JamesSweetJones / abYdraw

Input expressions of antibodies in AbML format and output drawings of their shape
GNU General Public License v3.0
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Bispecific that won't render #51

Open AndrewCRMartin opened 1 year ago

AndrewCRMartin commented 1 year ago
VH.a(1:5)-CH1(2:6)|VL.b(3:8)-CL(4:9){1}|
VL.a(5:1)-CL(6:2)-L(7)-VH.b(8:3)-CH1(9:4){1}-H(10:18){2}-CH2(11:19)-CH3(12:20)|
VL.a(13:21)-CL(14:22)-L(15)-VH.b(16:23)-CH1(17:24){1}-H(18:10){2}-CH2(19:11)-CH3(20:12)|
VH.a(21:13)-CH1(22:14)|VL.b(23:16)-CL(24:17){1}

Drawing this one creates the correct AbML (although somewhat different from this hand-created version), but it won't render.

JamesSweetJones commented 1 year ago

Is this the intended result? It's stored in the library as a Fab-IgG.

I think the issue with getting the expression is that it's issue is getting the chains mixed up. I'll take a look.

Screenshot 2023-04-19 at 16 31 29
AndrewCRMartin commented 1 year ago

Yes that's it. Not sure why my version didn't render (even when drawn and then Tidy'd

The following version (without a linker) doesn't render either:

VH.a(1:5)-CH1(2:6)|VL.b(3:7)-CL(4:8){1}|
VL.a(5:1)-CL(6:2)-VH.b(7:3)-CH1(8:4){1}-H(9:16){2}-CH2(10:17)-CH3(11:18)|
VL.a(12:19)-CL(13:20)-VH.b(14:21)-CH1(15:22){1}-H(16:9){2}-CH2(17:10)-CH3(18:11)|
VH.a(19:12)-CH1(20:13)|VL.b(21:14)-CL(22:15){1}
JamesSweetJones commented 1 year ago

I see the issue. The heavy chains start with a VL domain and that's confusing the step that sorts the chains out. I'll take a look