What's the resolution? At low res it is possible to miss a subtle movement
of e.g. some sidechains which are being replaced by the ligand. What quality
parameters did the MR have? Can you omit the entire ligand binding site,
refine, and re-generate the map - what does it look like after that?
A picture would help!
Artem
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Brenda
Patterson
Sent: Friday, December 28, 2007 10:56 AM
To: [log in to unmask]
Subject: [ccp4bb] Difference Map in COOT - Possible lignad but clash with
structure?
Hello,
I am fairly new to this lark so please forgive me if this question is
unclear,
but it is really puzzling me.
I have used phaser to generate a molecular replacement structure of my
target
(which has 100% identity to my template) and this particular crystal I had
soaked with a ligand.
I have a density in my difference map which resembles my ligand. The
thing is,
it overlaps the density map of my structure and if I were to place the
ligand
in that map, then there would be a steric clash. Obviously I would expect
the
ligand to be near to the structure, but not overlapping it? I am
uncertain how
to proceed?
Any helpful suggestions please?
Thanks in advance
Brenda
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