why don't you read in that chain in Coot and run the find ligand option with
flexible ligand turned on and select that 6kDa ligand ? You should also choose
Fo-Fc map to fit the ligand to maybe at 2.7 sigma. You might have to split up
the ligand into pieces, not sure what the limitations in Coot/Find Ligand are.
You already have a MR solution of the rest of your protein right ? So you are
just asking how to make your life easier to not built de novo 45-50 residues ?
Jürgen
On Oct 19, 2011, at 10:00 AM, Ed Pozharski wrote:
Why not do the molecular replacement - 6kDa is rather small but it most
likely will work
On Wed, 2011-10-19 at 06:13 -0700, Afshan Begum wrote:
Hello CCP4 user
I have collected a data set 2.1 for my complex. Actually after first
run of Rafmac i can see the density for my inhibitor but the problem
is my inhibitor is 6 KDa and i know the sequence of my inhibitor as
well this inhibitor already crystallize with other protein molecule
present in PDB data bank so how can i put in to that electron density
i mean are there any ways to combine two Pdb in one molecule?
I would be thankful for your help
Best Regards
AFSHAN
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
......................
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-2926
http://web.mac.com/bosch_lab/
