Opened 2 years ago

Closed 2 years ago

#9140 closed defect (can't reproduce)

ISOLDE: OpenMMException: Error initializing context: clCreateContext

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 (last modified by pett) 

The following bug report has been submitted:
Platform:        Linux-6.2.6-76060206-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

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 /home/azinas/projects/230404_dwbClpC-P_MecA-
> FtsZ/RealSpaceRefine_1/J104_rechain-coot-16_real_space_refined_001.pdb

Chain information for J104_rechain-coot-16_real_space_refined_001.pdb #1  
---  
Chain | Description  
A B C D E F | No description available  
Aa | No description available  
Ap | No description available  
Aq | No description available  
Ba Bb Bd Bi | No description available  
Bc | No description available  
Be | No description available  
Bf | No description available  
Bg Bk | No description available  
Bh | No description available  
Bj | No description available  
Bl | No description available  
Bm | No description available  
Bn | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
  

> open /home/azinas/projects/230404_dwbClpC-P_MecA-
> FtsZ/cryosparc_P14_J104_map_sharp.mrc

Opened cryosparc_P14_J104_map_sharp.mrc as #2, grid size 400,400,400, pixel
0.994, shown at level 0.0242, step 2, values float32  

> isolde start

> set selectionWidth 4

> 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  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 592 residues in model #1 to IUPAC-IUB
standards.  
Chain information for J104_rechain-coot-16_real_space_refined_001.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F | No description available  
1.2/Aa | No description available  
1.2/Ap | No description available  
1.2/Aq | No description available  
1.2/Ba 1.2/Bb 1.2/Bd 1.2/Bi | No description available  
1.2/Bc | No description available  
1.2/Be | No description available  
1.2/Bf | No description available  
1.2/Bg 1.2/Bk | No description available  
1.2/Bh | No description available  
1.2/Bj | No description available  
1.2/Bl | No description available  
1.2/Bm | No description available  
1.2/Bn | 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  
  

