Yes:
There are details in the coot manual
1) Get a dictionary for your ligand from PRODRG or somewhere. - you have
obviously done this..
2) CHECK IT IS CORRECT!!! Right chirality, planar groups, etc..
3) Import dictionary into coot, and a set of coordinates.
4) Import 2mFo-Dfc and mFo-Dfc maps ( auto mtz from REFMAC will do this)
5) Hit find ligand.
6) Real space refine it - you might need to do some brutal gradding and
shoving of bits..
Eleanor
George Kontopidis wrote:
You need protein structure, a different e. density map (1Fo-1Fc) and your
ligand structure. Then from COOT menu select Other Modelling Tools and click
Find Ligand. You can also move manually the ligand into the density map.
George
-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Anshul
Awasthi
Sent: Tuesday, September 30, 2008 10:57 AM
To: [email protected]
Subject: [ccp4bb] Putting ligand in the protein structure
Hi all the crystallographers,
I am trying to solve a structure of a protein with some inhibitor. I want to
know how I can put in my inhibitor in the density map of the data i got. I
can see some density in the active site where the inhibitor should be. I
generated the topoly file of the inhibitor (in both pdba nd refmac5 top
formats) from the Dundee PRODRG server. Now do i need to incorporate the
structure of the inhibitor in ccp4 or can i do in coot?? I am not sure of
how to do it.
ANy sugegstion will be very valuable for me.
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