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Format library
Pick a domain type, give it a specificity, and add it to the end of a chain. Build the chains in N→C order, then press Renumber & auto-pair — that allocates the identifiers and works out which domains face each other, so you never write the numbering by hand.
Add domain
Chains
Repair
Renumbers every domain left to right and pairs V with V, C with C across the facing chain — the same bookkeeping Tidy does in abYdraw.
Labels
Bonds
Geometry
Ground
Off = transparent, per the Aureka figure guide.
Tint rule
Domain origin is the CrossMab convention: colour travels with the domain when VH/VL or CH1/CL swap chains.
Specificity palette
Build a lettered multi-panel figure. Each row is one AbML string; the grid exports as a single SVG.
Panels
Grid
AbML describes a molecule as chains of domains. Chains are separated by |, domains within a chain by -, reading N-terminus to C-terminus.
Domain types
| VH VL | variable heavy / light |
| CH1–CH5 | constant heavy |
| CL | constant light |
| VHH | camelid single domain |
| H | hinge (drawn as a connector) |
| L | linker (drawn as a connector) |
| X | any other protein domain |
| C | chemical crosslinker |
| VA CA VB CB | TCR alpha / beta |
| VG CG VD CD | TCR gamma / delta |
Qualifiers
| .a – .h | specificity, picks the colour |
| (3) | domain identifier |
| (3:10) | identifier, paired with domain 10 |
| {2} | disulfides across that pairing |
| [ANTI:CD3] | comment — also MOD, TYPE, LENGTH, CLASS, NOTE, ASEQ, DSEQ |
| |[ADC] | trailing pseudo-chain: nonspecific conjugation |
A shared light chain carries both specificities: heavy chains VH.a and
VH.b against a common VL.ab. Knob and hole cannot sit on one domain, nor can
both charges, and ! is only valid on CH2.
Modifications
| > | knob |
| @ | hole |
| + _ | positive / negative charge pair |
| ^ | conjugation site |
| ! | aglycosyl CH2 |
| * | general modification |
Modifications sit straight after the type and before the specificity: CH3>(5:12), VL*.a(6:1).
Worked example
VH.a(1:6)-CH1(2:7){1}-H(3:10){2}-CH2(4:11)-CH3>(5:12)
One knob-bearing heavy chain: VH of specificity a paired with domain 6, CH1 paired with 7 through one disulfide, hinge paired with the other hinge through two, then CH2 and a knobbed CH3.