INN12120 trontinemab won't render

[AndrewCRMartin]

I drew the following and obtained the AbML, but it won't render back to a tidied picture.

VH.a(1:16)-CH1(2:17){1}-H(3:8){2}-CH2(4:9)-CH3@(5:10)|
VH.a(6:18)-CH1(7:19){1}-H(8:3){2}-CH2(9:4)-CH3>(10:5)-L(11)-VH.b(12:14)-CL(13:15){1}|
VL.b(14:12)-CH1(15:13){1}|
VL.a(16:1)-CL(17:2){1}|VL.a(18:6)-CL(19:7){1}

Also, on obtaining the AbML it insisted there were 3 disulphides between the hinges (3 and 8) even though I had only drawn two!

[AndrewCRMartin]

Full AbML with mutations should be:

VH.a(1:16)-CH1-(2:17){1}-H(3:8){2}-CH2(4:9)-CH3*@(5:10)|
VH.a(6:18)-CH1-(7:19){1}-H(8:3){2}-CH2(9:4)-CH3*>(10:5)-L(11)-VH.b(12:14)-CL*(13:15){1}|
VL.b(14:12)-CH1(15:13){1}|
VL.a(16:1)-CL+(17:2){1}|
VL.a(18:6)-CL+(19:7){1}

[JamesSweetJones]

Ah, I think the issue here is the order of the AbML strings. As I consider the "VL.b(14:12)-CH1(15:13){1}" a fragment, it should be put at the end of the expression like so:

VH.a(1:14)-CH1(2:15){1}-H(3:8){2}-CH2(4:9)-CH3@(5:10) | VH.a(6:16)-CH1(7:17){1}-H(8:3){2}-CH2(9:4)-CH3>(10:5)-L(11)-VH.b(12:18)-CL(13:19){1} | VL.a(14:1)-CL(15:2){1} | VL.a(16:6)-CL(17:7){1} | VL.b(18:12)-CH1(19:13){1}

I can try and change this so it's better at detecting this.

James

[AndrewCRMartin]

Just to point out that the string was created by abYdraw!

A.

On Wed, 22 Jun 2022 at 15:13, James Sweet-Jones @.***> wrote:

Ah, I think the issue here is the order of the AbML strings. As I consider the "VL.b(14:12)-CH1(15:13){1}" a fragment, it should be put at the end of the expression like so:

VH.a(1:14)-CH1(2:15){1}-H(3:8){2}-CH2(4:9)-CH3@(5:10)	VH.a(6:16)-CH1(7:17){1}-H(8:3){2}-CH2(9:4)-CH3>(10:5)-L(11)-VH.b(12:18)-CL(13:19){1}
VL.a(14:1)-CL(15:2){1}
VL.a(16:6)-CL(17:7){1}

VL.b(18:12)-CH1(19:13){1}

I can try and change this so it's better at detecting this.

James

— Reply to this email directly, view it on GitHub https://github.com/JamesSweetJones/abYdraw/issues/39#issuecomment-1163156288, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBQ7UPVZOMNGSCLQ7XQPF3VQMNRHANCNFSM5ZP2V4QA . You are receiving this because you authored the thread.Message ID: @.***>

-- Andrew C.R. Martin Professor of Bioinformatics and Computational Biology. Institute of Structural and Molecular Biology, UCL http://www.bioinf.org.uk/ Twitter: @PrfAndrewMartin