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[Solved] RosettaAntibody3 - Grafting step is failing to detect H3 from the input sequence

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[Solved] RosettaAntibody3 - Grafting step is failing to detect H3 from the input sequence
#1
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I am trying to run RosettaAntibody3 to build an Fv hhomology model from an input sequence. I am following the documentation form here.

I am using the command:  

antibody.static.linuxgccrelease \
  -database $ROSETTA_DATABASE \
  -fasta /mnt/data/input/myinput.fasta \
  -nstruct 1 \
  -out:path:all /mnt/data/output/output-graft/ \
  -detect_disulf false

 which fails fairly quickly with the error: 

protocols.antibody.grafting: Path to REGEX file is: /databases/rosetta/protocol_data/antibody/cdr_regex.txt
protocols.antibody.grafting: The detected H1 REGEX is: C[A-Z]{1,16}(W)(I|V|F|Y|A|M|L|N|G)(R|K|Q|V|N|C|G)(Q|K|H|E|L|R)
protocols.antibody.grafting: The detected H3 REGEX is: C[A-Z]{1,33}(W)(G|A|C)[A-Z]{1,2}(Q|S|G|R)
protocols.antibody.grafting: The detected L1 REGEX is: C[A-Z]{1,17}(WYL|WLQ|WFQ|WYQ|WYH|WVQ|WVR|WWQ|WVK|WYR|WLL|WFL|WVF|WIQ|WYR|WNQ|WHL|WHQ|WYM|WYY)
protocols.antibody.grafting: The detected L3 REGEX is: C[A-Z]{1,15}(L|F|V|S)G[A-Z](G|Y)
protocols.antibody.grafting: H1 detected: GFTLEYYAIG (10 residues at positions: 25 to 35)
H3 detection: failed

[ ERROR ]: Caught exception:


File: src/protocols/antibody/grafting/regex_based_cdr_detection.cc:100
H3 detection: failed. Pattern:C[A-Z]{1,33}(W)(G|A|C)[A-Z]{1,2}(Q|S|G|R)

I know this is a valid sequence - as the antibody itself is a real and functional antibody. 

Does anyone know why RosettaAntibody is failing to detect H3 as is? Is there a way to circumvent this problem?

As a hack, I changed the cdr_regex.txt to replace the H3 line with `H3 "<MyKnownH3Sequence>"`, and it still failed.

Category: 
Structure prediction
Post Situation: 
Unsolved
Mon, 2021-01-04 16:46
brspurri
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I was able to get some help on this via the back channels.

One way to circumvent this issue is to supply the positions of the CDRs manually using the -antibody:json_cdr <filename> flag with the format: 

{
    "h1" : {
        "begin" : 25,
        "end" : 35
    },
    "h2" : {
        "begin" : 49,
        "end" : 66
    },
    "h3" : {
        "begin" : 98,
        "end" : 102
    },
    "l1" : {
        "begin" : 23,
        "end" : 34
    },
    "l2" : {
        "begin" : 49,
        "end" : 56
    },
    "l3" : {
        "begin" : 88,
        "end" : 97
    }
}

Passing this file skipped the auto CDR detection, and all worked well. Solved.

Mon, 2021-01-18 18:14
brspurri