On 09/05/2017 16:56, Pellock, Sam wrote:
Hi,
I'm trying to model two states in a ligand-substrate-enzyme complex. That is,
there is
density that suggests that the substrate is partially linked to the enzyme and
also, but
independently, linked to the inhibitor. I've tried building both the
enzyme-substrate
covalent conjugate and the inhibitor-substrate covalent conjugate and
overlaying them on top
of each other, but this hasn't worked. I usually use the alternate
conformations tool for
issues like this, but since these are actually two distinct chemical entities
that occupy
the same space (I'm currently assuming they split the occupancy 50:50), I
couldn't determine
how to model them both simultaneously without significant clashes.
Hello Sam,
Both Coot and refmac should handle partial occupancy correctly, which is to say that atoms
with alt-conf "A" do not "see" atoms with alt-conf "B" and vice versa.
This sound exactly like the scenario described in Roberto Steiner's Refmac
lectures/tutorials (I don't know where you can find them off the cuff - it was a few years
ago now).
I mean to say, what you are describing should be doable, but I haven't tested such a
scenario in Coot (Refmac should be OK with this, I think).
Paul.
