I am using the RosettaAntibody3 workflow outlined here:
Everything is “working” when I use the command:
antibody_H3.linuxgccrelease
-database $ROSETTA_DATABASE
-s /input/TB184-140-0.relaxed.pdb
-ex1
-ex2
-extrachi_cutoff 0
-out:file:scorefile /output/my_antibody_h3.score
-nstruct 1
and based on the documetation, I am expecting the final output to have a extended (non-kinked) H3.
However, the output of the run shows extended?: False:
////////////////////////////////////////////////////////////////////////////////
/// Rosetta Antibody Info ///
/// ///
/// Antibody Type: Camelid Antibody
/// Light Chain Type: unknown
/// Predict H3 Cterminus Base: NEUTRAL
///
/// H1 info:
/// length: 10
/// sequence: GNXXXXXXXMG
/// north_cluster: H1-13-7
/// loop_info: LOOP start: 25 stop: 34 cut: 30 size: 10 skip rate: 0 extended?: False
///
/// H2 info:
/// length: 16
/// sequence: SXXXXXXXXXXXKG
/// north_cluster: H2-9-2
/// loop_info: LOOP start: 49 stop: 64 cut: 57 size: 16 skip rate: 0 extended?: False
///
/// H3 info:
/// length: 17
/// sequence: RVXXXXXXXXXXYE
/// north_cluster: H3-19-6
/// loop_info: LOOP start: 97 stop: 113 cut: 98 size: 17 skip rate: 0 extended?: False
///
////////////////////////////////////////////////////////////////////////////////
Does anyone know how to force RosettaAntibody (antibody_H3.linuxgccrelease) to model a extended H3?
I have also tried adding the flag -extend_h3_before_modeling with no change.
.
