Opened 4 years ago

Closed 3 years ago

#6540 closed defect (can't reproduce)

OpenMM crash

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x0000047c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py", line 4546 in getState
Windows fatal exception: access violation

===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\farnung_lab\\\Desktop\\\filipovski\\\38
> Model\\\cryosparc_P30_J253_006_volume_map.mrc"

Opened cryosparc_P30_J253_006_volume_map.mrc as #1, grid size 450,450,450,
pixel 0.83, shown at level 0.095, step 2, values float32  

> open "C:/Users/farnung_lab/Desktop/filipovski/38
> Model/cryosparc_P30_J253_006_volume_map.mrc"

Opened cryosparc_P30_J253_006_volume_map.mrc as #2, grid size 450,450,450,
pixel 0.83, shown at level 0.095, step 2, values float32  

> volume #2 step 1

> start isolde

Unknown command: start isolde  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 472 residues in model #1 to IUPAC-IUB
standards.  
Chain information for 38_structure_modified_bases_real_space_refined_019.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  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
1.2/J | No description available  
1.2/K | No description available  
1.2/L | No description available  
1.2/M | No description available  
1.2/N | No description available  
1.2/P | No description available  
1.2/Q | No description available  
1.2/R | No description available  
1.2/T | No description available  
1.2/U | No description available  
1.2/V | No description available  
1.2/W | No description available  
1.2/X | No description available  
1.2/Y | No description available  
1.2/Z | No description available  
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  
1.2/g | No description available  
1.2/h | No description available  
  
