Opened 3 years ago

Closed 3 years ago

#7709 closed defect (fixed)

Simulation stop: 'NoneType' object has no attribute 'atoms'

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 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/neck/pdb/gp13-14-15_v3_real_space_refined_002-coot-6.pdb

Summary of feedback from opening
/Users/wxg622/Desktop/NTLab/Phage/Maps/T4/neck/pdb/gp13-14-15_v3_real_space_refined_002-coot-6.pdb  
---  
warnings | Duplicate atom serial number found: 38414  
Duplicate atom serial number found: 38415  
Duplicate atom serial number found: 38416  
Duplicate atom serial number found: 38417  
Duplicate atom serial number found: 38418  
11130 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 31 31 LEU B 138 LEU B
155 1 18  
Start residue of secondary structure not found: HELIX 32 32 THR B 194 LYS B
196 1 3  
Start residue of secondary structure not found: HELIX 33 33 LEU B 215 ASN B
220 1 6  
Start residue of secondary structure not found: HELIX 34 34 PRO B 222 HIS B
224 1 3  
Start residue of secondary structure not found: HELIX 35 35 ALA B 241 ASN B
243 1 3  
60 messages similar to the above omitted  
  
Chain information for gp13-14-15_v3_real_space_refined_002-coot-6.pdb #1  
---  
Chain | Description  
A B J K M N P Q S T V W | No description available  
C D E F G H | No description available  
I L O R U X | No description available  
d e f g h i | No description available  
  

> open /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/neck/pdb/neck_fib_0904.pdb

Chain information for neck_fib_0904.pdb #2  
---  
Chain | Description  
0 AC AF AI AL AO | No description available  
1 2 3 4 5 6 7 8 x y z | No description available  
9 AA AB AD AE AG AH AJ AK AM AN AP | No description available  
A J M P S V | No description available  
AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah | No description
available  
B K N Q T W | No description available  
C D E F G H | No description available  
I L O R U X | No description available  
Y Z a b c j | No description available  
d e f g h i | No description available  
w | No description available  
  

> hide #!1 models

Drag select of 197755 atoms, 42 pseudobonds  

> select up

198915 atoms, 200870 bonds, 42 pseudobonds, 14755 residues, 2 models selected  

> select up

206966 atoms, 209038 bonds, 42 pseudobonds, 15449 residues, 2 models selected  

> select up

213382 atoms, 215635 bonds, 42 pseudobonds, 16147 residues, 2 models selected  

> delete sel

> hide #!2 atoms

> show #!2 cartoons

Drag select of 25 residues  
Drag select of 23 residues  
Drag select of 17 residues  
Drag select of 38 residues  
Drag select of 21 residues  
Drag select of 18 residues  

> select up

1538 atoms, 1582 bonds, 197 residues, 1 model selected  

> select up

2178 atoms, 2244 bonds, 282 residues, 1 model selected  

> delete sel

> show #!1 models

> combine #1 #2

> hide #!1 models

> hide #!2 models

> hide #!3 atoms

> show #!3 cartoons

Populating font family aliases took 297 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

> save
> /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/neck/pdb/gp3-13-14-15_v3_real_space_refined_002-coot-6.pdb
> models #3 relModel #1

> close

> open
> /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/neck/pdb/gp3-13-14-15_v3_real_space_refined_002-coot-6.pdb
> format pdb

Chain information for gp3-13-14-15_v3_real_space_refined_002-coot-6.pdb #1  
---  
Chain | Description  
A B J K M N P Q S T V W | No description available  
C D E F G H | No description available  
I L O R U X | No description available  
Y Z a b c j | No description available  
d e f g h i | No description available  
  

> open
> /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/neck/local/cryosparc_P48_J794_005_volume_map_sharp.mrc

Opened cryosparc_P48_J794_005_volume_map_sharp.mrc as #2, grid size
540,540,540, pixel 1.1, shown at level 0.576, step 4, values float32  

> volume #2 step 1

> hide atoms

> show cartoons

> volume #2 level 0.8737

> transparency 50

> isolde tutorial

> clipper associate #2 toModel #1

Opened cryosparc_P48_J794_005_volume_map_sharp.mrc as #1.1.1.1, grid size
540,540,540, pixel 1.1, shown at level 1.37, step 1, values float32  
Chain information for gp3-13-14-15_v3_real_space_refined_002-coot-6.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/J 1.2/K 1.2/M 1.2/N 1.2/P 1.2/Q 1.2/S 1.2/T 1.2/V 1.2/W | No
description available  
1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H | No description available  
1.2/I 1.2/L 1.2/O 1.2/R 1.2/U 1.2/X | No description available  
1.2/Y 1.2/Z 1.2/a 1.2/b 1.2/c 1.2/j | No description available  
1.2/d 1.2/e 1.2/f 1.2/g 1.2/h 1.2/i | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 459 residues in model #1.2 to IUPAC-IUB
standards.  

