Opened 2 years ago

Closed 2 years ago

#10130 closed defect (fixed)

'AdaptiveDistanceRestraintMgr' object has no attribute '_c_pointer'

Reported by: claudia.kielkopf@… 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: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
I was running an ISOLDE simulaiton and wanted to stop and discard the results, when there was an error message

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/AF_Afp11-12_3chains.pdb

Chain information for AF_Afp11-12_3chains.pdb #1  
---  
Chain | Description  
A | No description available  
I | No description available  
J | No description available  
  

> color bychain

> color bfactor palette alphafold

12286 atoms, 1570 residues, atom bfactor range 13.1 to 226  

> color bychain

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/Afp11-12_on920.pdb

Summary of feedback from opening
/Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/Afp11-12_on920.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4735 messages similar to the above omitted  
  
Chain information for Afp11-12_on920.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color bychain

> color bfactor palette alphafold

31945 atoms, 3140 residues, atom bfactor range 13.1 to 226  

> close #1

> select /A

4740 atoms, 4851 bonds, 607 residues, 1 model selected  

> ui tool show "Blast Protein"

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 2/A  

> save
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/Afp11-12_on920_onlyAfp11.pdb
> selectedOnly true relModel #2

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/Afp11-12_on920_onlyAfp11.pdb

Summary of feedback from opening
/Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/Afp11-12_on920_onlyAfp11.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 22 22 LEU B 7
ILE B 15 1 9  
Start residue of secondary structure not found: HELIX 23 23 PHE B 17 SER B 32
1 16  
Start residue of secondary structure not found: HELIX 24 24 PRO B 44 ALA B 63
1 20  
Start residue of secondary structure not found: HELIX 25 25 LEU B 67 LEU B 70
1 4  
Start residue of secondary structure not found: HELIX 26 26 GLU B 82 PHE B 84
1 3  
72 messages similar to the above omitted  
  
Chain information for Afp11-12_on920_onlyAfp11.pdb #1  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> select add #2

19659 atoms, 19945 bonds, 1570 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select #2/B

14919 atoms, 15094 bonds, 963 residues, 1 model selected  

> save
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/Afp11-12_on920_onlyAfp12.pdb
> models #2 selectedOnly true

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/Afp11-12_on920_onlyAfp12.pdb

Summary of feedback from opening
/Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/Afp11-12_on920_onlyAfp12.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 3
GLY A 12 1 10  
Start residue of secondary structure not found: HELIX 2 2 GLY A 27 GLU A 39 1
13  
Start residue of secondary structure not found: HELIX 3 3 TRP A 51 TRP A 55 1
5  
Start residue of secondary structure not found: HELIX 4 4 LEU A 61 GLN A 69 1
9  
Start residue of secondary structure not found: HELIX 5 5 PRO A 71 LEU A 73 1
3  
40 messages similar to the above omitted  
  
Chain information for Afp11-12_on920_onlyAfp12.pdb #3  
---  
Chain | Description  
B | No description available  
  

> hide #2 models

> close session

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/ProcessPredictedModel_17/Afp11-12_on920_onlyAfp11_processed_A_1.pdb

Chain information for Afp11-12_on920_onlyAfp11_processed_A_1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> color bfactor

4740 atoms, 607 residues, atom bfactor range 6.4 to 999  

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/ProcessPredictedModel_18/Afp11-12_on920_onlyAfp12_processed_A_1.pdb

Chain information for Afp11-12_on920_onlyAfp12_processed_A_1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/ProcessPredictedModel_18/Afp11-12_on920_onlyAfp12_processed.pdb

Chain information for Afp11-12_on920_onlyAfp12_processed.pdb #3  
---  
Chain | Description  
B | No description available  
  

> hide #1 models

> color bfactor #2-3

29838 atoms, 1926 residues, atom bfactor range 6.68 to 999  

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/Afp11-12_on920_onlyAfp12.pdb

Summary of feedback from opening
/Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/Afp11-12_on920_onlyAfp12.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 3
GLY A 12 1 10  
Start residue of secondary structure not found: HELIX 2 2 GLY A 27 GLU A 39 1
13  
Start residue of secondary structure not found: HELIX 3 3 TRP A 51 TRP A 55 1
5  
Start residue of secondary structure not found: HELIX 4 4 LEU A 61 GLN A 69 1
9  
Start residue of secondary structure not found: HELIX 5 5 PRO A 71 LEU A 73 1
3  
40 messages similar to the above omitted  
  
Chain information for Afp11-12_on920_onlyAfp12.pdb #4  
---  
Chain | Description  
B | No description available  
  

> hide #4 models

> show #4 models

> hide #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> close session

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/RealSpaceRefine_13/AF_Afp11-12_IS9_real_space_refined_007_IS3_real_space_refined_013.pdb

Chain information for
AF_Afp11-12_IS9_real_space_refined_007_IS3_real_space_refined_013.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/RealSpaceRefine_13/AF_Afp11-12_IS9_real_space_refined_007_IS3_real_space_refined_013_bfact.pdb

Chain information for
AF_Afp11-12_IS9_real_space_refined_007_IS3_real_space_refined_013_bfact.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!1 models

