[PyMOL] Help superimposing protein and sugar

[Savannah S. <sav...@gm...>]

Hello all,

TLDR; What’s the best way to place one molecule over a geometrically similar but unrelated second molecule?

I’m a scientist studying the docking of glycans to antibodies. I’m trying to use pymol to position my glycan, a 10-mer called gxm, close to its putative binding site. My glycan has a protein mimetic, p1, an 11-mer, that I already have docked to my antibody. 

Since p1 and gxm have similar structures, I’d like to align gxm as close as possible to where p1 goes on my p1-antibody co-crystal structure. However, since my glycan and my protein have no sequence alignment, I haven’t been able to use align, super, fit, etc. I tried using pair fit and pymol kept crashing when I called it. Cealign sounded like a good option, but, because I’m using a 10-mer and an 11-mer, I got an error that the sequences were too short.

The best I’ve been able to do is translate gxm to p1’s center of mass, then manually adjust gxm with my mouse. However, that’s obviously imprecise. Does anyone have any ideas for how I could overlap my glycan more closely to my protein?

Thanks!

Savannah Speir

Post Baccalaureate Fellow
Rosetta Commons
Johns Hopkins University