For the input of snugdock, what if there are several chains for heavy/light chains? For example, A and E for heavy chains and C and F for light chains?
Do we need to merge the chains or do we change the input command line?
How and why is your heavy or light chain multichain? snugdock assumes standard antibodies in Chothia numbering. If you don't have a normal looking Fv, it's not going to work. If you just mean "normal looking Fv, weird stuff behind it" - just toss the other stuff out.
If you want to dock multiple antibodies at once - you can't.
Is the input supposed to be Fv only? I downloaded antibody files from PDB and use it directly. Some may not be pure Fv. If that's the case, how can I isolate the Fv part?
Only one "tip" of an antibody binds your target, right? So Snugdock only works with a Fab fragment or better yet an Fv fragment - the rest of the protein is irrelevant and it's expensive to model it.
Just cut away the atoms you don't need with PyMOL (select the residues, remove the atoms, save the remaining molecule to a new file name), or by opening the PDB file up in your text editor of choice (like emacs or vi).
Hi here's an example which confuses me.
There are 2 chains each for heavy and light chains. And it looks like they are all part of Fab.
There are two copies of the whole complex in the asymmetric unit. Fab remains two chains, as it always has... https://en.wikipedia.org/wiki/Fragment_antigen-binding