2.2 :225
> isolde sim start sel
ISOLDE: started sim
> ui mousemode right zoom
> ui mousemode right translate
> 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 cisflip sel
Performing cis<\-->trans flip for 1 residues
> select clear
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> 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
> select clear
> isolde cisflip sel
Performing cis<\-->trans flip for 1 residues
> volume #2.1.1.1 level 0.1483
> 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 pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 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 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 sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view
> select clear
> 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 sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 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 pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
[Repeated 2 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 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 sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 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 sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view
> 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 #2.2 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 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 sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view
> save /Volumes/4TB/Harrislab/EM_5fold_1.pdb relModel #2.1.1.1
> view #2.2:224
> isolde sim start sel
ISOLDE: started sim
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #2.2,1,0,0,0.11117,0,1,0,-0.28154,0,0,1,0.45945
> undo
> 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
> isolde pepflip sel
Flipping the peptide bond 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 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 /Volumes/4TB/Harrislab/EM_5fold_2.pdb relModel #2.1.1.1
> close #2
> open /Users/uqnmodhi/Downloads/cryosparc_P42_J59_class_00_00022_volume.mrc
> format mrc
No such file/path:
/Users/uqnmodhi/Downloads/cryosparc_P42_J59_class_00_00022_volume.mrc
> open /Volumes/4TB/Harrislab/Zmab20/20_sharp2_map13b_ZIKVm20.mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/AB-coot-0.pdb
Summary of feedback from opening /Users/uqnmodhi/Documents/SPA/Harris_lab/AB-
coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER C 143
ILE C 146 1 4
Start residue of secondary structure not found: HELIX 2 2 PHE C 191 ASP C 193
1 3
Start residue of secondary structure not found: HELIX 3 3 LYS C 208 TRP C 210
1 3
Start residue of secondary structure not found: HELIX 4 4 PHE C 211 ASP C 213
1 3
Start residue of secondary structure not found: HELIX 5 5 LYS C 231 ALA C 233
1 3
36 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (183 )
Cannot find LINK/SSBOND residue CYS (300 )
Chain information for AB-coot-0.pdb #2
---
Chain | Description
A | No description available
F | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for AB-coot-0.pdb
---
Chain | Description
2.2/A | No description available
2.2/F | No description available
ISOLDE: created disulfide bonds between the following residues:
A300-A330; A183-A283
> clipper associate #1 toModel #2
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> view #2.2/B:12
No objects specified.
> volume #2.1.1.1 level 0.04165
> ~select
Nothing selected
> view #2.2/B:12
No objects specified.
> view
> ui mousemode right zoom
> hide #!2.2 target m
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/AB-coot-1.pdb
Summary of feedback from opening /Users/uqnmodhi/Documents/SPA/Harris_lab/AB-
coot-1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER C 143
ILE C 146 1 4
Start residue of secondary structure not found: HELIX 2 2 PHE C 191 ASP C 193
1 3
Start residue of secondary structure not found: HELIX 3 3 LYS C 208 TRP C 210
1 3
Start residue of secondary structure not found: HELIX 4 4 PHE C 211 ASP C 213
1 3
Start residue of secondary structure not found: HELIX 5 5 LYS C 231 ALA C 233
1 3
42 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (183 )
Cannot find LINK/SSBOND residue CYS (300 )
Chain information for AB-coot-1.pdb #1
---
Chain | Description
A | No description available
B | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for AB-coot-1.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
ISOLDE: created disulfide bonds between the following residues:
A300-A330; A183-A283
> view #1.2/B:12
> volume #2.1.1.1 level 0.1161
> 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
> volume #2.1.1.1 level 0.159
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> 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
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[Repeated 1 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> select clear
[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
> open 5IZ7
Summary of feedback from opening 5IZ7 fetched from pdb
---
note | Fetching compressed mmCIF 5iz7 from
http://files.rcsb.org/download/5iz7.cif
5iz7 title:
Cryo-EM structure of thermally stable Zika virus strain H/PF/2013 [more
info...]
