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#3805 closed defect (fixed)

Flip peptide bond: Simulation must be running

Reported by:	chimerax-bug-report@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description (last modified by pett)

The following bug report has been submitted:
Platform:        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 (3)

comment:1 by pett, 5 years ago

Component:	Unassigned → Third Party
Description:	modified (diff)
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Flip peptide bond: Simulation must be running

in reply to: 2 ; follow-up: 2 comment:2 by Tristan Croll, 5 years ago

Wow - that log tells a bit of a story...

Anyway, I think I can see what’s going wrong here - will happen when the user hits the “flip peptide bond” button but the simulation fails to start due to an unparameterised residue or missing hydrogens. Should be straightforward to tackle.

comment:3 by Tristan Croll, 3 years ago

Resolution:	→ fixed
Status:	assigned → closed

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