flip peptide bond: Simulation must be running

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-117-generic-x86_64-with-debian-stretch-sid
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
> /largedata/zhou/phenix_projects/gH1X_ncH14_Nuc197/ncH14-gH1x_Nuc197_P20_J256_map_autosharpened_1.3295angpix_v0.mrc
> format mrc

Opened ncH14-gH1x_Nuc197_P20_J256_map_autosharpened_1.3295angpix_v0.mrc, grid
size 256,256,256, pixel 1.33, shown at level 2.34, step 1, values float32  

> open
> /largedata/zhou/phenix_projects/gH1X_ncH14_Nuc197/RealSpaceRefine_5/H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb

Chain information for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
#2  
---  
Chain | Description  
A E | No description available  
B F | No description available  
C G | No description available  
D H | No description available  
I | No description available  
J | No description available  
M N | No description available  
U | No description available  
  

> lighting simple

> style stick

Changed 18334 atom styles  

> volume #1 level 4.618

> transparency 50

> color byhetero

> addh #2

Summary of feedback from adding hydrogens to
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
#2  
---  
notes | No usable SEQRES records for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
(#2) chain A; guessing termini instead  
No usable SEQRES records for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
(#2) chain B; guessing termini instead  
No usable SEQRES records for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
(#2) chain C; guessing termini instead  
No usable SEQRES records for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
(#2) chain D; guessing termini instead  
No usable SEQRES records for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
(#2) chain E; guessing termini instead  
8 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A LYS 37, /B LYS 20, /C ALA
10, /D LYS 30, /E LYS 37, /F LYS 20, /G ALA 10, /H LYS 30, /I DG 1, /J DG 1,
/M MET 19, /N MET 19, /U GLN 43  
Chain-initial residues that are not actual N termini: /M GLU 150, /N GLU 150  
Chain-final residues that are actual C termini: /B GLY 102, /F GLY 102, /I DC
197, /J DC 197, /M SER 268, /N SER 268  
Chain-final residues that are not actual C termini: /A GLU 133, /C LYS 118, /D
ALA 124, /E GLU 133, /G LYS 118, /H ALA 124, /M LYS 126, /N LYS 126, /U LYS
118  
1950 hydrogen bonds  
Adding 'H' to /M GLU 150  
Adding 'H' to /N GLU 150  
/A GLU 133 is not terminus, removing H atom from 'C'  
/C LYS 118 is not terminus, removing H atom from 'C'  
/D ALA 124 is not terminus, removing H atom from 'C'  
/E GLU 133 is not terminus, removing H atom from 'C'  
/G LYS 118 is not terminus, removing H atom from 'C'  
2 messages similar to the above omitted  
14966 hydrogens added  
  

> delete /I:1@H /J:1@H

> clipper associate #1 toModel #2

Chain information for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb  
---  
Chain | Description  
1.2/A 1.2/E | No description available  
1.2/B 1.2/F | No description available  
1.2/C 1.2/G | No description available  
1.2/D 1.2/H | No description available  
1.2/I | No description available  
1.2/J | No description available  
1.2/M 1.2/N | No description available  
1.2/U | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> set bgColor white

> isolde restrain distances "#2/A-H,M-N,U" kappa 10

No residues specified to restrain!  

> isolde restrain distances "#1/A-H,M-N,U" kappa 10

> isolde adjust distances #1 displayThreshold 0.1

> select "/A-H,M-N,U"

20804 atoms, 20977 bonds, 4 pseudobonds, 2 models selected  

> isolde sim start sel

> volume #1.1.1.1 level 7.041

> delete H

> save
> /largedata/zhou/phenix_projects/gH1X_ncH14_Nuc197/RealSpaceRefine_5/RSR5_protein_isolde_adjusted.pdb

> addh

Summary of feedback from adding hydrogens to
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
#1.2  
---  
notes | No usable SEQRES records for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
(#1.2) chain A; guessing termini instead  
No usable SEQRES records for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
(#1.2) chain B; guessing termini instead  
No usable SEQRES records for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
(#1.2) chain C; guessing termini instead  
No usable SEQRES records for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
(#1.2) chain D; guessing termini instead  
No usable SEQRES records for
H14RSR6_oct_DNA_scFv20-ncH14-gH1x_Uchain_combined_IJChain_ISOLDE_adjusted_edited_Uchain_offset1_protein_isolde_adjusted_deleteH_real_space_refined.pdb
(#1.2) chain E; guessing termini instead  
8 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A LYS 37, /B LYS 20, /C ALA
10, /D LYS 30, /E LYS 37, /F LYS 20, /G ALA 10, /H LYS 30, /I DG 1, /J DG 1,
/M MET 19, /N MET 19, /U GLN 43  
Chain-initial residues that are not actual N termini: /M GLU 150, /N GLU 150  
Chain-final residues that are actual C termini: /B GLY 102, /F GLY 102, /I DC
197, /J DC 197, /M SER 268, /N SER 268  
Chain-final residues that are not actual C termini: /A GLU 133, /C LYS 118, /D
ALA 124, /E GLU 133, /G LYS 118, /H ALA 124, /M LYS 126, /N LYS 126, /U LYS
118  
2008 hydrogen bonds  
Adding 'H' to /M GLU 150  
Adding 'H' to /N GLU 150  
/A GLU 133 is not terminus, removing H atom from 'C'  
/C LYS 118 is not terminus, removing H atom from 'C'  
/D ALA 124 is not terminus, removing H atom from 'C'  
/E GLU 133 is not terminus, removing H atom from 'C'  
/G LYS 118 is not terminus, removing H atom from 'C'  
2 messages similar to the above omitted  
14966 hydrogens added  
  
Traceback (most recent call last):  
File "/home/spuser/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2246, in _flip_peptide_bond  
self.flip_peptide_bond(res)  
File "/home/spuser/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 3218, in flip_peptide_bond  
pf = Peptide_Bond_Flipper(self, res)  
File "/home/spuser/.local/share/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 "/home/spuser/.local/share/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: 3.3.0 NVIDIA 440.31
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7048GR-TR
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
CPU: 48 Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz
Cache Size: 30720 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           251G        8.1G        241G        237M        2.5G        240G
	Swap:          255G          0B        255G

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:85e5]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tristan Croll]

No longer an issue. If a simulation isn't running, the flipper will start one.