Dear Afshan,
>From your question it is not completely clear where your problem lies.
However, I assume you have soaked/cocrystallized your protein (crystal)
with a ligand and collected a data set and want to know whether or not
your ligand has bound.
In that case I would do a few cycles of refinement using your existing
apo-structure. I use Buster for refinement, but refmac, cns or phenix
would do as well. Then I would load the refined coordinates and mtz file
in coot and do two searches, one for unmodelled blobs and one for
difference peaks. You can find those under the "Validate" pull down
menue: "unmodelled blobs" and "difference map peaks". Since your ligand
might have bound with partial occupancy, I would look for difference
peaks above 4 sigma. With the default of 5 sigma, you may miss your
ligand.
If you now where your ligand is expected to bind (active site, ATP
binding pocket...) you should also examine the electron density maps in
those regions. In my experience, you can scroll the electron density map
down to 0.6 sigma to look for partially bound ligands. Below that level
you start looking at noise or very disordered buffer components.
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Afshan Fayazi
Sent: Wednesday, February 16, 2011 4:34 PM
To: [email protected]
Subject: [ccp4bb] how can i cinfirm the ligand bindind
Dear CCP4 colleague
I just wanted to ask a simple question that if the ligand has bind the
molecules so how can i confirm it either my ligand has bind or not and
which program should i used to visualize it???
Best Regards
AFSHAN
