Hi, I would like to include the TaskOperations "RestrictToCDRsAndNeighbors" in my xml file which is to design the CDR in an antibody-antigen interface.
However, I do not know what to put as options under the arguments "numbering_scheme" and "cdr_definition"
From the manual, the explanations are
- numbering_scheme (&string): Set the antibody numbering scheme. Must also set the cdr_definition XML option. Both options can also be set through the command line (recommended). See General Antibody Tips for more info.
- cdr_definition (&string): Set the cdr definition you want to use. Must also set the numbering_scheme XML option. See General Antibody Tips
After reading the explanations and the General Antibody Tips I still have no idea what are the possible options to choose.
I improvised myself and written something as the following, which didn't work (i.e. the run stopped with no structures generated)
<RestrictToCDRsAndNeighbors name="to_cdrs" numbering_scheme="AHO_Scheme" cdr_definition="H1,H2,H3"/>
If you have ever used RestrictToCDRsAndNeighbors, would you mind showing me the possible options for the arguments "numbering_scheme" and "cdr_definition"?
Thanks in advance.