> clipper associate #2 toModel #1

Opened cryosparc_P14_J104_map_sharp.mrc as #1.1.1.1, grid size 400,400,400,
pixel 0.994, shown at step 1, values float32  
s1: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s2: ......RFAGF..............................  
s1: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s2: .........................ETLKDKRVM.......  
s1: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s2: ................................FIFLGP...  
s1: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1:
......................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.................................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
......................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.................................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
.....................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.................................................................................................................................  
s2:
IPTVIETTRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
......................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.................................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
......................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY................................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
........TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.................................................................................................................................  
s2:
YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
........TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY................................................................................................................................  
s2:
YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
.......TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY................................................................................................................................  
s2:
DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
......................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.................................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
..............TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.................................................................................................................................  
s2:
PTVIEAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
........TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY................................................................................................................................  
s2:
YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
..............TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.................................................................................................................................  
s2:
PTVIETYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
............TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY................................................................................................................................  
s2:
PTVIEDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
.............TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY..............................................................................................................................  
s2:
PTVIEYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQD...SEKDIYLYINSPGGSVTAGFAIYDTKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1:
..........................................................................................................................................................................................................................................................................................................................................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY...............................................................................................................................................................................................................................................................................................................................................  
s2:
AQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGTLHYTPRAKKVIEVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMNNTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVNLKEIEQEIEKVKNEKDAAVHAQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNGTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTTVDFRNTIIIMTSNVRFAGFGRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKE  
s1:
..................................................................................................................................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................  
s2:
TERAQRVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEHYTPRAKKVIELSMDEARVGTEHILLGLIRENEGVAARVFANLDITKARAQVVKALGNPENNTPTLDSLARDLTVIAKDGTLDPVIG...RDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSNNLKEIEQEIEKVKNEKDAAVFENAANLRDKQTKLEKQYEEAKNEWKNAQNSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGHDDGGQLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFGYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIA  
s1:
...................................................................................................................................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................  
s2:
RVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGYTPRAKKVIELSMDEARKGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMSNTPTLDSLARDLTVIAKDGTLDPVIG...RDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSHTTPNNLKEIEQEIEKVKNEKDAAVHQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNGMSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGHDDGGQLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFQDYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIAEQ  
s1:
.................................................................................................................................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................  
s2:
TERAQRVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEHYTPRAKKVIELSMDEARVGTEHILLGLIRENEGVAARVFANLDITKARAQVVKALGNPENTPTLDSLARDLTVIAKDGTLDPVIG...RDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSPNNLKEIEQEIEKVKNEKDAAVHQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNGSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGGQLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFDYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIAEQ  
s1:
.........................................................................................................................................TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................  
s2:
TERAQRVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHYTPRAKKVIELSMDEARKLVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPENTPTLDSLARDLTVIAKDGTLDPVIG...RDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSEIEQEIEKVKNEKDAAVHAQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGHDDGGQLTKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFDYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIAEQ  
s1:
...............TRTIIVKFNDLEDVINYAYHSNPITTE..FEDLLYMV.DGTYYY.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................  
s2:
AQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGTLHYTPRAKKVIELSMDEARKLHHNFVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMSRDKEITRVIEVLSRRTKNNPVLIGEPGVETLKDKRVMSLDMGTVVAGEFEERLKKVMEEIQQAGNVILFIDELHTLVSNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPVDTVAILKGLRDRYRINISDEAIEAAVKLSNRYFLPDKAIDLIDEASSKVRLKSHTKEIEQEIEKVKNEKDAAFENAANLRDKQTKLEKQYEEAKNEWKNAQNGINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLTGVGKTELARALMIRVDMSEFMEKHAVSRLSVILFDHPDVFNILLQVLDDGDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGEFKYDIAEQ  
s1: ......RFAGF..............................  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: RFAGF  
s2: RFAGF  
s1: ......RFAGF  
s2: ETLKDKRVM..  
s1: RFAGF.....  
s2: ....FIFLGP  
s1: ......RFAGF..............................  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1:
