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:[log in to unmask]] On Behalf Of Anshul
> Awasthi
> Sent: Tuesday, September 30, 2008 10:57 AM
> To: [log in to unmask]
> 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.
>
> No virus found in this incoming message.
> Checked by AVG - http://www.avg.com
> Version: 8.0.173 / Virus Database: 270.7.5/1697 - Release Date: 29/9/2008
> 7:25 μμ
>
>
>
>
|