Done loading forcefield  
Opened cryosparc_P30_J253_006_volume_map.mrc as #1.1.1.1, grid size
450,450,450, pixel 0.83, shown at step 1, values float32  
Fetching CCD ASP_LEO2_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LEO2_DHD2/ASP_LEO2_DHD2.cif  
Fetching CCD ASP_LFZW_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LFZW_DHD2/ASP_LFZW_DHD2.cif  
Fetching CCD ASN_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ASN_LEO2/ASN_LEO2.cif  
Fetching CCD MEN from http://ligand-expo.rcsb.org/reports/M/MEN/MEN.cif  
Fetching CCD LYZ from http://ligand-expo.rcsb.org/reports/L/LYZ/LYZ.cif  
Fetching CCD ALY from http://ligand-expo.rcsb.org/reports/A/ALY/ALY.cif  
Fetching CCD LAY from http://ligand-expo.rcsb.org/reports/L/LAY/LAY.cif  
Fetching CCD SAC from http://ligand-expo.rcsb.org/reports/S/SAC/SAC.cif  
Deleted the following atoms from residue TPO Z775: O  
Deleted the following atoms from residue TPO A1525: O  
Deleted the following atoms from residue SEP A1547: O  
Fetching CCD GLU_LEO2_DHE2 from http://ligand-
expo.rcsb.org/reports/G/GLU_LEO2_DHE2/GLU_LEO2_DHE2.cif  
Fetching CCD GLU_LFZW_DHE2 from http://ligand-
expo.rcsb.org/reports/G/GLU_LFZW_DHE2/GLU_LFZW_DHE2.cif  
Fetching CCD NLG from http://ligand-expo.rcsb.org/reports/N/NLG/NLG.cif  
Fetching CCD GLN_LEO2 from http://ligand-
expo.rcsb.org/reports/G/GLN_LEO2/GLN_LEO2.cif  
Fetching CCD CGU from http://ligand-expo.rcsb.org/reports/C/CGU/CGU.cif  
Fetching CCD GLN_LFZW from http://ligand-
expo.rcsb.org/reports/G/GLN_LFZW/GLN_LFZW.cif  
Fetching CCD NLQ from http://ligand-expo.rcsb.org/reports/N/NLQ/NLQ.cif  
Fetching CCD FME from http://ligand-expo.rcsb.org/reports/F/FME/FME.cif  
Fetching CCD AME from http://ligand-expo.rcsb.org/reports/A/AME/AME.cif  
Deleted the following atoms from residue DT T-64: OP1  
Deleted the following atoms from residue DT T-65: OP1  
Deleted the following atoms from residue DT T-70: OP1  
Deleted the following atoms from residue DT T-72: OP1  
Deleted the following atoms from residue DT T-79: OP1  
Deleted the following atoms from residue DT T-89: OP1  
Deleted the following atoms from residue DT T-90: OP1  
Deleted the following atoms from residue DT T-99: OP1  
Deleted the following atoms from residue DT T-101: OP1  
Deleted the following atoms from residue DT T-109: OP1  
Deleted the following atoms from residue DT T-112: OP1  
Deleted the following atoms from residue DT T-115: OP1  
Deleted the following atoms from residue DT T-116: OP1  
Deleted the following atoms from residue DT T-120: OP1  
Deleted the following atoms from residue DT T-132: OP1  
Deleted the following atoms from residue DT T-138: OP1  
Deleted the following atoms from residue DT N142: OP1  
Deleted the following atoms from residue DT N140: OP1  
Deleted the following atoms from residue DT N139: OP1  
Deleted the following atoms from residue DT N127: OP1  
Deleted the following atoms from residue DT N118: O2P, O1P  
Deleted the following atoms from residue DT N117: OP1  
Deleted the following atoms from residue DT N108: OP1  
Deleted the following atoms from residue DT N106: OP1  
Deleted the following atoms from residue DT N104: OP1  
Deleted the following atoms from residue DT N98: OP1  
Deleted the following atoms from residue DT N95: OP1  
Deleted the following atoms from residue DT N88: OP1  
Deleted the following atoms from residue DT N87: OP1  
Deleted the following atoms from residue DT N86: OP1  
Deleted the following atoms from residue DT N82: OP1  
Deleted the following atoms from residue DT N78: OP1  
Deleted the following atoms from residue DT N61: OP1  
Deleted the following atoms from residue DT N60: OP1  
Deleted the following atoms from residue DT N59: O2P, O1P  
Deleted the following atoms from residue DT N58: O2P, O1P  
Deleted the following atoms from residue DT N57: O2P, O1P  
Deleted the following atoms from residue DT N56: O2P, O1P  
Deleted the following atoms from residue DT N50: OP1  
Deleted the following atoms from residue DT N49: OP1  
Deleted the following atoms from residue DT N44: OP1  
Deleted the following atoms from residue DT N43: OP1  
Deleted the following atoms from residue DT N42: OP1  
Deleted the following atoms from residue DT N41: OP1  
Deleted the following atoms from residue DT N39: OP1  
Deleted the following atoms from residue DT N27: OP1  
Deleted the following atoms from residue DT N23: OP1  
Deleted the following atoms from residue DT N20: OP1  
Deleted the following atoms from residue DT N18: OP1  
Deleted the following atoms from residue DT N16: OP1  
Deleted the following atoms from residue DT N14: OP1  
Deleted the following atoms from residue DC T-17: OP1  
Deleted the following atoms from residue DC T-22: OP1  
Deleted the following atoms from residue DC T-24: OP1  
Deleted the following atoms from residue DC T-28: OP1  
Deleted the following atoms from residue DC T-29: OP1  
Deleted the following atoms from residue DC T-31: OP1  
Deleted the following atoms from residue DC T-36: OP1  
Deleted the following atoms from residue DC T-37: OP1  
Deleted the following atoms from residue DC T-38: OP1  
Deleted the following atoms from residue DC T-40: OP1  
Deleted the following atoms from residue DC T-51: OP1  
Deleted the following atoms from residue DC T-52: OP1  
Deleted the following atoms from residue DC T-54: O2P, O1P  