...................................................................RFAGF.....................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
...................................................................RFAGF.....................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
..................................................................RFAGF.....................................................................................................................  
s2:
IPTVIETTRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
...................................................................RFAGF.....................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
...................................................................RFAGF....................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
.....................................................RFAGF.....................................................................................................................  
s2:
YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
.....................................................RFAGF....................................................................................................................  
s2:
YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
....................................................RFAGF....................................................................................................................  
s2:
DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
...................................................................RFAGF.....................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
...........................................................RFAGF.....................................................................................................................  
s2:
PTVIEAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
.....................................................RFAGF....................................................................................................................  
s2:
YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
...........................................................RFAGF.....................................................................................................................  
s2:
PTVIETYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
.........................................................RFAGF....................................................................................................................  
s2:
PTVIEDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
..........................................................RFAGF..................................................................................................................  
s2:
PTVIEYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1: ......RFAGF..............................  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: ......RFAGF..............................  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: ......RFAGF..............................  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: ......RFAGF..............................  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1:
.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................RFAGF....................................................................................................................  
s2:
AQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGTLHYTPRAKKVIEVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMNNTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVNLKEIEQEIEKVKNEKDAAVHAQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNGTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTTVDFRNTIIIMTSNVRFAGFGRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKE  
s1:
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................RFAGF..............................................................................................................................  
s2:
TERAQRVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEHYTPRAKKVIELSMDEARVGTEHILLGLIRENEGVAARVFANLDITKARAQVVKALGNPENNTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSNNLKEIEQEIEKVKNEKDAAVFENAANLRDKQTKLEKQYEEAKNEWKNAQNSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGHDDGGQLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFGYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIA  
s1:
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................RFAGF.................................................................................................................................  
s2:
RVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGYTPRAKKVIELSMDEARKGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMSNTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSHTTPNNLKEIEQEIEKVKNEKDAAVHQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNGMSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGHDDGGQLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFQDYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIAEQ  
s1:
...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................RFAGF................................................................................................................................  
s2:
TERAQRVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEHYTPRAKKVIELSMDEARVGTEHILLGLIRENEGVAARVFANLDITKARAQVVKALGNPENTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSPNNLKEIEQEIEKVKNEKDAAVHQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNGSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGGQLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFDYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIAEQ  
s1:
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................RFAGF................................................................................................................................  
s2:
TERAQRVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHYTPRAKKVIELSMDEARKLVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPENTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSEIEQEIEKVKNEKDAAVHAQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGHDDGGQLTKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFDYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIAEQ  
s1:
...............................................................................RFAGF................................................................................................................................................................................................................................................................................................................................................................................................................................................................................  
s2:
AQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGTLHYTPRAKKVIELSMDEARKLHHNFVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMSRDKEITRVIEVLSRRTKNNPVLIGEPGVETLKDKRVMSLDMGTVVAGEFEERLKKVMEEIQQAGNVILFIDELHTLVSNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPVDTVAILKGLRDRYRINISDEAIEAAVKLSNRYFLPDKAIDLIDEASSKVRLKSHTKEIEQEIEKVKNEKDAAFENAANLRDKQTKLEKQYEEAKNEWKNAQNGINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLTGVGKTELARALMIRVDMSEFMEKHAVSRLSVILFDHPDVFNILLQVLDDGDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGEFKYDIAEQ  
s1: .........................ETLKDKRVM.......  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: ETLKDKRVM..  
s2: ......RFAGF  
s1: ETLKDKRVM  
s2: ETLKDKRVM  
s1: ETLKDKRVM...  
s2: ......FIFLGP  
s1: .........................ETLKDKRVM.......  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1:
...................ETLKDKRVM.................................................................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
...................ETLKDKRVM.................................................................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
..................ETLKDKRVM.................................................................................................................................................................  
s2:
IPTVIETTRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
...................ETLKDKRVM.................................................................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
...................ETLKDKRVM................................................................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