> color bfactor #!2

22147 atoms, 1420 residues, atom bfactor range 6.4 to 276  

> close session

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/RealSpaceRefine_13/AF_Afp11-12_IS9_real_space_refined_007_IS3_real_space_refined_013_bfact.pdb

Chain information for
AF_Afp11-12_IS9_real_space_refined_007_IS3_real_space_refined_013_bfact.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/cryosparc_P15_J920__localfilter_zflip.mrc

Opened cryosparc_P15_J920__localfilter_zflip.mrc as #2, grid size 360,360,360,
pixel 1.08, shown at level 1.02, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.5876

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp12/Afp11-12/cryosparc_P15_J918_009_volume_map_sharp_zflip.mrc

Opened cryosparc_P15_J918_009_volume_map_sharp_zflip.mrc as #3, grid size
360,360,360, pixel 1.08, shown at level 0.968, step 2, values float32  

> volume #2 level 0.4127

> volume #3 step 1

> volume #3 level 0.9555

> volume #3 level 0.5086

> volume #3 level 0.6898

> volume #2 level 0.6051

> close #3

> clipper associate #2 toModel #1

Opened cryosparc_P15_J920__localfilter_zflip.mrc as #1.1.1.1, grid size
360,360,360, pixel 1.08, shown at level 0.881, step 1, values float32  
Chain information for
AF_Afp11-12_IS9_real_space_refined_007_IS3_real_space_refined_013_bfact.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
  

> set bgColor white

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 105 residues in model #1.2 to IUPAC-IUB
standards.  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> addh

Summary of feedback from adding hydrogens to
AF_Afp11-12_IS9_real_space_refined_007_IS3_real_space_refined_013_bfact.pdb
#1.2  
---  
notes | No usable SEQRES records for
AF_Afp11-12_IS9_real_space_refined_007_IS3_real_space_refined_013_bfact.pdb
(#1.2) chain A; guessing termini instead  
No usable SEQRES records for
AF_Afp11-12_IS9_real_space_refined_007_IS3_real_space_refined_013_bfact.pdb
(#1.2) chain B; guessing termini instead  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A LEU 4, /A GLN 18, /A
LEU 201, /A THR 216, /A PRO 331, /A THR 541, /B ASN 5, /B VAL 160, /B ILE 632,
/B VAL 644, /B HIS 661, /B SER 674, /B TRP 778, /B PHE 806  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLU 604, /A GLY 12, /A
ALA 192, /A THR 212, /A LYS 315, /A TRP 532, /B VAL 916, /B PRO 154, /B ALA
626, /B GLN 636, /B ILE 654, /B LYS 669, /B ALA 757, /B LYS 798  
1062 hydrogen bonds  
/A GLU 604 is not terminus, removing H atom from 'C'  
/B VAL 916 is not terminus, removing H atom from 'C'  
1 hydrogens added  
  

> ui tool show "Ramachandran Plot"

