RosettaAntibody – No matching templates for CDR1

[Anonymous]

hi,

I am trying to use RosettaAntibody in order to model a camiled heavy chain only antibody (pdb code: 1YC7_1).

when using the following command:

antibody.linuxgccrelease -exclude_homologs true -vhh_only -fasta 1YC7_1.fa | tee grafting.log

(I am using exclude_homologs in order to test its preformance, because this antibody structure is already solved and found in the database).

I get the following error:

protocols.antibody.grafting: SCS_Base::select: Final results count: h1:0    h2:10   h3:10   l1:168  l2:13   l3:114  frh:882  frl:708  orientation:821

antibody: SCS frh best template: 3k1k

antibody: SCS frl best template: 1mju

antibody: SCS Orientation best template: 1kfa





File: src/protocols/antibody/grafting/grafter.cc:207

SimpleGrafter::graft: not all nessesary SCS results is specified!



rm: No match.

rm: No match.

It seems like Rosetta can’t find any template for h1, it can’t even find the 1YC7_1 himself (even when removing the -exclude_homologs flag, although it finds it for the other regions…).

when seraching h1 sequence in Blast it confirmed that this antibody indeed doesnt have a good match.

so when trying to specifie a template for h1 manually  (tried multiple templates, all found in the database):

antibody.linuxgccrelease -exclude_homologs true -vhh_only -antibody:h1_template 1kfa -fasta 1YC7_1.fa | tee grafting.log

 

I get the following error:

protocols.antibody.grafting: SCS_Base::select: Final results count: h1:0    h2:10   h3:10   l1:168  l2:13   l3:114  frh:882  frl:708  orientation:821

antibody: SCS frh best template: 3k1k

antibody: SCS frl best template: 1mju

antibody: SCS Orientation best template: 1kfa

antibody: Note: Grafting manually specified H1 CDR!

ROSETTA_CRASH.log FOR DETAILS.





Segmentation fault

rm: No match.

rm: No match.

 

ROSETTA_CRASH.log:

##############################################################################################################

#

# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/

# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py

#



[START_CRASH_REPORT]

[ROSETTA_VERSION]: 2020.50+release.1295438

[COMMIT_DATE]: 2020-12-13T21:33:15.479874

[APPLICATION]: antibody.linuxgccrelease

[MODE]: Release

[EXTRAS]: default

[OS]: GNU/Linux

[COMPILER]: GCC version "8.3.0"

[STDLIB]: libstdc++ version 20190406

[START_OPTIONS]

-antibody:h1_template=1kfa -antibody:exclude_homologs -fasta=1YC7_1.fa -vhh_only



[END_OPTIONS]



[START_BACKTRACE]: RAW_LIBC

/cs/labs/dina/tomer.cohen13/Rosetta/main/source/build/src/release/linux/4.19/64/x86/gcc/8/default/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x23) [0x7fcf1ae33123]

/cs/labs/dina/tomer.cohen13/Rosetta/main/source/build/src/release/linux/4.19/64/x86/gcc/8/default/libutility.so(utility::signal_handler(int)+0xd4) [0x7fcf1ae33234]

/lib/x86_64-linux-gnu/libc.so.6(+0x37840) [0x7fcf192dd840]

/lib/x86_64-linux-gnu/libstdc++.so.6(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x14) [0x7fcf19724184]

antibody.linuxgccrelease(+0x2074c) [0x562753b3074c]

antibody.linuxgccrelease(+0x1c1b0) [0x562753b2c1b0]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb) [0x7fcf192ca09b]

antibody.linuxgccrelease(+0x1c27a) [0x562753b2c27a]



[END_BACKTRACE]



[FILE]: SIGSEGV

[LINE]: 11

[START_MESSAGE]

Segmentation Fault



[END_MESSAGE]

[END_CRASH_REPORT]



##############################################################################################################

#

# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/

# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py

#



[START_CRASH_REPORT]

[ROSETTA_VERSION]: 2020.50+release.1295438

[COMMIT_DATE]: 2020-12-13T21:33:15.479874

[APPLICATION]: antibody.linuxgccrelease

[MODE]: Release

[EXTRAS]: default

[OS]: GNU/Linux

[COMPILER]: GCC version "8.3.0"

[STDLIB]: libstdc++ version 20190406

[START_OPTIONS]

-antibody:h1_template=5c1m -antibody:exclude_homologs -fasta=1YC7_1.fa -vhh_only



[END_OPTIONS]



[START_BACKTRACE]: RAW_LIBC

/cs/labs/dina/tomer.cohen13/Rosetta/main/source/build/src/release/linux/4.19/64/x86/gcc/8/default/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x23) [0x7fdcead7e123]

/cs/labs/dina/tomer.cohen13/Rosetta/main/source/build/src/release/linux/4.19/64/x86/gcc/8/default/libutility.so(utility::signal_handler(int)+0xd4) [0x7fdcead7e234]

/lib/x86_64-linux-gnu/libc.so.6(+0x37840) [0x7fdce9228840]

/lib/x86_64-linux-gnu/libstdc++.so.6(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)+0x14) [0x7fdce966f184]

antibody.linuxgccrelease(+0x2074c) [0x55f36d89274c]

antibody.linuxgccrelease(+0x1c1b0) [0x55f36d88e1b0]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb) [0x7fdce921509b]

antibody.linuxgccrelease(+0x1c27a) [0x55f36d88e27a]



[END_BACKTRACE]



[FILE]: SIGSEGV

[LINE]: 11

[START_MESSAGE]

Segmentation Fault



[END_MESSAGE]

[END_CRASH_REPORT]

 

Thanks for the help!

 

[Author]

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