> ui tool show "Ramachandran Plot"

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

> isolde restrain distances
> "#1.2/A","#1.2/B","#1.2/C","#1.2/D","#1.2/E","#1.2/F","#1.2/G","#1.2/H","#1.2/I","#1.2/J","#1.2/K","#1.2/L","#1.2/M","#1.2/N","#1.2/O","#1.2/P","#1.2/Q","#1.2/R","#1.2/S","#1.2/T","#1.2/U","#1.2/V","#1.2/W","#1.2/X","#1.2/Y","#1.2/Z","#1.2/a","#1.2/b","#1.2/c","#1.2/d","#1.2/e","#1.2/f","#1.2/g","#1.2/h","#1.2/i","#1.2/j"
> templateAtoms
> "#1.2/A","#1.2/B","#1.2/C","#1.2/D","#1.2/E","#1.2/F","#1.2/G","#1.2/H","#1.2/I","#1.2/J","#1.2/K","#1.2/L","#1.2/M","#1.2/N","#1.2/O","#1.2/P","#1.2/Q","#1.2/R","#1.2/S","#1.2/T","#1.2/U","#1.2/V","#1.2/W","#1.2/X","#1.2/Y","#1.2/Z","#1.2/a","#1.2/b","#1.2/c","#1.2/d","#1.2/e","#1.2/f","#1.2/g","#1.2/h","#1.2/i","#1.2/j"
> perChain false adjustForConfidence false useCoordinateAlignment false kappa
> 4.40 fallOff 2.50 groupName "Reference Distance Restraints"

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

> isolde restrain torsions #1.2/A templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/B templateResidues #1.2/B adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/C templateResidues #1.2/C adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/D templateResidues #1.2/D adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/E templateResidues #1.2/E adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/F templateResidues #1.2/F adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/G templateResidues #1.2/G adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/H templateResidues #1.2/H adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/I templateResidues #1.2/I adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/J templateResidues #1.2/J adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/K templateResidues #1.2/K adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/L templateResidues #1.2/L adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/M templateResidues #1.2/M adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/N templateResidues #1.2/N adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/O templateResidues #1.2/O adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/P templateResidues #1.2/P adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/Q templateResidues #1.2/Q adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/R templateResidues #1.2/R adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/S templateResidues #1.2/S adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/T templateResidues #1.2/T adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/U templateResidues #1.2/U adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/V templateResidues #1.2/V adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/W templateResidues #1.2/W adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/X templateResidues #1.2/X adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/Y templateResidues #1.2/Y adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/Z templateResidues #1.2/Z adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/a templateResidues #1.2/a adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/b templateResidues #1.2/b adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/c templateResidues #1.2/c adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/d templateResidues #1.2/d adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/e templateResidues #1.2/e adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/f templateResidues #1.2/f adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/g templateResidues #1.2/g adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/h templateResidues #1.2/h adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/i templateResidues #1.2/i adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde restrain torsions #1.2/j templateResidues #1.2/j adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

