Re: [modeller_usage] Including a Thioester linkage

João Rodrigues wrote: > Another question though, maybe this is a bit out of the scope of > MODELLER but: > > PRES DISU -0.36 ! Patch for disulfides. Patch must be 1-CYS and 2-CYS. > > > ATOM 1:CB CT2 -0.10 ! > ATOM 1:SG SM -0.08 ! 2:SG--2:CB-- > ATOM 2:SG SM -0.08 ! / > ATOM 2:CB CT2 -0.10 ! -1:CB--1:SG > > So, I get the syntax but I fail to understand one thing. Is that number > -0.36 the overall charge of the residue or something?

Yes, that's the total charge. Modeller doesn't actually depend on this being correct, however, so you can set it to 0 if you like. You can't leave it blank though.

Ben Webb, Modeller Caretaker