peptide flip: Simulation must be running!

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/ISOLDE files/ISOLDE_J55_DeepEMhancer-
> widetarget_coot_itr4_rsr_016.pdb"

Chain information for ISOLDE_J55_DeepEMhancer-widetarget_coot_itr4_rsr_016.pdb
#1  
---  
Chain | Description  
A D | No description available  
B E | No description available  
C | No description available  
F G H I | No description available  
J | No description available  
  

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12
> 2020/Maps/DeepEMhancer/From
> Yogesh/deppEMhancer_J55-Cryosparc/J55_009_widetarget_maps.mrc"

Opened J55_009_widetarget_maps.mrc as #2, grid size 250,250,250, pixel 1.07,
shown at level 0.0457, step 1, values float32  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for ISOLDE_J55_DeepEMhancer-widetarget_coot_itr4_rsr_016.pdb  
---  
Chain | Description  
1.2/A 1.2/D | No description available  
1.2/B 1.2/E | No description available  
1.2/C | No description available  
1.2/F 1.2/G 1.2/H 1.2/I | No description available  
1.2/J | No description available  
  
Done loading forcefield  

> volume #2 level 0.1926

> surface dust #2 size 10.7

> volume #2 level 0.2425

> volume #2 level 0.2367

> hide #!2 models

> set bgColor white

ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to ISOLDE_J55_DeepEMhancer-
widetarget_coot_itr4_rsr_016.pdb #1.2  
---  
notes | No usable SEQRES records for ISOLDE_J55_DeepEMhancer-
widetarget_coot_itr4_rsr_016.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for ISOLDE_J55_DeepEMhancer-
widetarget_coot_itr4_rsr_016.pdb (#1.2) chain B; guessing termini instead  
No usable SEQRES records for ISOLDE_J55_DeepEMhancer-
widetarget_coot_itr4_rsr_016.pdb (#1.2) chain C; guessing termini instead  
No usable SEQRES records for ISOLDE_J55_DeepEMhancer-
widetarget_coot_itr4_rsr_016.pdb (#1.2) chain D; guessing termini instead  
No usable SEQRES records for ISOLDE_J55_DeepEMhancer-
widetarget_coot_itr4_rsr_016.pdb (#1.2) chain E; guessing termini instead  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A PRO 31, /B PHE 39, /C ILE
35, /D PRO 31, /E PHE 39, /F MET 1, /G MET 1, /H MET 1, /I MET 1, /J MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ASN 237, /B ASN 237, /C
ASN 237, /D ASN 237, /E ASN 237, /F GLY 89, /G GLY 89, /H GLY 89, /I GLY 89,
/J GLU 258  
1354 hydrogen bonds  
/A ASN 237 is not terminus, removing H atom from 'C'  
/B ASN 237 is not terminus, removing H atom from 'C'  
/C ASN 237 is not terminus, removing H atom from 'C'  
/D ASN 237 is not terminus, removing H atom from 'C'  
/E ASN 237 is not terminus, removing H atom from 'C'  
5 messages similar to the above omitted  
13723 hydrogens added  
  
Traceback (most recent call last):  
File "/Users/yogesh/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2265, in _flip_peptide_bond  
self.flip_peptide_bond(res)  
File "/Users/yogesh/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 3257, in flip_peptide_bond  
pf = Peptide_Bond_Flipper(self, res)  
File "/Users/yogesh/Library/Application Support/ChimeraX/1.2/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/yogesh/Library/Application Support/ChimeraX/1.2/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: 4.1 ATI-4.5.14
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1554.120.19.0.0 (iBridge: 18.16.14663.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 4 days 1:01

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
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          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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    ChimeraX-AlignmentMatrices: 2.0
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