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

> isolde sim start sel

ISOLDE: stopped sim  

> addh H

Summary of feedback from adding hydrogens to
gp3-13-14-15_v3_real_space_refined_002-coot-6.pdb #1.2  
---  
notes | No usable SEQRES records for
gp3-13-14-15_v3_real_space_refined_002-coot-6.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for gp3-13-14-15_v3_real_space_refined_002-coot-6.pdb
(#1.2) chain B; guessing termini instead  
No usable SEQRES records for gp3-13-14-15_v3_real_space_refined_002-coot-6.pdb
(#1.2) chain C; guessing termini instead  
No usable SEQRES records for gp3-13-14-15_v3_real_space_refined_002-coot-6.pdb
(#1.2) chain D; guessing termini instead  
No usable SEQRES records for gp3-13-14-15_v3_real_space_refined_002-coot-6.pdb
(#1.2) chain E; guessing termini instead  
31 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /Y SER 2, /Z SER 2, /a SER
2, /b SER 2, /c SER 2, /d MET 1, /e MET 1, /f MET 1, /g MET 1, /h MET 1, /i
MET 1, /j SER 2  
Chain-initial residues that are not actual N termini: /A SER 2, /A GLY 93, /B
SER 2, /B GLY 93, /C ALA 2, /D ALA 2, /E ALA 2, /F ALA 2, /G ALA 2, /H ALA 2,
/I GLY 135, /J SER 2, /J GLY 93, /K SER 2, /K GLY 93, /L GLY 135, /M SER 2, /M
GLY 93, /N SER 2, /N GLY 93, /O GLY 135, /P SER 2, /P GLY 93, /Q SER 2, /Q GLY
93, /R GLY 135, /S SER 2, /S GLY 93, /T SER 2, /T GLY 93, /U GLY 135, /V SER
2, /V GLY 93, /W SER 2, /W GLY 93, /X GLY 135  
Chain-final residues that are actual C termini: /I GLY 309, /L GLY 309, /O GLY
309, /R GLY 309, /U GLY 309, /X GLY 309, /Y VAL 176, /Z VAL 176, /a VAL 176,
/b VAL 176, /c VAL 176, /j VAL 176  
Chain-final residues that are not actual C termini: /A GLY 93, /A THR 90, /B
GLY 93, /B THR 90, /C GLU 246, /D GLU 246, /E GLU 246, /F GLU 246, /G GLU 246,
/H GLU 246, /J GLY 93, /J THR 90, /K GLY 93, /K THR 90, /M GLY 93, /M THR 90,
/N GLY 93, /N THR 90, /P GLY 93, /P THR 90, /Q GLY 93, /Q THR 90, /S GLY 93,
/S THR 90, /T GLY 93, /T THR 90, /V GLY 93, /V THR 90, /W GLY 93, /W THR 90,
/d THR 272, /e THR 272, /f THR 272, /g THR 272, /h THR 272, /i THR 272  
3957 hydrogen bonds  
Adding 'H' to /A GLY 93  
Adding 'H' to /B GLY 93  
Adding 'H' to /J GLY 93  
Adding 'H' to /K GLY 93  
Adding 'H' to /M GLY 93  
7 messages similar to the above omitted  
/A GLY 93 is not terminus, removing H atom from 'C'  
/B GLY 93 is not terminus, removing H atom from 'C'  
/C GLU 246 is not terminus, removing H atom from 'C'  
/D GLU 246 is not terminus, removing H atom from 'C'  
/E GLU 246 is not terminus, removing H atom from 'C'  
19 messages similar to the above omitted  
17532 hydrogens added  
  
Fetching CCD PHE_LL from http://ligand-
expo.rcsb.org/reports/P/PHE_LL/PHE_LL.cif  
Fetching CCD PHE_LEO2 from http://ligand-
expo.rcsb.org/reports/P/PHE_LEO2/PHE_LEO2.cif  
Fetching CCD TYR_LL from http://ligand-
expo.rcsb.org/reports/T/TYR_LL/TYR_LL.cif  
Fetching CCD PHE_LFZW from http://ligand-
expo.rcsb.org/reports/P/PHE_LFZW/PHE_LFZW.cif  
Fetching CCD TYR_LEO2 from http://ligand-
expo.rcsb.org/reports/T/TYR_LEO2/TYR_LEO2.cif  
Fetching CCD TYR_LFZW from http://ligand-
expo.rcsb.org/reports/T/TYR_LFZW/TYR_LFZW.cif  
Fetching CCD 5CR from http://ligand-expo.rcsb.org/reports/5/5CR/5CR.cif  
Deleted the following atoms from residue PHE H93: H1  
Deleted the following atoms from residue PHE G93: H1  
Deleted the following atoms from residue PHE F93: H1  
Deleted the following atoms from residue PHE E93: H1  
Deleted the following atoms from residue PHE D93: H1  
Deleted the following atoms from residue PHE C93: H1  
Fetching CCD DAH from http://ligand-expo.rcsb.org/reports/D/DAH/DAH.cif  
Fetching CCD 3NF from http://ligand-expo.rcsb.org/reports/3/3NF/3NF.cif  
Deleted the following atoms from residue TYR d43: H, HN  
Deleted the following atoms from residue TYR i43: H, HN  
Deleted the following atoms from residue TYR h43: HN, H  
Deleted the following atoms from residue TYR g43: HN, H  
Deleted the following atoms from residue TYR f43: H, HN  
Deleted the following atoms from residue TYR e43: HN, H  