[Repeated 1 time(s)]s1:
LEQLKQILGQTFLLEPRTGKGLLNLMAKYTEAVPFAGHTDADWKDFWMAGCTLEALSDIYQYPGLAEKKLPVQQAFLLALLHLLETPRAMLNTVPARHRSLYYRDLLGFAPRAPQPDSVAVSFTLQRNSSPYALPAGSLLDGGQDSAGNSITYQTDDSLLITGQQLEQLCWTAQVGETWKRYTALPAEGLRLFTATTDTKEKAPELYLGFSGTSAQDTLSLYWSVRASSALDVTWWYYQGTKWASLDAELQDNTASLSVSNLWRARLPADSQPGSGLPQDDEPLEAGYYWIKGTLKPQLQAVLANAMTATLNVAQAIDDSHFSQPLPANTINQLVTPVAAISDVRQPLPSVGGQPRETEMAMLQRAAPRIAHRQRAITWNNMRSLLMEHYPEIFDVRFPDVDKLSRLPALEVQSLMVIPDGRYGDNDDALRPALSNGRLSRMAQWLSQYTSLWAAPTLKNPKYIDVTARYRVTFVVGIRPDYGYRQLAAQLQHDYMPWTPGNQVDYYQLLATLQQSPLVQSVNALVLSHDVIDETGKPTSMETQSTVTARDDEVLILCPEGE  
s2:
LEQLKQILGQTFLLEPRTGKGLLNLMAKYTEAVPFAGHTDADWKDFWMAGCTLEALSDIYQYPGLAEKKLPVQQAFLLALLHLLETPRAMLNTVPARHRSLYYRDLLGFAPRAPQPDSVAVSFTLQRNSSPYALPAGSLLDGGQDSAGNSITYQTDDSLLITGQQLEQLCWTAQVGETWKRYTALPAEGLRLFTATTDTKEKAPELYLGFSGTSAQDTLSLYWSVRASSALDVTWWYYQGTKWASLDAELQDNTASLSVSNLWRARLPADSQPGSGLPQDDEPLEAGYYWIKGTLKPQLQAVLANAMTATLNVAQAIDDSHFSQPLPANTINQLVTPVAAISDVRQPLPSVGGQPRETEMAMLQRAAPRIAHRQRAITWNNMRSLLMEHYPEIFDVRFPDVDKLSRLPALEVQSLMVIPDGRYGDNDDALRPALSNGRLSRMAQWLSQYTSLWAAPTLKNPKYIDVTARYRVTFVVGIRPDYGYRQLAAQLQHDYMPWTPGNQVDYYQLLATLQQSPLVQSVNALVLSHDVIDETGKPTSMETQSTVTARDDEVLILCPEGE  
s1:
.............................................................................................................................................................................................................................LEQLKQILGQTFLLEPRTGKGLLNLMAKYTEAVPFA.GHTD......ADWKDFWMAGCTLEALSDIYQ..YPGLAEKKLPVQQAFLLALLHLLETPRAMLNTVPARHRSLYYRDLLGFAP...RAPQPDSVAVSFTLQRNSSPYALPA.GSLLDGGQDSAGNSITYQTD.....DSLLITGQQLEQLCWTAQVGETWKRYTALPAEGLRLFTATTDTKE.KAPELYLGFSGTS..AQDTLSLYWSVRASSALDVTWWYYQGTKWASLDAELQDNTASLSVSNLWRARLPADSQPGSGL.PQDDEPLEAGY.......YWIKGTLKPQLQAVLANAMTATLNVAQAIDDSHFSQ..PLPANTINQLVTPVAAISD...VRQPLPSVGGQPRETEMAMLQRAAPRIAHRQRAITWNNMRSLLMEHYPEIFDVRFPDVD.KLSRLPALEVQSLMVIPDGRYG.DNDDALRPALSNGRLSRMAQWLS.QYTSLWAAPTLKNPKYIDVTARYRVTFVVGIRPDYGYRQLAAQLQHDYMPW.TPGNQV...DYYQLLATLQQSPLVQSVNALVLSHDVIDETGKPTSMETQSTVTARDDEVLILCPEGE.............................................................................  
s2:
NALFPAVKDAIVFDALWQQAHEKVTALSGEIWTDTGDHDPGVTLLQSATWNCSDLSYRASLSLNDLLTHQDQSTLFPEEFGPEQVLTCNTVTAEDYRRALLDVHSSDIQALDTPEQDFLFSDVSLTQEPKEHRFHWWYNAEKREYSFRKPVNELKLRGNLWLSLVPTRYTQSLSPENLAAVEQCLAEFLAAHRNLGEVVSRITWLQPATFSPRMTIELADNIGDINQVAAQIYQVTDAFLRP...AVARYTTEQRRALGDADDAIFEGPRLKHGWQQTAPSQITSGGYVLNLGPLVNLLLAIPG...VASLSTLSVDKGDGHITAVTGDNLRWQVADGYYPLLWGAP.PLSLLAG.....DDSPLTLVSKGGIRNTLESEAMAGYLTQADLIVTTPTVLPAGRFRDQTLYIP.IGQRQPECYALQQPDTVIDDQTRAVHQFLLPVDQLLADGTAELAQLPTLLAFKNRGDAI........RGTRWPYTNAMVQQ.....AIHQPYAKTLEAIAQQDAAIFTQDKQPVGGNYARELDFLQYLLGYFGTQRAAL...PLTLDLPDFLATQRAYLAQQPALGYDRINIRIDQVSALQKRIAARIGLDSICFADNPD...LGQLPFYLIEHRQL.LPQTPDSTFDSEQTPSGFAITLTQVQGQLIDLIAIHVSRLLVIKSFTVSTENSQQLHNTLSRLETAWASHNLRWQNSNVWLQD.......MDYRLNYAEAKLQPANPQ..QRLLASNAQSPYPAMVSVGDGIVLRPAWQLAATVKAVDPIAG.TLLIEKFPSAESSFRYQWAFSQANYATTDRFSFVVSAVLNRRLIENPNIVPEQLVAWIQETIMAEFPAHVSLINHWLDDATFNNFGVTYSRWQNSGMPLGDDAFALMQILTLGHLPV  
s1:
NALFPAVKDAIVFDALWQQAHEKVTALSGEIWTDTGDHDPGVTLLQSATWNCSDLSYRASLSLNDLLTHQDQSTLFPEEFGPEQVLTCNTVTAEDYRRALLDVHSSDIQALDTPEQDFLFSDVSLTQEPKEHRFHWWYNAEKREYSFRKPVNELKLRGNLWLSLVPTRYTQSLSPENLAAVEQCLAEFLAAHRNLGEVVSRITWLQPATFSPRMTIELADNIGDINQVAAQIYQVTDAFLRP...AVARYTTEQRRALGDADDAIFEGPRLKHGWQQTAPSQITSGGYVLNLGPLVNLLLAIPG...VASLSTLSVDKGDGHITAVTGDNLRWQVADGYYPLLWGAP.PLSLLAG.....DDSPLTLVSKGGIRNTLESEAMAGYLTQADLIVTTPTVLPAGRFRDQTLYIP.IGQRQPECYALQQPDTVIDDQTRAVHQFLLPVDQLLADGTAELAQLPTLLAFKNRGDAI........RGTRWPYTNAMVQQ.....AIHQPYAKTLEAIAQQDAAIFTQDKQPVGGNYARELDFLQYLLGYFGTQRAAL...PLTLDLPDFLATQRAYLAQQPALGYDRINIRIDQVSALQKRIAARIGLDSICFADNPD...LGQLPFYLIEHRQL.LPQTPDSTFDSEQTPSGFAITLTQVQGQLIDLIAIHVSRLLVIKSFTVSTENSQQLHNTLSRLETAWASHNLRWQNSNVWLQD.......MDYRLNYAEAKLQPANPQ..QRLLASNAQSPYPAMVSVGDGIVLRPAWQLAATVKAVDPIAG.TLLIEKFPSAESSFRYQWAFSQANYATTDRFSFVVSAVLNRRLIENPNIVPEQLVAWIQETIMAEFPAHVSLINHWLDDATFNNFGVTYSRWQNSGMPLGDDAFALMQILTLGHLPV  
s2:
.............................................................................................................................................................................................................................LEQLKQILGQTFLLEPRTGKGLLNLMAKYTEAVPFA.GHTD......ADWKDFWMAGCTLEALSDIYQ..YPGLAEKKLPVQQAFLLALLHLLETPRAMLNTVPARHRSLYYRDLLGFAP...RAPQPDSVAVSFTLQRNSSPYALPA.GSLLDGGQDSAGNSITYQTD.....DSLLITGQQLEQLCWTAQVGETWKRYTALPAEGLRLFTATTDTKE.KAPELYLGFSGTS..AQDTLSLYWSVRASSALDVTWWYYQGTKWASLDAELQDNTASLSVSNLWRARLPADSQPGSGL.PQDDEPLEAGY.......YWIKGTLKPQLQAVLANAMTATLNVAQAIDDSHFSQ..PLPANTINQLVTPVAAISD...VRQPLPSVGGQPRETEMAMLQRAAPRIAHRQRAITWNNMRSLLMEHYPEIFDVRFPDVD.KLSRLPALEVQSLMVIPDGRYG.DNDDALRPALSNGRLSRMAQWLS.QYTSLWAAPTLKNPKYIDVTARYRVTFVVGIRPDYGYRQLAAQLQHDYMPW.TPGNQV...DYYQLLATLQQSPLVQSVNALVLSHDVIDETGKPTSMETQSTVTARDDEVLILCPEGE.............................................................................  
s1:
NALFPAVKDAIVFDALWQQAHEKVTALSGEIWTDTGDHDPGVTLLQSATWNCSDLSYRASLSLNDLLTHQDQSTLFPEEFGPEQVLTCNTVTAEDYRRALLDVHSSDIQALDTPEQDFLFSDVSLTQEPKEHRFHWWYNAEKREYSFRKPVNELKLRGNLWLSLVPTRYTQSLSPENLAAVEQCLAEFLAAHRNLGEVVSRITWLQPATFSPRMTIELADNIGDINQVAAQIYQVTDAFLRPAVARYTTEQRRALGDADDAIFEGPRLKHGWQQTAPSQITSGGYVLNLGPLVNLLLAIPGVASLSTLSVDKGDGHITAVTGDNLRWQVADGYYPLLWGAPPLSLLAGDDSPLTLVSKGGIRNTLESEAMAGYLTQADLIVTTPTVLPAGRFRDQTLYIPIGQRQPECYALQQPDTVIDDQTRAVHQFLLPVDQLLADGTAELAQLPTLLAFKNRGDAIRGTRWPYTNAMVQQAIHQPYAKTLEAIAQQDAAIFTQDKQPVGGNYARELDFLQYLLGYFGTQRAALPLTLDLPDFLATQRAYLAQQPALGYDRINIRIDQVSALQKRIAARIGLDSICFADNPDLGQLPFYLIEHRQLLPQTPDSTFDSEQTPSGFAITLTQVQGQLIDLIAIHVSRLLVIKSFTVSTENSQQLHNTLSRLETAWASHNLRWQNSNVWLQDMDYRLNYAEAKLQPANPQQRLLASNAQSPYPAMVSVGDGIVLRPAWQLAATVKAVDPIAGTLLIEKFPSAESSFRYQWAFSQANYATTDRFSFVVSAVLNRRLIENPNIVPEQLVAWIQETIMAEFPAHVSLINHWLDDATFNNFGVTYSRWQNSGMPLGDDAFALMQILTLGHLPV  
s2:
NALFPAVKDAIVFDALWQQAHEKVTALSGEIWTDTGDHDPGVTLLQSATWNCSDLSYRASLSLNDLLTHQDQSTLFPEEFGPEQVLTCNTVTAEDYRRALLDVHSSDIQALDTPEQDFLFSDVSLTQEPKEHRFHWWYNAEKREYSFRKPVNELKLRGNLWLSLVPTRYTQSLSPENLAAVEQCLAEFLAAHRNLGEVVSRITWLQPATFSPRMTIELADNIGDINQVAAQIYQVTDAFLRPAVARYTTEQRRALGDADDAIFEGPRLKHGWQQTAPSQITSGGYVLNLGPLVNLLLAIPGVASLSTLSVDKGDGHITAVTGDNLRWQVADGYYPLLWGAPPLSLLAGDDSPLTLVSKGGIRNTLESEAMAGYLTQADLIVTTPTVLPAGRFRDQTLYIPIGQRQPECYALQQPDTVIDDQTRAVHQFLLPVDQLLADGTAELAQLPTLLAFKNRGDAIRGTRWPYTNAMVQQAIHQPYAKTLEAIAQQDAAIFTQDKQPVGGNYARELDFLQYLLGYFGTQRAALPLTLDLPDFLATQRAYLAQQPALGYDRINIRIDQVSALQKRIAARIGLDSICFADNPDLGQLPFYLIEHRQLLPQTPDSTFDSEQTPSGFAITLTQVQGQLIDLIAIHVSRLLVIKSFTVSTENSQQLHNTLSRLETAWASHNLRWQNSNVWLQDMDYRLNYAEAKLQPANPQQRLLASNAQSPYPAMVSVGDGIVLRPAWQLAATVKAVDPIAGTLLIEKFPSAESSFRYQWAFSQANYATTDRFSFVVSAVLNRRLIENPNIVPEQLVAWIQETIMAEFPAHVSLINHWLDDATFNNFGVTYSRWQNSGMPLGDDAFALMQILTLGHLPV  