Chain information for 5iz7 #3
---
Chain | Description | UniProt
A B C | structural protein E | A0A024B7W1_ZIKV
D E F | structural protein M | A0A0U4DG08_ZIKV
Non-standard residues in 5iz7 #3
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
5iz7 mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> mmaker #3 to #2.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AB-coot-0.pdb, chain A (#2.2) with 5iz7, chain A (#3), sequence
alignment score = 1945.1
RMSD between 430 pruned atom pairs is 1.149 angstroms; (across all 491 pairs:
1.473)
> select add #3
13269 atoms, 13571 bonds, 1741 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> view
> ui mousemode right zoom
> ~select
Nothing selected
> hide #3 models
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /Users/uqnmodhi/Documents/SPA/Harris_lab/AB-coot-2.pdb models #1
> relModel #2.1.1.1
> view :82
> ui mousemode right zoom
> volume #2.1.1.1 level 0.2108
> select :82
48 atoms, 43 bonds, 5 residues, 3 models selected
> select : #2.2:82
Expected an objects specifier or a keyword
> select #2.2:82
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2.2/A:82
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2.2/C:82
Nothing selected
> select #2.2/A:82
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2.2/A:82
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2.2/A:82-84
43 atoms, 42 bonds, 3 residues, 1 model selected
> select #2.2/A:82-84
43 atoms, 42 bonds, 3 residues, 1 model selected
> select #1.2/A:82-84
43 atoms, 42 bonds, 3 residues, 1 model selected
> 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
> volume #2.1.1.1 level 0.1427
> 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 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
> save /Users/uqnmodhi/Documents/SPA/Harris_lab/AB-coot-3.pdb models #2
> relModel #2.1.1.1
> select #1.2/A:272-274
39 atoms, 38 bonds, 3 residues, 1 model selected
> view #1.2/A:272-274
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /Users/uqnmodhi/Documents/SPA/Harris_lab/AB-coot-4.pdb models #2
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> show #!2.2 models
> hide #!2.2 models
> save /Users/uqnmodhi/Documents/SPA/Harris_lab/AB-coot-5.pdb models #1
> relModel #2.1.1.1
> view #1.2/A:73-74
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> isolde sim start sel
[Repeated 1 time(s)]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 clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /Users/uqnmodhi/Documents/SPA/Harris_lab/AB_20250205_1.pdb models #1
> relModel #2.1.1.1
> close #1
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/AB_20250205_1-coot-0.pdb
Chain information for AB_20250205_1-coot-0.pdb #1
---
Chain | Description
A C | No description available
B D | No description available
Window position QRect(3232,294 149x44) outside any known screen, using primary
screen
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for AB_20250205_1-coot-0.pdb
---
Chain | Description
1.2/A 1.2/C | No description available
1.2/B 1.2/D | No description available
ISOLDE: created disulfide bonds between the following residues:
C300-C330; C183-C283
Window position QRect(3106,419 0x3) outside any known screen, using primary
screen
> close #3#1.1,3#2.3#1-2#1.2#2.1-2
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/AB_20250205_1-coot-0.pdb
Chain information for AB_20250205_1-coot-0.pdb #1
---
Chain | Description
A C | No description available
B D | No description available
> open /Volumes/4TB/Harrislab/Zmab20/20_sharp2_map13b_ZIKVm20.mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for AB_20250205_1-coot-0.pdb
---
Chain | Description
1.2/A 1.2/C | No description available
1.2/B 1.2/D | No description available
ISOLDE: created disulfide bonds between the following residues:
C300-C330; C183-C283
> clipper associate #2 toModel #1
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> ui mousemode right zoom
> ~select
Nothing selected
> ui tool show "Ramachandran Plot"
> ~select
Nothing selected
> select #1.2/C
7403 atoms, 7483 bonds, 492 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> 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
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> select clear
> isolde sim resume
> 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
> ui mousemode right zoom
> select clear
> 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
> isolde ignore 1.2/B:13
Expected a residues specifier or a keyword
> isolde ignore sel
Changes to the set of ignored residues will notbe applied until you stop the
current simulation.
ISOLDE: currently ignoring 1 residues in model 1.2
> isolde sim resume
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond 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 6 residues
Window position QRect(2381,413 600x300) outside any known screen, using
primary screen
Peptide bond must be mobile in the simulation!
