On Sep 30, 2008, at 9:56, Anshul Awasthi wrote:
> 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.
As one of many alternatives you can use "ARP/wARP Ligand Fit" from
the CCP4I
(provided you downloaded and installed the current version of ARP/wARP)
and then input your protein structure, the observed data, and the PDB
of your ligand.
The script will calculate the mFo-DFc map, find the most likely site
for the ligand,
and then fir the ligand there, and refine it in real space.
Tassos
>
>
> ANy sugegstion will be very valuable for me.
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