> isolde restrain distances "#1.2/A","#1.2/B" templateAtoms "#1.2/A","#1.2/B"
> 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 sim start sel

ISOLDE: started sim  

> hide ~@CA

> isolde sim stop

Sim termination reason: None  
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 sim start /B:206

ISOLDE: started sim  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/backends/backend_qt.py", line 454, in _draw_idle  
self.draw()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 405, in draw  
self.figure.draw(self.renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 74, in draw_wrapper  
result = draw(artist, renderer, *args, **kwargs)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 51, in draw_wrapper  
return draw(artist, renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 3076, in draw  
self.get_layout_engine().execute(self)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/layout_engine.py", line 175, in execute  
kwargs = get_tight_layout_figure(  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/_tight_layout.py", line 308, in get_tight_layout_figure  
kwargs = _auto_adjust_subplotpars(fig, renderer,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/_tight_layout.py", line 85, in _auto_adjust_subplotpars  
tight_bbox = fig.transFigure.inverted().transform_bbox(tight_bbox_raw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/transforms.py", line 1876, in inverted  
self._inverted = Affine2D(inv(mtx), shorthand_name=shorthand_name)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/backends/backend_qt.py", line 454, in _draw_idle  
self.draw()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 405, in draw  
self.figure.draw(self.renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 74, in draw_wrapper  
result = draw(artist, renderer, *args, **kwargs)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 51, in draw_wrapper  
return draw(artist, renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 3076, in draw  
self.get_layout_engine().execute(self)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/layout_engine.py", line 175, in execute  
kwargs = get_tight_layout_figure(  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/_tight_layout.py", line 308, in get_tight_layout_figure  
kwargs = _auto_adjust_subplotpars(fig, renderer,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/_tight_layout.py", line 85, in _auto_adjust_subplotpars  
tight_bbox = fig.transFigure.inverted().transform_bbox(tight_bbox_raw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/transforms.py", line 1876, in inverted  
self._inverted = Affine2D(inv(mtx), shorthand_name=shorthand_name)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  

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

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:206

ISOLDE: started sim  

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

> close #1.2.8

> isolde pepflip /B:206

> isolde pepflip /B:205

> isolde pepflip /B:204

[Repeated 3 time(s)]

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/mvc492/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 770, in _sim_end_cb  
self._starting_checkpoint.revert()  
File "/Users/mvc492/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/checkpoint.py", line 61, in revert  
rm.restore_checkpoint(data)  
File "/Users/mvc492/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/molobject.py", line 3435, in restore_checkpoint  
restraints = self.atoms_restraints(atoms)  
File "/Users/mvc492/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/molobject.py", line 2979, in atoms_restraints  
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers,
len(atoms)))  
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'  
  
Error processing trigger "sim terminated":  
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'  
  
File "/Users/mvc492/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/molobject.py", line 2979, in atoms_restraints  
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers,
len(atoms)))  
  
See log for complete Python traceback.  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:204

ISOLDE: started sim  

> isolde pepflip /B:206

[Repeated 1 time(s)]