> ui mousemode right zoom
> select clear
[Repeated 4 time(s)]
> isolde sim resume
> hide #!1.2 models
> show #!1.2 models
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/AB_20250205_1-coot-1.pdb
Chain information for AB_20250205_1-coot-1.pdb #2
---
Chain | Description
A C | No description available
B D | No description available
> hide #!1.2 models
> show #!1.2 models
> close #1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/position.py", line 118, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/distance.py", line 150, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/secondary_structure.py", line 79,
in _selection_changed_cb
sel = self.isolde.selected_atoms.unique_residues
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/register_shift.py", line 105, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/20_sharp2_map13b_ZIKVm20.mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb
self._expanded_cb()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb
tm = self.torsion_restraint_mgr
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr
return AdaptiveDihedralRestraintMgr(model)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__
super().__init__(model, c_pointer=c_pointer,
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__
super().__init__(display_name, model, c_pointer)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
AttributeError: 'AtomicStructure' object has no attribute 'session'
Error processing trigger "add models":
AttributeError: 'AtomicStructure' object has no attribute 'session'
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x101458820>
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1199, in __del__
if not self.was_deleted:
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb
self._expanded_cb()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb
tm = self.torsion_restraint_mgr
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr
return AdaptiveDihedralRestraintMgr(model)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__
super().__init__(model, c_pointer=c_pointer,
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__
super().__init__(display_name, model, c_pointer)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
AttributeError: 'AtomicStructure' object has no attribute 'session'
Error processing trigger "add models":
AttributeError: 'AtomicStructure' object has no attribute 'session'
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x101458820>
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1199, in __del__
if not self.was_deleted:
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb
self._expanded_cb()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb
tm = self.torsion_restraint_mgr
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr
return AdaptiveDihedralRestraintMgr(model)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__
super().__init__(model, c_pointer=c_pointer,
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__
super().__init__(display_name, model, c_pointer)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
AttributeError: 'AtomicStructure' object has no attribute 'session'
Error processing trigger "add models":
AttributeError: 'AtomicStructure' object has no attribute 'session'
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__
session = model.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x101458820>
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1199, in __del__
if not self.was_deleted:
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'
> isolde sim stop
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1038, in
_sim_end_cb
self._pr_sim_end_cb()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1095, in
_pr_sim_end_cb
restraints =
self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 2382, in get_restraints
return self._get_restraints(atoms)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 2335, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 2335, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 1009, in _sim_end_cb
run(self.session, f'clipper spot #{self.selected_model.id_string}', log=False)
AttributeError: 'NoneType' object has no attribute 'id_string'
Error processing trigger "sim terminated":
AttributeError: 'NoneType' object has no attribute 'id_string'
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 1009, in _sim_end_cb
run(self.session, f'clipper spot #{self.selected_model.id_string}', log=False)
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2 to IUPAC-IUB
standards.
Chain information for AB_20250205_1-coot-1.pdb
---
Chain | Description
2.2/A 2.2/C | No description available
2.2/B 2.2/D | No description available
ISOLDE: created disulfide bonds between the following residues:
C300-C330; C183-C283
> clipper associate #1 toModel #2
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> view
> select #2.2/C/
Expected an objects specifier or a keyword
> select #2.2/C
7403 atoms, 7483 bonds, 492 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #2/C
7403 atoms, 7483 bonds, 492 residues, 1 model selected
> 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 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
Unable to flip peptide bond after 50 rounds. Giving up.