.....ETLKDKRVM.................................................................................................................................................................  
s2:
YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
.....ETLKDKRVM................................................................................................................................................................  
s2:
YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
....ETLKDKRVM................................................................................................................................................................  
s2:
DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
...................ETLKDKRVM.................................................................................................................................................................  
s2:
IPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
...........ETLKDKRVM.................................................................................................................................................................  
s2:
PTVIEAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
.....ETLKDKRVM................................................................................................................................................................  
s2:
YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
...........ETLKDKRVM.................................................................................................................................................................  
s2:
PTVIETYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1:
.........ETLKDKRVM................................................................................................................................................................  
s2:
PTVIEDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP  
s1:
..........ETLKDKRVM..............................................................................................................................................................  
s2:
PTVIEYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE  
s1: .........................ETLKDKRVM.......  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: .........................ETLKDKRVM.......  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: .........................ETLKDKRVM.......  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1: .........................ETLKDKRVM.......  
s2: TRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYY  
s1:
...........................................................................................................................................................................................ETLKDKRVM..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................  
s2:
AQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGTLHYTPRAKKVIEVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMNNTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVNLKEIEQEIEKVKNEKDAAVHAQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNGTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTTVDFRNTIIIMTSNVRFAGFGRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKE  
[a bunch of this deleted]
s2:
TERAQRVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVE........HYTPRAKKVIELSMDEAR......VGTEHILLGLIRENEGVAARVFANLD..ITKARAQVVKALGNPENNTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSNNLKEIEQEIEKVKNEKDAAVFENAANLRDKQTKLEKQYEEAKNEWKNAQNSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGHDDGGQLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFGYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIA..  
s1:
.....AQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGTLHYTPRAKKVIELSMDEARKLHHNFVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMS..........................RDKEITRVIEVLSRRTKNNPVLIGEPGV...................ETLKDKRVMSLDMGTVVA.....GEFEERLKKVMEEIQQAGNVILFIDELHTLV...........SNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEP..VDTVAILKGLRDRY....RINISDEAIEAAVKLSNRY....FLPDKAIDLIDEASSKVRLKSHT.....KEIEQEIEKVKNEKDAA....FENAANLRDKQTKLEKQYEEAKNEWKNAQNG........................INETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGL...............TGVGKTELARAL..........MIRVDMSEFMEKHAVSRL.........................SVILFD.....HPDVFNILLQVLDDG..............................................................DDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDG.EFKYDIAEQ  
s2:
RVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIG.....YTPRAKKVIELSMDEARK......GTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMSNTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSHTTPNNLKEIEQEIEKVKNEKDAAVHQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNGMSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGHDDGGQLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFQDYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIAEQ  
s1:
..........AQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGTLHYTPRAKKVIELSMDEARKLHHNFVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPE........................MSRDKEITRVIEVLSRRTKNNPVLIGEPGV...................ETLKDKRVMSLDMGTVVA....GEFEERLKKVMEEIQQAGNVILFIDELHTLV...........SNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEP..VDTVAILKGLRDRY....RINISDEAIEAAVKLSNRY....FLPDKAIDLIDEASSKVRLKS..HTKEIEQEIEKVKNEKDAA....FENAANLRDKQTKLEKQYEEAKNEWKNAQNG.......................INETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGL...............TGVGKTELARAL..........MIRVDMSEFMEKHAVSRL.....................SVILFD.....HPDVFNILLQVLDDG.............................................................DDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDG.EFKYDIAEQ  
s2:
TERAQRVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVE........HYTPRAKKVIELSMDEAR......VGTEHILLGLIRENEGVAARVFANLD..ITKARAQVVKALGNPENTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSPNNLKEIEQEIEKVKNEKDAAVHQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNGSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGGQLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFDYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIAEQ  
s1:
..........AQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGTLHYTPRAKKVIELSMDEARKLHHNFVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPE........................MSRDKEITRVIEVLSRRTKNNPVLIGEPGV..................ETLKDKRVMSLDMGTVVA.....GEFEERLKKVMEEIQQAGNVILFIDELHTLV...........SNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEP..VDTVAILKGLRDRY....RINISDEAIEAAVKLSNRY....FLPDKAIDLIDEASSKVRLKSHTKEIEQEIEKVKNEKDAA.....FENAANLRDKQTKLEKQYEEAKNEWKNAQNG......................INETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGL...............TGVGKTELARAL..........MIRVDMSEFMEKHAVSRL........................SVILFD.....HPDVFNILLQVLDDG.............................................................DDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDG.EFKYDIAEQ  
s2:
TERAQRVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIG....HYTPRAKKVIELSMDEARKL....VGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPENTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKS...EIEQEIEKVKNEKDAAVHAQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGHDDGGQLTKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFDYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIAEQ  
s1:
AQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGTLHYTPRAKKVIELSMDEARKLHHNFVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMSRDKEITRVIEVLSRRTKNNPVLIGEPGVETLKDKRVMSLDMGTVVAGEFEERLKKVMEEIQQAGNVILFIDELHTLVSNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPVDTVAILKGLRDRYRINISDEAIEAAVKLSNRYFLPDKAIDLIDEASSKVRLKSHTKEIEQEIEKVKNEKDAAFENAANLRDKQTKLEKQYEEAKNEWKNAQNGINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLTGVGKTELARALMIRVDMSEFMEKHAVSRLSVILFDHPDVFNILLQVLDDGDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGEFKYDIAEQ  
s2:
AQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGTLHYTPRAKKVIELSMDEARKLHHNFVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMSRDKEITRVIEVLSRRTKNNPVLIGEPGVETLKDKRVMSLDMGTVVAGEFEERLKKVMEEIQQAGNVILFIDELHTLVSNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPVDTVAILKGLRDRYRINISDEAIEAAVKLSNRYFLPDKAIDLIDEASSKVRLKSHTKEIEQEIEKVKNEKDAAFENAANLRDKQTKLEKQYEEAKNEWKNAQNGINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLTGVGKTELARALMIRVDMSEFMEKHAVSRLSVILFDHPDVFNILLQVLDDGDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGEFKYDIAEQ  