> isolde pepflip /B:205

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:204

ISOLDE: started sim  

> isolde pepflip /B:207

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
s1:
LEQLKQILGQTFLLEPRTGKGLLNLMAKYTEAVPFAGHTDADWKDFWMAGCTLEALSDIYQYPGLAEKKLPVQQAFLLALLHLLETPRAMLNTVPARHRSLYYRDLLGFAPRAPQPDSVAVSFTLQRNSSPYALPAGSLLDGGQDSAGNSITYQTDDSLLITGQQLEQLCWTAQVGETWKRYTALPAEGLRLFTATTDTKEKAPELYLGFSGTSAQDTLSLYWSVRASSALDVTWWYYQGTKWASLDAELQDNTASLSVSNLWRARLPADSQPGSGLPQDDEPLEAGYYWIKGTLKPQLQAVLANAMTATLNVAQAIDDSHFSQPLPANTINQLVTPVAAISDVRQPLPSVGGQPRETEMAMLQRAAPRIAHRQRAITWNNMRSLLMEHYPEIFDVRFPDVDKLSRLPALEVQSLMVIPDGRYGDNDDALRPALSNGRLSRMAQWLSQYTSLWAAPTLKNPKYIDVTARYRVTFVVGIRPDYGYRQLAAQLQHDYMPWTPGNQVDYYQLLATLQQSPLVQSVNALVLSHDVIDETGKPTSMETQSTVTARDDEVLILCPEGE  
s2:
LEQLKQILGQTFLLEPRTGKGLLNLMAKYTEAVPFAGHTDADWKDFWMAGCTLEALSDIYQYPGLAEKKLPVQQAFLLALLHLLETPRAMLNTVPARHRSLYYRDLLGFAPRAPQPDSVAVSFTLQRNSSPYALPAGSLLDGGQDSAGNSITYQTDDSLLITGQQLEQLCWTAQVGETWKRYTALPAEGLRLFTATTDTKEKAPELYLGFSGTSAQDTLSLYWSVRASSALDVTWWYYQGTKWASLDAELQDNTASLSVSNLWRARLPADSQPGSGLPQDDEPLEAGYYWIKGTLKPQLQAVLANAMTATLNVAQAIDDSHFSQPLPANTINQLVTPVAAISDVRQPLPSVGGQPRETEMAMLQRAAPRIAHRQRAITWNNMRSLLMEHYPEIFDVRFPDVDKLSRLPALEVQSLMVIPDGRYGDNDDALRPALSNGRLSRMAQWLSQYTSLWAAPTLKNPKYIDVTARYRVTFVVGIRPDYGYRQLAAQLQHDYMPWTPGNQVDYYQLLATLQQSPLVQSVNALVLSHDVIDETGKPTSMETQSTVTARDDEVLILCPEGE  
s1:
.............................................................................................................................................................................................................................LEQLKQILGQTFLLEPRTGKGLLNLMAKYTEAVPFA.GHTD......ADWKDFWMAGCTLEALSDIYQ..YPGLAEKKLPVQQAFLLALLHLLETPRAMLNTVPARHRSLYYRDLLGFAP...RAPQPDSVAVSFTLQRNSSPYALPA.GSLLDGGQDSAGNSITYQTD.....DSLLITGQQLEQLCWTAQVGETWKRYTALPAEGLRLFTATTDTKE.KAPELYLGFSGTS..AQDTLSLYWSVRASSALDVTWWYYQGTKWASLDAELQDNTASLSVSNLWRARLPADSQPGSGL.PQDDEPLEAGY.......YWIKGTLKPQLQAVLANAMTATLNVAQAIDDSHFSQ..PLPANTINQLVTPVAAISD...VRQPLPSVGGQPRETEMAMLQRAAPRIAHRQRAITWNNMRSLLMEHYPEIFDVRFPDVD.KLSRLPALEVQSLMVIPDGRYG.DNDDALRPALS...NGRLSRMAQWLSQYTSLWAAPTLKNPKYIDVTARYRVTFVVGIRPDYGYRQLAAQLQHDYMPW.TPGNQV...DYYQLLATLQQSPLVQSVNALVLSHDVIDETGKPTSMETQSTVTARDDEVLILCPEGE.............................................................................  
s2:
NALFPAVKDAIVFDALWQQAHEKVTALSGEIWTDTGDHDPGVTLLQSATWNCSDLSYRASLSLNDLLTHQDQSTLFPEEFGPEQVLTCNTVTAEDYRRALLDVHSSDIQALDTPEQDFLFSDVSLTQEPKEHRFHWWYNAEKREYSFRKPVNELKLRGNLWLSLVPTRYTQSLSPENLAAVEQCLAEFLAAHRNLGEVVSRITWLQPATFSPRMTIELADNIGDINQVAAQIYQVTDAFLRP...AVARYTTEQRRALGDADDAIFEGPRLKHGWQQTAPSQITSGGYVLNLGPLVNLLLAIPG...VASLSTLSVDKGDGHITAVTGDNLRWQVADGYYPLLWGAP.PLSLLAG.....DDSPLTLVSKGGIRNTLESEAMAGYLTQADLIVTTPTVLPAGRFRDQTLYIP.IGQRQPECYALQQPDTVIDDQTRAVHQFLLPVDQLLADGTAELAQLPTLLAFKNRGDAI........RGTRWPYTNAMVQQ.....AIHQPYAKTLEAIAQQDAAIFTQDKQPVGGNYARELDFLQYLLGYFGTQRAAL...PLTLDLPDFLATQRAYLAQQPALGYDRINIRIDQVSALQKRIAARIGLDSICFADNPD...LGQLPFYLIEHRQL.LPQTPDSTFDSEQTPSGFAITLTQVQGQLIDLIAIHVSRLLVIKSFTVSTENSQQLHNTLSRLETAWASHNLRWQN..SNVWLQD.......MDYRLNYAEAKLQPANPQ..QRLLASNAQSPYPAMVSVGDGIVLRPAWQLAATVKAVDPIAG.TLLIEKFPSAESSFRYQWAFSQANYATTDRFSFVVSAVLNRRLIENPNIVPEQLVAWIQETIMAEFPAHVSLINHWLDDATFNNFGVTYSRWQNSGMPLGDDAFALMQILTLGHLPV  
s1:
NALFPAVKDAIVFDALWQQAHEKVTALSGEIWTDTGDHDPGVTLLQSATWNCSDLSYRASLSLNDLLTHQDQSTLFPEEFGPEQVLTCNTVTAEDYRRALLDVHSSDIQALDTPEQDFLFSDVSLTQEPKEHRFHWWYNAEKREYSFRKPVNELKLRGNLWLSLVPTRYTQSLSPENLAAVEQCLAEFLAAHRNLGEVVSRITWLQPATFSPRMTIELADNIGDINQVAAQIYQVTDAFLRP...AVARYTTEQRRALGDADDAIFEGPRLKHGWQQTAPSQITSGGYVLNLGPLVNLLLAIPG...VASLSTLSVDKGDGHITAVTGDNLRWQVADGYYPLLWGAP.PLSLLAG.....DDSPLTLVSKGGIRNTLESEAMAGYLTQADLIVTTPTVLPAGRFRDQTLYIP.IGQRQPECYALQQPDTVIDDQTRAVHQFLLPVDQLLADGTAELAQLPTLLAFKNRGDAI........RGTRWPYTNAMVQQ.....AIHQPYAKTLEAIAQQDAAIFTQDKQPVGGNYARELDFLQYLLGYFGTQRAAL...PLTLDLPDFLATQRAYLAQQPALGYDRINIRIDQVSALQKRIAARIGLDSICFADNPD...LGQLPFYLIEHRQL.LPQTPDSTFDSEQTPSGFAITLTQVQGQLIDLIAIHVSRLLVIKSFTVSTENSQQLHNTLSRLETAWASHNLRWQN..SNVWLQD.......MDYRLNYAEAKLQPANPQ..QRLLASNAQSPYPAMVSVGDGIVLRPAWQLAATVKAVDPIAG.TLLIEKFPSAESSFRYQWAFSQANYATTDRFSFVVSAVLNRRLIENPNIVPEQLVAWIQETIMAEFPAHVSLINHWLDDATFNNFGVTYSRWQNSGMPLGDDAFALMQILTLGHLPV  
s2:
.............................................................................................................................................................................................................................LEQLKQILGQTFLLEPRTGKGLLNLMAKYTEAVPFA.GHTD......ADWKDFWMAGCTLEALSDIYQ..YPGLAEKKLPVQQAFLLALLHLLETPRAMLNTVPARHRSLYYRDLLGFAP...RAPQPDSVAVSFTLQRNSSPYALPA.GSLLDGGQDSAGNSITYQTD.....DSLLITGQQLEQLCWTAQVGETWKRYTALPAEGLRLFTATTDTKE.KAPELYLGFSGTS..AQDTLSLYWSVRASSALDVTWWYYQGTKWASLDAELQDNTASLSVSNLWRARLPADSQPGSGL.PQDDEPLEAGY.......YWIKGTLKPQLQAVLANAMTATLNVAQAIDDSHFSQ..PLPANTINQLVTPVAAISD...VRQPLPSVGGQPRETEMAMLQRAAPRIAHRQRAITWNNMRSLLMEHYPEIFDVRFPDVD.KLSRLPALEVQSLMVIPDGRYG.DNDDALRPALS...NGRLSRMAQWLSQYTSLWAAPTLKNPKYIDVTARYRVTFVVGIRPDYGYRQLAAQLQHDYMPW.TPGNQV...DYYQLLATLQQSPLVQSVNALVLSHDVIDETGKPTSMETQSTVTARDDEVLILCPEGE.............................................................................  
s1:
NALFPAVKDAIVFDALWQQAHEKVTALSGEIWTDTGDHDPGVTLLQSATWNCSDLSYRASLSLNDLLTHQDQSTLFPEEFGPEQVLTCNTVTAEDYRRALLDVHSSDIQALDTPEQDFLFSDVSLTQEPKEHRFHWWYNAEKREYSFRKPVNELKLRGNLWLSLVPTRYTQSLSPENLAAVEQCLAEFLAAHRNLGEVVSRITWLQPATFSPRMTIELADNIGDINQVAAQIYQVTDAFLRPAVARYTTEQRRALGDADDAIFEGPRLKHGWQQTAPSQITSGGYVLNLGPLVNLLLAIPGVASLSTLSVDKGDGHITAVTGDNLRWQVADGYYPLLWGAPPLSLLAGDDSPLTLVSKGGIRNTLESEAMAGYLTQADLIVTTPTVLPAGRFRDQTLYIPIGQRQPECYALQQPDTVIDDQTRAVHQFLLPVDQLLADGTAELAQLPTLLAFKNRGDAIRGTRWPYTNAMVQQAIHQPYAKTLEAIAQQDAAIFTQDKQPVGGNYARELDFLQYLLGYFGTQRAALPLTLDLPDFLATQRAYLAQQPALGYDRINIRIDQVSALQKRIAARIGLDSICFADNPDLGQLPFYLIEHRQLLPQTPDSTFDSEQTPSGFAITLTQVQGQLIDLIAIHVSRLLVIKSFTVSTENSQQLHNTLSRLETAWASHNLRWQNSNVWLQDMDYRLNYAEAKLQPANPQQRLLASNAQSPYPAMVSVGDGIVLRPAWQLAATVKAVDPIAGTLLIEKFPSAESSFRYQWAFSQANYATTDRFSFVVSAVLNRRLIENPNIVPEQLVAWIQETIMAEFPAHVSLINHWLDDATFNNFGVTYSRWQNSGMPLGDDAFALMQILTLGHLPV  
s2:
NALFPAVKDAIVFDALWQQAHEKVTALSGEIWTDTGDHDPGVTLLQSATWNCSDLSYRASLSLNDLLTHQDQSTLFPEEFGPEQVLTCNTVTAEDYRRALLDVHSSDIQALDTPEQDFLFSDVSLTQEPKEHRFHWWYNAEKREYSFRKPVNELKLRGNLWLSLVPTRYTQSLSPENLAAVEQCLAEFLAAHRNLGEVVSRITWLQPATFSPRMTIELADNIGDINQVAAQIYQVTDAFLRPAVARYTTEQRRALGDADDAIFEGPRLKHGWQQTAPSQITSGGYVLNLGPLVNLLLAIPGVASLSTLSVDKGDGHITAVTGDNLRWQVADGYYPLLWGAPPLSLLAGDDSPLTLVSKGGIRNTLESEAMAGYLTQADLIVTTPTVLPAGRFRDQTLYIPIGQRQPECYALQQPDTVIDDQTRAVHQFLLPVDQLLADGTAELAQLPTLLAFKNRGDAIRGTRWPYTNAMVQQAIHQPYAKTLEAIAQQDAAIFTQDKQPVGGNYARELDFLQYLLGYFGTQRAALPLTLDLPDFLATQRAYLAQQPALGYDRINIRIDQVSALQKRIAARIGLDSICFADNPDLGQLPFYLIEHRQLLPQTPDSTFDSEQTPSGFAITLTQVQGQLIDLIAIHVSRLLVIKSFTVSTENSQQLHNTLSRLETAWASHNLRWQNSNVWLQDMDYRLNYAEAKLQPANPQQRLLASNAQSPYPAMVSVGDGIVLRPAWQLAATVKAVDPIAGTLLIEKFPSAESSFRYQWAFSQANYATTDRFSFVVSAVLNRRLIENPNIVPEQLVAWIQETIMAEFPAHVSLINHWLDDATFNNFGVTYSRWQNSGMPLGDDAFALMQILTLGHLPV  