[Repeated 2 time(s)]
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip sel
Flipping the peptide bond for 1 residues
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 12 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> save /Users/uqnmodhi/Documents/SPA/Harris_lab/ABCD_20250205_1-coot-0.pdb
> relModel #2.1.1.1
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/ABCD_20250205_1-coot-1.pdb
Chain information for ABCD_20250205_1-coot-1.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
> close #1
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/ABCDEF_20250205_1-coot-2.pdb
Chain information for ABCDEF_20250205_1-coot-2.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for ABCDEF_20250205_1-coot-2.pdb
---
Chain | Description
1.2/A 1.2/C 1.2/E | No description available
1.2/B 1.2/D 1.2/F | No description available
ISOLDE: created disulfide bonds between the following residues:
E183-E283; E300-E330
> select
42925 atoms, 43400 bonds, 2820 residues, 27 models selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim resume
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/ACE_2.pdb
Summary of feedback from opening
/Users/uqnmodhi/Documents/SPA/Harris_lab/ACE_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER C 143
ILE C 146 1 4
Start residue of secondary structure not found: HELIX 2 2 PHE C 191 ASP C 193
1 3
Start residue of secondary structure not found: HELIX 3 3 LYS C 208 TRP C 210
1 3
Start residue of secondary structure not found: HELIX 4 4 PHE C 211 ASP C 213
1 3
Start residue of secondary structure not found: HELIX 5 5 LYS C 231 ALA C 233
1 3
48 messages similar to the above omitted
End residue of secondary structure not found: HELIX 7 7 GLY C 383 LYS C 385 1
3
End residue of secondary structure not found: HELIX 8 8 THR C 397 LEU C 415 1
19
Start residue of secondary structure not found: HELIX 9 9 GLY C 416 ASP C 421
1 6
End residue of secondary structure not found: HELIX 10 10 ALA C 428 PHE C 448
1 21
Start residue of secondary structure not found: HELIX 11 11 TRP C 453 ASN C
469 1 17
Start residue of secondary structure not found: HELIX 12 12 GLY C 473 THR C
491 1 19
Start residue of secondary structure not found: HELIX 13 13 HIS F 5 THR F 7 1
3
Start residue of secondary structure not found: HELIX 14 14 GLU F 18 ARG F 20
1 3
Start residue of secondary structure not found: HELIX 15 15 LYS F 24 ARG F 35
1 12
11 messages similar to the above omitted
End residue of secondary structure not found: SHEET 9 9 1 GLY C 104 ALA C 112
0
Start residue of secondary structure not found: SHEET 10 10 1 LYS C 113 LYS C
118 0
Start residue of secondary structure not found: SHEET 11 11 1 LYS C 119 SER C
124 0
Start residue of secondary structure not found: SHEET 12 12 1 LEU C 129 VAL C
137 0
Start residue of secondary structure not found: SHEET 13 13 1 ARG C 157 ILE C
162 0
Start residue of secondary structure not found: SHEET 14 14 1 ARG C 168 THR C
172 0
14 messages similar to the above omitted
End residue of secondary structure not found: SHEET 29 29 1 ILE C 387 TRP C
391 0
Start residue of secondary structure not found: HELIX 1 1 SER C 143 ILE C 146
1 4
Start residue of secondary structure not found: HELIX 2 2 PHE C 191 ASP C 193
1 3
Start residue of secondary structure not found: HELIX 3 3 LYS C 208 TRP C 210
1 3
Start residue of secondary structure not found: HELIX 4 4 PHE C 211 ASP C 213
1 3
Start residue of secondary structure not found: HELIX 5 5 LYS C 231 ALA C 233
1 3
48 messages similar to the above omitted
Chain information for ACE_2.pdb
---
Chain | Description
3.4/A 3.6/A 3.7/A 3.1/C 3.2/C 3.3/C 3.7/C 3.7/E | No description available
3.5/A 3.5/B 3.5/C | No description available
3.4/B 3.6/B 3.1/F 3.2/F 3.3/F | No description available
3.5/D 3.5/E 3.5/F | No description available
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> close #3.1-7
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/ACE_2.pdb
Summary of feedback from opening
/Users/uqnmodhi/Documents/SPA/Harris_lab/ACE_2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER C 143
ILE C 146 1 4
Start residue of secondary structure not found: HELIX 2 2 PHE C 191 ASP C 193
1 3
Start residue of secondary structure not found: HELIX 3 3 LYS C 208 TRP C 210
1 3
Start residue of secondary structure not found: HELIX 4 4 PHE C 211 ASP C 213
1 3
Start residue of secondary structure not found: HELIX 5 5 LYS C 231 ALA C 233
1 3
48 messages similar to the above omitted
End residue of secondary structure not found: HELIX 7 7 GLY C 383 LYS C 385 1
3
End residue of secondary structure not found: HELIX 8 8 THR C 397 LEU C 415 1
19
Start residue of secondary structure not found: HELIX 9 9 GLY C 416 ASP C 421
1 6
End residue of secondary structure not found: HELIX 10 10 ALA C 428 PHE C 448
1 21
Start residue of secondary structure not found: HELIX 11 11 TRP C 453 ASN C
469 1 17
Start residue of secondary structure not found: HELIX 12 12 GLY C 473 THR C
491 1 19
