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!
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