> select add #1.2

99732 atoms, 100944 bonds, 12 pseudobonds, 6282 residues, 12 models selected  

> select add #1.2

99732 atoms, 100944 bonds, 12 pseudobonds, 6282 residues, 12 models selected  

> select add #1.2

99732 atoms, 100944 bonds, 12 pseudobonds, 6282 residues, 12 models selected  

> select add #1.2

99732 atoms, 100944 bonds, 12 pseudobonds, 6282 residues, 12 models selected  

> isolde sim start sel

ISOLDE: started sim  

> select add #1.2

99732 atoms, 100944 bonds, 12 pseudobonds, 6282 residues, 12 models selected  

> select add #1.2

99732 atoms, 100944 bonds, 12 pseudobonds, 6282 residues, 12 models selected  

> select clear

> select up

258 atoms, 261 bonds, 19 residues, 1 model selected  

> select down

11 atoms, 1 residue, 1 model selected  

> select up

258 atoms, 261 bonds, 19 residues, 1 model selected  

> select down

11 atoms, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> isolde release distances #1.2&sel externalOnly true groupName "Reference
> Distance Restraints"

> select up

258 atoms, 261 bonds, 19 residues, 1 model selected  

> select up

8 atoms, 7 bonds, 3 residues, 1 model selected  

> select up

47 atoms, 48 bonds, 3 residues, 1 model selected  

> isolde release distances #1.2&sel externalOnly true groupName "Reference
> Distance Restraints"

> volume #1.1.1.1 level 0.725

> select up

205 atoms, 209 bonds, 13 residues, 1 model selected  

> isolde release distances #1.2&sel externalOnly true groupName "Reference
> Distance Restraints"

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 58 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> isolde sim pause

> isolde sim resume

> isolde sim pause

> select clear

[Repeated 2 time(s)]

> isolde sim resume

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

205 atoms, 209 bonds, 13 residues, 1 model selected  

> isolde release distances #1.2&sel externalOnly true groupName "Reference
> Distance Restraints"

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> select clear

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim pause

> isolde sim resume

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> select up

258 atoms, 261 bonds, 19 residues, 1 model selected  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

258 atoms, 261 bonds, 19 residues, 1 model selected  

> isolde release distances #1.2&sel externalOnly true groupName "Reference
> Distance Restraints"

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde release distances #1.2&sel internalOnly true groupName "Reference
> Distance Restraints"

> select clear

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

74 atoms, 74 bonds, 4 residues, 1 model selected  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

[Repeated 1 time(s)]

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

258 atoms, 261 bonds, 19 residues, 1 model selected  

> select down

12 atoms, 11 bonds, 1 residue, 1 model selected  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

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

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> select up

258 atoms, 261 bonds, 19 residues, 1 model selected  

> select up

2704 atoms, 2734 bonds, 175 residues, 1 model selected  

> select down

258 atoms, 261 bonds, 19 residues, 1 model selected  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Unable to flip peptide bond after 50 rounds. Giving up.  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde sim stop

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 sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #1.1.1.1 level 0.5749

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> select clear

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.5012

> hide #1.3 models

> show #1.3 models

> hide #!1.1 models

> isolde sim stop

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

> hide #!1.2 models

> show #!1.2 models

> show #!1.1 models

> isolde sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

258 atoms, 261 bonds, 19 residues, 1 model selected  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> isolde release distances #1.2&sel externalOnly true groupName "Reference
> Distance Restraints"

[Repeated 1 time(s)]

> volume #1.1.1.1 level 0.3447

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> select clear

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel internalOnly true groupName "Reference
> Distance Restraints"

> isolde sim stop

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 sim start sel

ISOLDE: started sim  

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/wxg622/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 1009, in _sim_end_cb  
run(self.session, f'clipper spot #{self.selected_model.id_string}', log=False)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/wxg622/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/cmd.py", line 109, in spotlight  
sh = get_symmetry_handler(m, create=create, auto_add_to_session=True)  
File "/Users/wxg622/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/wxg622/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/wxg622/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 594, in __init__  
self.add_model(model, ignore_model_symmetry=ignore_model_symmetry,  
File "/Users/wxg622/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 649, in add_model  
self.set_default_atom_display(mode=self._hydrogen_mode)  
File "/Users/wxg622/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 922, in set_default_atom_display  
atoms = model.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "sim terminated":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/wxg622/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 922, in set_default_atom_display  
atoms = model.atoms  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
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: 64 GB
      System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0)
      OS Loader Version: 540.120.3~22

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 1 day 6:57

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: x16
      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:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LEN P27q-10:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version:  2.4a


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Simulation stop: 'NoneType' object has no attribute 'atoms'

comment:2 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

Another instance of the rotamer preview bug.

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