Start residue of secondary structure not found: HELIX 13 13 HIS F 5 THR F 7 1
3
Start residue of secondary structure not found: HELIX 14 14 GLU F 18 ARG F 20
1 3
Start residue of secondary structure not found: HELIX 15 15 LYS F 24 ARG F 35
1 12
11 messages similar to the above omitted
End residue of secondary structure not found: SHEET 9 9 1 GLY C 104 ALA C 112
0
Start residue of secondary structure not found: SHEET 10 10 1 LYS C 113 LYS C
118 0
Start residue of secondary structure not found: SHEET 11 11 1 LYS C 119 SER C
124 0
Start residue of secondary structure not found: SHEET 12 12 1 LEU C 129 VAL C
137 0
Start residue of secondary structure not found: SHEET 13 13 1 ARG C 157 ILE C
162 0
Start residue of secondary structure not found: SHEET 14 14 1 ARG C 168 THR C
172 0
14 messages similar to the above omitted
End residue of secondary structure not found: SHEET 29 29 1 ILE C 387 TRP C
391 0
Start residue of secondary structure not found: HELIX 1 1 SER C 143 ILE C 146
1 4
Start residue of secondary structure not found: HELIX 2 2 PHE C 191 ASP C 193
1 3
Start residue of secondary structure not found: HELIX 3 3 LYS C 208 TRP C 210
1 3
Start residue of secondary structure not found: HELIX 4 4 PHE C 211 ASP C 213
1 3
Start residue of secondary structure not found: HELIX 5 5 LYS C 231 ALA C 233
1 3
48 messages similar to the above omitted
Chain information for ACE_2.pdb
---
Chain | Description
4.4/A 4.6/A 4.7/A 4.1/C 4.2/C 4.3/C 4.7/C 4.7/E | No description available
4.5/A 4.5/B 4.5/C | No description available
4.4/B 4.6/B 4.1/F 4.2/F 4.3/F | No description available
4.5/D 4.5/E 4.5/F | No description available
> close #4
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/ACD_3.pdb
Chain information for ACD_3.pdb #4
---
Chain | Description
A C E | No description available
> close #3
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for ACD_3.pdb
---
Chain | Description
3.2/A 3.2/C 3.2/E | No description available
ISOLDE: created disulfide bonds between the following residues:
E300-E330; E183-E283
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
> close #3.2
Deleting atomic symmetry model...
Deleting atomic symmetry model...
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/position.py", line 118, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/distance.py", line 150, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/secondary_structure.py", line 79,
in _selection_changed_cb
sel = self.isolde.selected_atoms.unique_residues
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/register_shift.py", line 105, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1038, in
_sim_end_cb
self._pr_sim_end_cb()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1095, in
_pr_sim_end_cb
restraints =
self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 2382, in get_restraints
return self._get_restraints(atoms)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 2335, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer'
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 2335, in _get_restraints
num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> close #1
Deleting atomic symmetry model...
> close #2
Deleting atomic symmetry model...
> close #3
Deleting atomic symmetry model...
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/ACD_3.pdb
Chain information for ACD_3.pdb #1
---
Chain | Description
A C E | No description available
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/20_sharp2_map13b_ZIKVm20.mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for ACD_3.pdb
---
Chain | Description
1.2/A 1.2/C 1.2/E | No description available
ISOLDE: created disulfide bonds between the following residues:
E183-E283; E300-E330
> 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
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/ACD_3-coot-0.pdb
Chain information for ACD_3-coot-0.pdb #3
---
Chain | Description
A C E | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #3 to IUPAC-IUB
standards.
Chain information for ACD_3-coot-0.pdb
---
Chain | Description
3.2/A 3.2/C 3.2/E | No description available
ISOLDE: created disulfide bonds between the following residues:
E183-E283; E300-E330
> view
> ui mousemode right zoom
> hide #!3.2 models
> show #!3.2 models
> 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 10 residues in model #3.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> close #1
> ui mousemode right zoom
> clipper associate #2 toModel #3
Opened 20_sharp2_map13b_ZIKVm20.mrc as #3.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> select add #3.2
22209 atoms, 22449 bonds, 1476 residues, 11 models selected
> select add #3.2
22209 atoms, 22449 bonds, 1476 residues, 11 models selected
> ~select
Nothing selected
> select #3.2
22209 atoms, 22449 bonds, 1476 residues, 11 models selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
[Repeated 3 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...
