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Opened 5 years ago
Last modified 3 years ago
#3805 closed defect
Flip peptide bond: Simulation must be running — at Version 1
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6a93 format mmcif fromDatabase pdb
6a93 title:
Crystal structure of 5-HT2AR in complex with risperidone [more info...]
Chain information for 6a93 #1
---
Chain | Description
A B | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
Non-standard residues in 6a93 #1
---
1PE — pentaethylene glycol (PEG400)
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
CLR — cholesterol
PLM — palmitic acid
ZN — zinc ion
6a93 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> log metadata #1
Metadata for 6a93 #1
---
Title | Crystal structure of 5-HT2AR in complex with risperidone
Citation | Kimura, K.T., Asada, H., Inoue, A., Kadji, F.M.N., Im, D., Mori,
C., Arakawa, T., Hirata, K., Nomura, Y., Nomura, N., Aoki, J., Iwata, S.,
Shimamura, T. (2019). Structures of the 5-HT2Areceptor in complex with the
antipsychotics risperidone and zotepine. Nat.Struct.Mol.Biol., 26, 121-128.
PMID: 30723326. DOI: 10.1038/s41594-018-0180-z
Non-standard residues | 1PE — pentaethylene glycol (PEG400)
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
CLR — cholesterol
PLM — palmitic acid
ZN — zinc ion
Gene sources | Homo sapiens (human)
Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.707Å
> select /B
2886 atoms, 2950 bonds, 2 pseudobonds, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> ui tool show ISOLDE
> set selectionWidth 4
6a93 title:
Crystal structure of 5-HT2AR in complex with risperidone [more info...]
Chain information for 6a93
---
Chain | Description
1.2/A | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
Non-standard residues in 6a93 #1.2
---
1PE — pentaethylene glycol (PEG400)
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
CLR — cholesterol
ZN — zinc ion
6a93 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Done loading forcefield
> select /A
3003 atoms, 3069 bonds, 5 pseudobonds, 2 models selected
> surface style (#!1.2 & sel) mesh
> ui tool show "Side View"
> ui tool show "Color Actions"
> set bgColor white
> set bgColor black
> close 1
Expected a models specifier or a keyword
> close ~1
Expected a models specifier or a keyword
> close #1
Deleting atomic symmetry model...
> open 6a93 format mmcif fromDatabase pdb
6a93 title:
Crystal structure of 5-HT2AR in complex with risperidone [more info...]
Chain information for 6a93 #1
---
Chain | Description
A B | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
Non-standard residues in 6a93 #1
---
1PE — pentaethylene glycol (PEG400)
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
CLR — cholesterol
PLM — palmitic acid
ZN — zinc ion
6a93 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select /B
2886 atoms, 2950 bonds, 2 pseudobonds, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select ligand
97 atoms, 101 bonds, 1 model selected
> delete sel
> select :ZN
1 atom, 1 model selected
> delete sel
> ui tool show ISOLDE
> set selectionWidth 4
6a93 title:
Crystal structure of 5-HT2AR in complex with risperidone [more info...]
Chain information for 6a93
---
Chain | Description
1.2/A | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
6a93 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Done loading forcefield
> display #1
> structureFactors true
Unknown command: structureFactors true
> close #1
Deleting atomic symmetry model...
> open 6a93 structureFactors true
Summary of feedback from opening 6a93 fetched from pdb
---
notes | Fetching compressed 6a93 structure factors from
http://files.rcsb.org/download/6a93-sf.cif
Resolution: 3.0000161028648624
6a93 title:
Crystal structure of 5-HT2AR in complex with risperidone [more info...]