> isolde cisflip #1.2/d:252

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to J104_rechain-
coot-16_real_space_refined_001.pdb #1.2  
---  
notes | No usable SEQRES records for J104_rechain-
coot-16_real_space_refined_001.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for J104_rechain-coot-16_real_space_refined_001.pdb
(#1.2) chain Aa; guessing termini instead  
No usable SEQRES records for J104_rechain-coot-16_real_space_refined_001.pdb
(#1.2) chain Ap; guessing termini instead  
No usable SEQRES records for J104_rechain-coot-16_real_space_refined_001.pdb
(#1.2) chain Aq; guessing termini instead  
No usable SEQRES records for J104_rechain-coot-16_real_space_refined_001.pdb
(#1.2) chain B; guessing termini instead  
24 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A THR 336, /Aa ARG 669, /Ap
GLU 232, /Aq PHE 541, /B THR 336, /Ba ILE 4, /Bb ILE 4, /Bc ILE 4, /Bd ILE 4,
/Be ILE 4, /Bf TYR 18, /Bg TYR 18, /Bh ASP 19, /Bi ILE 4, /Bj PRO 5, /Bk TYR
18, /Bl PRO 5, /Bm PRO 5, /Bn PRO 5, /C THR 336, /D THR 336, /E THR 336, /F
THR 336, /a ALA 17, /b THR 7, /c ARG 12, /d THR 7, /e THR 7, /f ALA 17  
Chain-initial residues that are not actual N termini: /Bj ALA 17, /Bl TYR 18,
/Bm ASP 19, /Bn TYR 18, /a GLY 76, /a VAL 103, /a ASN 158, /a ASP 295, /a ASN
412, /a THR 469, /a LEU 602, /a THR 646, /a ARG 669, /a ARG 686, /b HIS 79, /b
VAL 103, /b ASN 158, /b ASN 411, /b PHE 436, /b SER 468, /b TYR 682, /c TYR
80, /c GLY 104, /c ASN 159, /c GLN 680, /d HIS 79, /d VAL 103, /d ASN 159, /d
PRO 410, /d SER 468, /d GLY 600, /d ASP 681, /e TYR 80, /e VAL 103, /e ASN
159, /e GLU 415, /e SER 468, /e ASP 681, /f GLY 76, /f ARG 185, /f GLU 232, /f
GLY 255, /f SER 297, /f VAL 345, /f ARG 363, /f PHE 386, /f LYS 414, /f PHE
436, /f ILE 491, /f THR 547, /f MET 569, /f SER 612, /f HIS 623, /f ASP 706  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A TYR 376, /Aa PHE 673,
/Ap MET 240, /Aq PRO 546, /B TYR 376, /Ba GLU 193, /Bb GLU 193, /Bc GLU 193,
/Bd GLU 193, /Be PRO 192, /Bf GLU 193, /Bg PRO 192, /Bh PRO 192, /Bi GLU 193,
/Bj GLU 193, /Bj GLU 9, /Bk PRO 192, /Bl GLU 193, /Bl THR 10, /Bm PRO 192, /Bm
GLU 9, /Bn GLU 193, /Bn GLU 9, /C TYR 376, /D TYR 376, /E TYR 376, /F TYR 376,
/a GLU 800, /a HIS 70, /a GLU 89, /a MET 147, /a VAL 285, /a VAL 402, /a GLY
466, /a GLY 595, /a THR 640, /a VAL 660, /a GLY 674, /b ALA 806, /b GLU 65, /b
ARG 96, /b GLU 146, /b SER 406, /b VAL 431, /b ASN 465, /b GLY 674, /c GLN
808, /c GLY 69, /c LYS 97, /c SER 148, /c PHE 673, /d GLN 808, /d GLU 65, /d
ARG 96, /d GLU 146, /d SER 406, /d GLY 466, /d GLY 595, /d PHE 673, /e GLN
808, /e HIS 70, /e LEU 98, /e GLU 146, /e SER 406, /e ASN 465, /e PHE 673, /f
GLN 808, /f HIS 70, /f SER 148, /f VAL 212, /f ALA 249, /f VAL 285, /f PRO
342, /f TYR 358, /f TYR 381, /f THR 408, /f ALA 430, /f GLY 466, /f LEU 531,
/f LEU 558, /f LEU 586, /f ASP 617, /f GLY 637  
5572 hydrogen bonds  
Adding 'H' to /Bj ALA 17  
Adding 'H' to /Bl TYR 18  
Adding 'H' to /Bm ASP 19  
Adding 'H' to /Bn TYR 18  
Adding 'H' to /a GLY 76  
48 messages similar to the above omitted  
/A TYR 376 is not terminus, removing H atom from 'C'  
/Aa PHE 673 is not terminus, removing H atom from 'C'  
/Ap MET 240 is not terminus, removing H atom from 'C'  
/Aq PRO 546 is not terminus, removing H atom from 'C'  
/B TYR 376 is not terminus, removing H atom from 'C'  
25 messages similar to the above omitted  
56264 hydrogens added  
  
