Adding 2 X domains with a contect instead of a linker between them renders incorrectly

[AndrewCRMartin]

• start with a standard IgG
• add 2 X domains to the Nter of each of the light chains
• put a connect between the two X domains on each side
• add a linker between the Cter of each X and the Nter of each light chain
• click Tidy

I obtain the following AbML:

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

but the two X domains on each side render on top of one another.

Strictly the AbML is incorrect as it says X(11:12)-X(12:11) and X(16:17)-X(17:16) while there should not be contacts between the domains.

If I modify the AbML to remove those spurious contacts between X domains:

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

and render the structure, it generates something crazy with the light chains separated from the heavy chains and different lengths of X-X connections on each side.

[AndrewCRMartin]

(If I put linkers between the two X domains, it works OK)

[JamesSweetJones]

Leave it with me. I'll take a look at this one

[JamesSweetJones]

I've achieved this structure and updated the main abYdraw script (abYdrawV1.01). I hope this has worked!

[AndrewCRMartin]

Perfect!

A.

On Fri, 2 Sept 2022 at 10:04, James Sweet-Jones @.***> wrote:

[image: Screenshot 2022-09-02 at 10 00 51] https://user-images.githubusercontent.com/73530578/188104553-5e0e337d-8be5-4691-9aa9-68ad5664131c.png

I've achieved this structure and updated the main abYdraw script (abYdrawV1.01). I hope this has worked!

— Reply to this email directly, view it on GitHub https://github.com/JamesSweetJones/abYdraw/issues/41#issuecomment-1235255583, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBQ7ULTVNWW6NCUHT5EGG3V4G7KBANCNFSM6AAAAAAQCO4QAU . 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

[AndrewCRMartin]

Just a thought... Does the one still work where there was an X trimer?

Also can you generate the Mac/Windows apps?

A.

On Fri, 2 Sept 2022 at 11:41, James Sweet-Jones @.***> wrote:

Closed #41 https://github.com/JamesSweetJones/abYdraw/issues/41 as completed.

— Reply to this email directly, view it on GitHub https://github.com/JamesSweetJones/abYdraw/issues/41#event-7312222159, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBQ7UJJ2ZF27PSY2B5NSEDV4HKVRANCNFSM6AAAAAAQCO4QAU . 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