Chain information for 6a93
---
Chain | Description
1.2/A 1.2/B | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
Non-standard residues in 6a93 #1.2
---
1PE — pentaethylene glycol (PEG400)
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
CLR — cholesterol
PLM — palmitic acid
ZN — zinc ion
6a93 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select /B
2886 atoms, 2950 bonds, 2 pseudobonds, 2 models selected
> delete atoms (#!1.2 & sel)
> delete bonds (#!1.2 & sel)
> select /A
3003 atoms, 3069 bonds, 5 pseudobonds, 2 models selected
> show (#!1.2 & sel) target ab
> show (#!1.2 & sel-residues & sidechain) target ab
> show (#!1.2 & sel) target ab
> select clear
> select clear
> select up
92 atoms, 93 bonds, 1 model selected
> select up
3003 atoms, 3069 bonds, 1 model selected
> show (#!1.2 & sel) target ab
> surface style (#!1.2 & sel) mesh
> close #1
Deleting atomic symmetry model...
Deleting (LIVE) 2mFo-DFc_sharp_29
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) MDFF potential
Deleting Crystallographic maps (6a93-sf.cif)
> open 6a93
6a93 title:
Crystal structure of 5-HT2AR in complex with risperidone [more info...]
Chain information for 6a93 #1
---
Chain | Description
A B | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
Non-standard residues in 6a93 #1
---
1PE — pentaethylene glycol (PEG400)
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
CLR — cholesterol
PLM — palmitic acid
ZN — zinc ion
6a93 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
6a93 title:
Crystal structure of 5-HT2AR in complex with risperidone [more info...]
Chain information for 6a93
---
Chain | Description
1.2/A 1.2/B | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
Non-standard residues in 6a93 #1.2
---
1PE — pentaethylene glycol (PEG400)
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
CLR — cholesterol
PLM — palmitic acid
ZN — zinc ion
6a93 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select clear
> select up
92 atoms, 93 bonds, 1 model selected
> select up
3003 atoms, 3069 bonds, 1 model selected
> show (#!1.2 & sel) target ab
> close #1
Deleting atomic symmetry model...
> open 6a93
6a93 title:
Crystal structure of 5-HT2AR in complex with risperidone [more info...]
Chain information for 6a93 #1
---
Chain | Description
A B | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
Non-standard residues in 6a93 #1
---
1PE — pentaethylene glycol (PEG400)
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
CLR — cholesterol
PLM — palmitic acid
ZN — zinc ion
6a93 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select /B
2886 atoms, 2950 bonds, 2 pseudobonds, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select ligands
Expected an objects specifier or a keyword
> select ligand
97 atoms, 101 bonds, 1 model selected
> delete sel
> select :ZN
1 atom, 1 model selected
> delete sel
> save "/Users/lukedamerum/Desktop/UoN/PhD Project/The University of
> Nottingham/Shailesh Mistry - Luke Damerum/PhD Project/Computational
> Chemistry/ChimeraX/Tutorial/6A93 Test.mtz"
You need to specify at least one crystallographic map set to save!
> save "/Users/lukedamerum/Desktop/UoN/PhD Project/The University of
> Nottingham/Shailesh Mistry - Luke Damerum/PhD Project/Computational
> Chemistry/ChimeraX/Tutorial/6a93 test.mtz"
You need to specify at least one crystallographic map set to save!
No known data format for file suffix '.mtx'
> save /Users/lukedamerum/desktop/6a93.mtz #1
You need to specify at least one crystallographic map set to save!
> open 6a93 structureFactors true
Summary of feedback from opening 6a93 fetched from pdb
---
notes | Resolution: 3.0000161028648624
6a93 title:
Crystal structure of 5-HT2AR in complex with risperidone [more info...]