Deleted the following atoms from residue DC T-55: O1P, O2P  
Deleted the following atoms from residue DC T-63: OP1  
Deleted the following atoms from residue DC T-66: OP1  
Deleted the following atoms from residue DC T-67: OP1  
Deleted the following atoms from residue DC T-68: OP1  
Deleted the following atoms from residue DC T-69: OP1  
Deleted the following atoms from residue DC T-73: OP1  
Deleted the following atoms from residue DC T-75: OP1  
Deleted the following atoms from residue DC T-77: OP1  
Deleted the following atoms from residue DC T-81: OP1  
Deleted the following atoms from residue DC T-83: OP1  
Deleted the following atoms from residue DC T-85: OP1  
Deleted the following atoms from residue DC T-91: OP1  
Deleted the following atoms from residue DC T-93: OP1  
Deleted the following atoms from residue DC T-94: OP1  
Deleted the following atoms from residue DC T-96: OP1  
Deleted the following atoms from residue DC T-100: OP1  
Deleted the following atoms from residue DC T-102: OP1  
Deleted the following atoms from residue DC T-105: OP1  
Deleted the following atoms from residue DC T-111: OP1  
Deleted the following atoms from residue DC T-119: OP1  
Deleted the following atoms from residue DC T-121: OP1  
Deleted the following atoms from residue DC T-123: OP1  
Deleted the following atoms from residue DC T-124: OP1  
Deleted the following atoms from residue DC T-129: OP1  
Deleted the following atoms from residue DC T-130: OP1  
Deleted the following atoms from residue DC T-135: OP1  
Deleted the following atoms from residue DC T-136: OP1  
Deleted the following atoms from residue DC T-137: OP1  
Deleted the following atoms from residue DC T-143: OP1  
Deleted the following atoms from residue DC N141: OP1  
Deleted the following atoms from residue DC N134: OP1  
Deleted the following atoms from residue DC N133: OP1  
Deleted the following atoms from residue DC N131: OP1  
Deleted the following atoms from residue DC N128: OP1  
Deleted the following atoms from residue DC N126: OP1  
Deleted the following atoms from residue DC N125: OP1  
Deleted the following atoms from residue DC N122: OP1  
Deleted the following atoms from residue DC N114: OP1  
Deleted the following atoms from residue DC N113: OP1  
Deleted the following atoms from residue DC N110: OP1  
Deleted the following atoms from residue DC N107: OP1  
Deleted the following atoms from residue DC N103: OP1  
Deleted the following atoms from residue DC N97: OP1  
Deleted the following atoms from residue DC N92: OP1  
Deleted the following atoms from residue DC N84: OP1  
Deleted the following atoms from residue DC N80: OP1  
Deleted the following atoms from residue DC N76: OP1  
Deleted the following atoms from residue DC N74: OP1  
Deleted the following atoms from residue DC N71: OP1  
Deleted the following atoms from residue DC N62: OP1  
Deleted the following atoms from residue DC N53: OP1  
Deleted the following atoms from residue DC N48: OP1  
Deleted the following atoms from residue DC N47: OP1  
Deleted the following atoms from residue DC N46: OP1  
Deleted the following atoms from residue DC N45: OP1  
Deleted the following atoms from residue DC N26: OP1  
Deleted the following atoms from residue DC N25: OP1  
Deleted the following atoms from residue DC N21: OP1  
Deleted the following atoms from residue DC N19: OP1  
Deleted the following atoms from residue DC N15: OP1  
Deleted the following atoms from residue DG T-15: OP1  
Deleted the following atoms from residue DG T-19: OP1  
Deleted the following atoms from residue DG T-21: OP1  
Deleted the following atoms from residue DG T-25: OP1  
Deleted the following atoms from residue DG T-26: OP1  
Deleted the following atoms from residue DG T-33: OP1  
Deleted the following atoms from residue DG T-45: OP1  
Deleted the following atoms from residue DG T-46: OP1  
Deleted the following atoms from residue DG T-47: OP1  
Deleted the following atoms from residue DG T-48: OP1  
Deleted the following atoms from residue DG T-53: OP1  
Deleted the following atoms from residue DG T-62: OP1  
Deleted the following atoms from residue DG T-71: OP1  
Deleted the following atoms from residue DG T-74: OP1  
Deleted the following atoms from residue DG T-76: OP1  
Deleted the following atoms from residue DG T-80: OP1  
Deleted the following atoms from residue DG T-84: OP1  
Deleted the following atoms from residue DG T-92: OP1  
Deleted the following atoms from residue DG T-97: OP1  
Deleted the following atoms from residue DG T-103: OP1  
Deleted the following atoms from residue DG T-107: OP1  
Deleted the following atoms from residue DG T-110: OP1  
Deleted the following atoms from residue DG T-113: OP1  
Deleted the following atoms from residue DG T-114: OP1  
Deleted the following atoms from residue DG T-122: OP1  
Deleted the following atoms from residue DG T-125: OP1  
Deleted the following atoms from residue DG T-126: OP1  
Deleted the following atoms from residue DG T-128: OP1  
Deleted the following atoms from residue DG T-131: OP1  
Deleted the following atoms from residue DG T-133: OP1  
Deleted the following atoms from residue DG T-134: OP1  
Deleted the following atoms from residue DG T-141: OP1  
Deleted the following atoms from residue DG N143: OP1  
Deleted the following atoms from residue DG N137: OP1  
Deleted the following atoms from residue DG N136: OP1  