ISOLDE: Corrected atom nomenclature of 14 residues in model #3.2 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
> select clear
> 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 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: Corrected atom nomenclature of 2 residues in model #3.2 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 pepflip sel
Flipping the peptide bond 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 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 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
Unable to flip peptide bond after 50 rounds. Giving up.
> 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 #3.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #3.2 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: Corrected atom nomenclature of 1 residues in model #3.2 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: Corrected atom nomenclature of 1 residues in model #3.2 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 sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /Users/uqnmodhi/Documents/SPA/Harris_lab/ACE_done.pdb relModel #3.1.1.1
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/ABCDEF_done-coot-2.pdb
Chain information for ABCDEF_done-coot-2.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1 to IUPAC-IUB
standards.
Chain information for ABCDEF_done-coot-2.pdb
---
Chain | Description
1.2/A 1.2/C 1.2/E | No description available
1.2/B 1.2/D 1.2/F | No description available
> close #1
> close
> close #
Expected a models specifier or a keyword
> close #
Expected a models specifier or a keyword
> open /Volumes/4TB/Harrislab/Zmab20/20_sharp2_map13b_ZIKVm20.mrc format mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/ABCDEF_done-coot-2.pdb
Chain information for ABCDEF_done-coot-2.pdb #2
---
Chain | Description
A C E | No description available
B D F | No description available
> volume #1
> volume #1 level 0.2491
> volume #1 step 1
> hide cartoons
> hide atoms
> show cartoons
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2 to IUPAC-IUB
standards.
Chain information for ABCDEF_done-coot-2.pdb
---
Chain | Description
2.2/A 2.2/C 2.2/E | No description available
2.2/B 2.2/D 2.2/F | No description available
> clipper associate #1 toModel #2
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> ui mousemode right zoom
> 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 9 residues in model #2.2 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 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
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 stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> 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 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 pepflip sel
Flipping the peptide bond for 1 residues
ISOLDE: started sim
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 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 #2.2 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> 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 #2.2 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 #2.2 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 pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond 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 #2.2 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
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: 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
> 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 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 clear
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.1446
> 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 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
> select clear
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde pepflip sel
Flipping the peptide bond for 1 residues
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde 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 #2.2 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
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> 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
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> ~select
Nothing selected
> select clear
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> save /Users/uqnmodhi/Documents/SPA/Harris_lab/ABCDEF_5.pdb relModel
> #2.1.1.1.1
> close #2
> open /Volumes/4TB/Harrislab/Zmab20/20_sharp2_map13b_ZIKVm20.mrc format mrc
Opened 20_sharp2_map13b_ZIKVm20.mrc as #1, grid size 336,336,336, pixel 0.8,
shown at level 0.169, step 2, values float32
> open /Users/uqnmodhi/Documents/SPA/Harris_lab/ABCDEF_5.pdb
Chain information for ABCDEF_5.pdb #2
---
Chain | Description
A C E | No description available
B D F | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for ABCDEF_5.pdb
---
Chain | Description
2.2/A 2.2/C 2.2/E | No description available
2.2/B 2.2/D 2.2/F | No description available
> clipper associate #1 toModel #2
Opened 20_sharp2_map13b_ZIKVm20.mrc as #2.1.1.1, grid size 336,336,336, pixel
0.8, shown at step 1, values float32
> ui mousemode right zoom
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider
toolbar_command(session, name)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command
run(session, 'isolde sim start sel')
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim
isolde.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim
sm.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim
self._prepare_sim()
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
openmm.OpenMMException: Error initializing context: clCreateCommandQueue (-30)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1186, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1993, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range
Error processing trigger "changes":
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1186, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1993, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range
Error processing trigger "changes":
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1186, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1993, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range
Error processing trigger "changes":
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range
File "/Users/uqnmodhi/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
> select clear
OpenGL version: unknown
Could not make opengl context current
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: Z14W000TLX/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.81.2
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.3 (23H417)
Kernel Version: Darwin 23.6.0
Time since boot: 3 days, 14 hours, 2 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2414H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (1)
comment:1 by , 8 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE: 'AtomicStructure' object has no attribute '_c_pointer_ref' |
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