> isolde restrain distances "#1.2/A","#1.2/B" templateAtoms "#1.2/A","#1.2/B"
> 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 0.46

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 0.46

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

> isolde sim start /A:335

ISOLDE: started sim  

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

> close #1.2.1

> isolde pepflip /A:335

> isolde pepflip /A:334

[Repeated 1 time(s)]

> isolde pepflip /A:335

> isolde pepflip /A:336

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde restrain distances "#1.2/A","#1.2/B" templateAtoms "#1.2/A","#1.2/B"
> 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 0.46

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 0.46

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

> isolde sim start /A:347

ISOLDE: started sim  

> hide ~@CA

> close #1.2.1

> isolde release torsions #1.2&sel

> show ~@CA

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/mvc492/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 770, in _sim_end_cb  
self._starting_checkpoint.revert()  
File "/Users/mvc492/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/checkpoint.py", line 61, in revert  
rm.restore_checkpoint(data)  
File "/Users/mvc492/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/molobject.py", line 3435, in restore_checkpoint  
restraints = self.atoms_restraints(atoms)  
File "/Users/mvc492/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/molobject.py", line 2979, in atoms_restraints  
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers,
len(atoms)))  
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'  
  
Error processing trigger "sim terminated":  
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'  
  
File "/Users/mvc492/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/molobject.py", line 2979, in atoms_restraints  
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers,
len(atoms)))  
  
See log for complete Python traceback.  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  




OpenGL version: 4.1 INTEL-22.1.28
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2020.60.9.0.0 (iBridge: 21.16.2030.5.3,0)
      OS Loader Version: 580~743

Software:

    System Software Overview:

      System Version: macOS 14.1 (23B74)
      Kernel Version: Darwin 23.1.0
      Time since boot: 3 hours, 2 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2715H:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: GH85D8540F1S
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (3)

comment:1 by Eric Pettersen, 2 years ago

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

comment:2 by Tristan Croll, 2 years ago

Status: assigned → accepted

The cause of the traceback is that you deleted the model managing the adaptive distance restraints while a simulation was running ("close #1.2.8" in the log). There is a bug here: my intent was for ISOLDE to respond sensibly in this case, and for the most part it does - but of course restoring the restraints from a snapshot will no longer work since their manager has been deleted. I'll figure out how to make it handle this more gracefully (probably by simply printing a warning to the log to explain why those restraints couldn't be restored).

I also noticed repeated calls to "close #1.2.1" in the log - presumably to get rid of the Ramachandran or rotamer markup? You can do this with less risk of unintended consequences with the commands "~rama" and "~rota" - or simply hide the model rather than close it.

comment:3 by Tristan Croll, 2 years ago

Resolution: → fixed
Status: accepted → closed

For ISOLDE 1.7, if the manager for a given set of restraints is closed during a running simulation and the user subsequently hits the snapshot-restore button, it will result in a warning like the following in the log:

Reference Distance Restraints manager has been deleted. Unable to restore its restraints.

The restraints themselves are lost for good in this scenario, I'm afraid.

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