Deleted the following atoms from residue DG N135: OP1  
Deleted the following atoms from residue DG N130: OP1  
Deleted the following atoms from residue DG N129: OP1  
Deleted the following atoms from residue DG N124: OP1  
Deleted the following atoms from residue DG N123: OP1  
Deleted the following atoms from residue DG N121: OP1  
Deleted the following atoms from residue DG N119: OP1  
Deleted the following atoms from residue DG N111: OP1  
Deleted the following atoms from residue DG N105: OP1  
Deleted the following atoms from residue DG N102: OP1  
Deleted the following atoms from residue DG N100: OP1  
Deleted the following atoms from residue DG N96: OP1  
Deleted the following atoms from residue DG N94: OP1  
Deleted the following atoms from residue DG N93: OP1  
Deleted the following atoms from residue DG N91: OP1  
Deleted the following atoms from residue DG N85: OP1  
Deleted the following atoms from residue DG N83: OP1  
Deleted the following atoms from residue DG N81: OP1  
Deleted the following atoms from residue DG N77: OP1  
Deleted the following atoms from residue DG N75: OP1  
Deleted the following atoms from residue DG N73: OP1  
Deleted the following atoms from residue DG N69: OP1  
Deleted the following atoms from residue DG N68: OP1  
Deleted the following atoms from residue DG N67: OP1  
Deleted the following atoms from residue DG N66: OP1  
Deleted the following atoms from residue DG N63: OP1  
Deleted the following atoms from residue DG N55: O1P, O2P  
Deleted the following atoms from residue DG N54: O1P, O2P  
Deleted the following atoms from residue DG N52: OP1  
Deleted the following atoms from residue DG N51: OP1  
Deleted the following atoms from residue DG N40: OP1  
Deleted the following atoms from residue DG N24: OP1  
Deleted the following atoms from residue DG N22: OP1  
Deleted the following atoms from residue DG N17: OP1  
Deleted the following atoms from residue DA T-14: OP1  
Deleted the following atoms from residue DA T-16: OP1  
Deleted the following atoms from residue DA T-18: OP1  
Deleted the following atoms from residue DA T-20: OP1  
Deleted the following atoms from residue DA T-23: OP1  
Deleted the following atoms from residue DA T-27: OP1  
Deleted the following atoms from residue DA T-30: OP1  
Deleted the following atoms from residue DA T-32: OP1  
Deleted the following atoms from residue DA T-34: OP1  
Deleted the following atoms from residue DA T-35: OP1  
Deleted the following atoms from residue DA T-39: OP1  
Deleted the following atoms from residue DA T-41: OP1  
Deleted the following atoms from residue DA T-42: OP1  
Deleted the following atoms from residue DA T-43: OP1  
Deleted the following atoms from residue DA T-44: OP1  
Deleted the following atoms from residue DA T-49: OP1  
Deleted the following atoms from residue DA T-50: OP1  
Deleted the following atoms from residue DA T-56: O1P, O2P  
Deleted the following atoms from residue DA T-57: O2P, O1P  
Deleted the following atoms from residue DA T-58: O1P, O2P  
Deleted the following atoms from residue DA T-59: O1P, O2P  
Deleted the following atoms from residue DA T-60: OP1  
Deleted the following atoms from residue DA T-61: OP1  
Deleted the following atoms from residue DA T-78: OP1  
Deleted the following atoms from residue DA T-82: OP1  
Deleted the following atoms from residue DA T-86: OP1  
Deleted the following atoms from residue DA T-87: OP1  
Deleted the following atoms from residue DA T-88: OP1  
Deleted the following atoms from residue DA T-95: OP1  
Deleted the following atoms from residue DA T-98: OP1  
Deleted the following atoms from residue DA T-104: OP1  
Deleted the following atoms from residue DA T-106: OP1  
Deleted the following atoms from residue DA T-108: OP1  
Deleted the following atoms from residue DA T-117: OP1  
Deleted the following atoms from residue DA T-118: OP1  
Deleted the following atoms from residue DA T-127: OP1  
Deleted the following atoms from residue DA T-139: OP1  
Deleted the following atoms from residue DA T-140: OP1  
Deleted the following atoms from residue DA T-142: OP1  
Deleted the following atoms from residue DA N144: OP1  
Deleted the following atoms from residue DA N138: OP1  
Deleted the following atoms from residue DA N132: OP1  
Deleted the following atoms from residue DA N120: OP1  
Deleted the following atoms from residue DA N116: OP1  
Deleted the following atoms from residue DA N115: OP1  
Deleted the following atoms from residue DA N112: OP1  
Deleted the following atoms from residue DA N109: OP1  
Deleted the following atoms from residue DA N101: OP1  
Deleted the following atoms from residue DA N99: OP1  
Deleted the following atoms from residue DA N90: OP1  
Deleted the following atoms from residue DA N89: OP1  
Deleted the following atoms from residue DA N79: OP1  
Deleted the following atoms from residue DA N72: OP1  
Deleted the following atoms from residue DA N70: OP1  
Deleted the following atoms from residue DA N65: OP1  
Deleted the following atoms from residue DA N64: OP1  
ISOLDE: started sim  
ISOLDE: paused sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
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: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
Peptide bond must be mobile in the simulation!  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  