Loading residue template for ADP from internal database  
Loading residue template for AGS from internal database  
Failed to add atoms ['HG23'] to atom CG2 because this will lead to having 5
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (THR). If this template is built
into ISOLDE, please report this using Help/Report a bug  
Deleted the following atoms from residue THR d547: H  
Deleted the following atoms from residue LEU a730: HN, H  
Deleted the following atoms from residue LYS c551: H, HZ  
Deleted the following atoms from residue THR c552: H  
Deleted the following atoms from residue LYS d551: H, HB  

> isolde cisflip #1.2/d:252

Traceback (most recent call last):  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/peptide_bond.py", line 96, in cb  
run(self.session, f'isolde cisflip #{m.id_string}/{r.chain_id}:{r.number}')  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/manipulations/cmd.py", line 57, in cis_flip  
isolde_sim(session, 'start', residues.atoms)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 896, in start_sim  
sm.start_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5931, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error initializing context: clCreateContext (-5)  
  
openmm.OpenMMException: Error initializing context: clCreateContext (-5)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5931, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  

> isolde cisflip #1.2/f:513

Traceback (most recent call last):  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/peptide_bond.py", line 96, in cb  
run(self.session, f'isolde cisflip #{m.id_string}/{r.chain_id}:{r.number}')  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/manipulations/cmd.py", line 57, in cis_flip  
isolde_sim(session, 'start', residues.atoms)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 896, in start_sim  
sm.start_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5931, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error initializing context: clCreateContext (-5)  
  
openmm.OpenMMException: Error initializing context: clCreateContext (-5)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5931, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  

> isolde sim start
> /a:511,712-716,718-745,747-756,761,764-765,767-796/f:498,500-504,521,524-526,528-531

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 21, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 896, in start_sim  
sm.start_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5931, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error initializing context: clCreateContext (-5)  
  
openmm.OpenMMException: Error initializing context: clCreateContext (-5)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5931, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 909, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1816, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 909, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1816, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 22.3.5
OpenGL renderer: RENOIR (renoir, LLVM 15.0.6, DRM 3.49, 6.2.6-76060206-generic)
OpenGL vendor: AMD

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=pop
XDG_SESSION_DESKTOP=pop
XDG_CURRENT_DESKTOP=pop:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 20YM
OS: Pop!_OS 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 9 5900HX with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            30Gi       9.6Gi        12Gi       390Mi       8.2Gi        18Gi
	Swap:           31Gi          0B        31Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA106M [GeForce RTX 3060 Mobile / Max-Q] [10de:2520] (rev a1)	
	Subsystem: Lenovo GA106M [GeForce RTX 3060 Mobile / Max-Q] [17aa:3801]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    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: 2023.5.7
    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-LinuxSupport: 1.0.1
    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-XMAS: 1.1.2
    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
    distro: 1.7.0
    docutils: 0.19
    et-xmlfile: 1.1.0
    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: 2022.9.26
    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
    openpyxl: 3.1.2
    openvr: 1.23.701
    packaging: 23.1
    pandas: 2.0.2
    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
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    seaborn: 0.12.2
    setuptools: 67.4.0
    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 (2)

comment:1 by pett, 2 years ago

Component: Unassigned → Third Party
Description: modified (diff)
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: OpenMMException: Error initializing context: clCreateContext

comment:2 by Tristan Croll, 2 years ago

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

-5 is CL_OUT_OF_RESOURCES. Looks like a laptop with some weird hybrid GPU architecture (one I haven't seen before) - a low-end GPU associated with the CPU (AMD Renoir architecture - maybe misconfigured given that OpenGL is running on the Mesa driver), with a RTX 3060. It's not clear which GPU it's trying to run on (something I should fix)... the 3060 has 6GB of RAM and from what I gather the Renoir shares the CPU memory. In either case I'd expect it to take a *really* large model to hit the resource limit - hard to do much without further input from the user.

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