Chain information for 6a93
---
Chain | Description
2.2/A 2.2/B | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
Non-standard residues in 6a93 #2.2
---
1PE — pentaethylene glycol (PEG400)
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
CLR — cholesterol
PLM — palmitic acid
ZN — zinc ion
6a93 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> close #1
> open 1a0m structureFactors true
Summary of feedback from opening 1a0m fetched from pdb
---
warning | No free flags detected in this dataset! Automatically generated a
new random set with 445 free from 9264 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.
notes | Fetching compressed mmCIF 1a0m from
http://files.rcsb.org/download/1a0m.cif
Fetching compressed 1a0m structure factors from
http://files.rcsb.org/download/1a0m-sf.cif
Resolution: 1.0944213038232693
1a0m title:
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]
Chain information for 1a0m
---
Chain | Description
1.2/A 1.2/B | α-conotoxin [TYR15]-epi
Non-standard residues in 1a0m #1.2
---
NH2 — amino group
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
Please select a single residue!
> select clear
> select #2.2/A
3003 atoms, 3069 bonds, 5 pseudobonds, 2 models selected
> select #2.2/B
2886 atoms, 2950 bonds, 2 pseudobonds, 2 models selected
> delete atoms (#!2.2 & sel)
> delete bonds (#!2.2 & sel)
> select #2.2/A:228
8 atoms, 7 bonds, 1 model selected
> select up
96 atoms, 96 bonds, 1 model selected
> select up
3003 atoms, 3069 bonds, 1 model selected
Please select a single residue!
Please select a single residue!
> addh H
No structures specified
> addh H #2
Expected a keyword
> close #1
Deleting atomic symmetry model...
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc_smooth_27
Deleting Crystallographic maps (1a0m-sf.cif)
> addh H
No structures specified
> addh H 6a93
Expected a keyword
> select clear
> select up
2 atoms, 1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select ligand
97 atoms, 101 bonds, 1 model selected
> delete sel
> delete :ZN
> select clear
> select up
2 atoms, 1 bond, 1 model selected
> select up
8 atoms, 7 bonds, 1 model selected
Please select a single atom!
> ui tool show ISOLDE
> set selectionWidth 4
Done loading forcefield
> select up
8 atoms, 7 bonds, 1 model selected
Updating bulk solvent parameters...
> addh
Summary of feedback from adding hydrogens to 6a93 #2.2
---
notes | Termini for 6a93 (#2.2) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A THR 69
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A TYR 399
367 hydrogen bonds
Adding 'H' to /A THR 69
/A TYR 399 is not terminus, removing H atom from 'C'
2988 hydrogens added
Traceback (most recent call last):
File "/Users/lukedamerum/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2246, in _flip_peptide_bond
self.flip_peptide_bond(res)
File "/Users/lukedamerum/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 3218, in flip_peptide_bond
pf = Peptide_Bond_Flipper(self, res)
File "/Users/lukedamerum/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/manipulations/peptide_flip.py", line 44, in __init__
raise TypeError('Simulation must be running!')
TypeError: Simulation must be running!
TypeError: Simulation must be running!
File "/Users/lukedamerum/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/manipulations/peptide_flip.py", line 44, in __init__
raise TypeError('Simulation must be running!')
See log for complete Python traceback.
OpenGL version: 3.3 NVIDIA-10.4.14 310.90.30.05b27
OpenGL renderer: NVIDIA GeForce 320M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro7,1
Processor Name: Intel Core 2 Duo
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache: 3 MB
Memory: 8 GB
Boot ROM Version: 68.0.0.0.0
SMC Version (system): 1.62f7
Sudden Motion Sensor:
State: Enabled
Software:
System Software Overview:
System Version: macOS 10.13.6 (17G14019)
Kernel Version: Darwin 17.7.0
Time since boot: 8:28
Graphics/Displays:
NVIDIA GeForce 320M:
Chipset Model: NVIDIA GeForce 320M
Type: GPU
VRAM (Dynamic, Max): 256 MB
Vendor: NVIDIA (0x10de)
Device ID: 0x08a0
Revision ID: 0x00a2
ROM Revision: 3533
Displays:
Color LCD:
Display Type: LCD
Resolution: 1280 x 800
UI Looks like: 1280 x 800
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History (1)
comment:1 by , 5 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Flip peptide bond: Simulation must be running |
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