> select clear

> volume #1.1.1.1 level 0.2566

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  
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  
ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
Peptide bond must be mobile in the simulation!  
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  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
Peptide bond must be mobile in the simulation!  
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: started sim  
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: started sim  
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: started sim  

> volume #1.1.1.1 level 0.103

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.1898

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  

> select clear

> volume #1.1.1.1 level 0.2347

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

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  
Traceback (most recent call last):  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2154, in _backrub_rotamer  
self._apply_backrub(None, None)  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2164, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\refine\backrub_rotamer.py", line 410, in
apply_backrub  
b = Backrub(r, mdff_p, clash_weight=clash_weight, map_weight=map_weight)  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\refine\backrub_rotamer.py", line 81, in __init__  
raise TypeError('Backrub requires N- and C-terminal flanking residues to be
present!')  
TypeError: Backrub requires N- and C-terminal flanking residues to be present!  
  
TypeError: Backrub requires N- and C-terminal flanking residues to be present!  
  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\refine\backrub_rotamer.py", line 81, in __init__  
raise TypeError('Backrub requires N- and C-terminal flanking residues to be
present!')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2154, in _backrub_rotamer  
self._apply_backrub(None, None)  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2164, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\refine\backrub_rotamer.py", line 410, in
apply_backrub  
b = Backrub(r, mdff_p, clash_weight=clash_weight, map_weight=map_weight)  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\refine\backrub_rotamer.py", line 81, in __init__  
raise TypeError('Backrub requires N- and C-terminal flanking residues to be
present!')  
TypeError: Backrub requires N- and C-terminal flanking residues to be present!  
  
TypeError: Backrub requires N- and C-terminal flanking residues to be present!  
  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\refine\backrub_rotamer.py", line 81, in __init__  
raise TypeError('Backrub requires N- and C-terminal flanking residues to be
present!')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2154, in _backrub_rotamer  
self._apply_backrub(None, None)  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2164, in _apply_backrub  
apply_backrub(self, mdff_mgr, res)  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\refine\backrub_rotamer.py", line 410, in
apply_backrub  
b = Backrub(r, mdff_p, clash_weight=clash_weight, map_weight=map_weight)  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\refine\backrub_rotamer.py", line 81, in __init__  
raise TypeError('Backrub requires N- and C-terminal flanking residues to be
present!')  
TypeError: Backrub requires N- and C-terminal flanking residues to be present!  
  
TypeError: Backrub requires N- and C-terminal flanking residues to be present!  
  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\refine\backrub_rotamer.py", line 81, in __init__  
raise TypeError('Backrub requires N- and C-terminal flanking residues to be
present!')  
  
See log for complete Python traceback.  
  
ISOLDE: started sim  
ISOLDE: paused sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
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  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

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: started sim  
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  
ISOLDE: started sim  

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  

> volume #1.1.1.1 level 0.1068

> volume #1.1.1.1 level 0.1842

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
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: started sim  
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: started sim  
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: started sim  

> volume #1.1.1.1 level 0.08234

> volume #1.1.1.1 level 0.1944

> volume #1.1.1.1 level 0.2496

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  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
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: started sim  

> volume #1.1.1.1 level 0.2739

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: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

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  

> volume #1.1.1.1 level 0.09707

> volume #1.1.1.1 level 0.1406

ISOLDE: started sim  
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: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
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  
ISOLDE: started sim  

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  
Peptide bond must be mobile in the simulation!  
Unable to flip peptide bond after 50 rounds. Giving up.  
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: started sim  
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: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  

> volume #1.1.1.1 level 0.3374

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  

> volume #1.1.1.1 level 0.1371

> volume #1.1.1.1 level 0.3531

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2784, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 576, in __init__  
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 971, in
expand_mobile_selection  
sel = selections.expand_selection_along_chains(core_atoms,  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\selections.py", line 39, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
TypeError: Selected atoms must all be in the same model!  
  
TypeError: Selected atoms must all be in the same model!  
  
File "C:\Users\farnung_lab\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\selections.py", line 39, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
  
See log for complete Python traceback.  
  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  

> isolde~ignore

Unknown command: isolde~ignore  

> isolde ignore

Changes to the set of ignored residues will notbe applied until you stop the
current simulation.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Microsoft Windows 10 Enterprise (Build 19043)
Memory: 137,342,418,944
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-6850K CPU @ 3.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → OpenMM crash

comment:2 by Tristan Croll, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed
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