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.
