Dear Giovanna and Bosch: Thank you for your advices.
I tried the way as you suggested, but not work. Here is how I did: 1. Center on the ligand density, and "Find ligand" "Right here". 2. Increase Fo-Fc at 3 sigma or reduce 2Fo-Fc maps to 0.8 sigma. Coot failed to recognize the density. > You do specify the ligand you are looking for (as PDB file) right? The ligand that I put into protein is NADH. I use NAD to do the search. It found two but failed on the other two. Thanks for advice Uma On Wed, Oct 24, 2012 at 10:44 AM, Bosch, Juergen <jubo...@jhsph.edu> wrote: > If you show symmetry mates I'm sure the ones Coot found "outside" your > protein are actually in the sites you are missing. > Nothing to worry, just safe the symmetry mate and read in those > coordinates& merge with your current model. > > Jürgen > > ...................... > 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://lupo.jhsph.edu > > On Oct 24, 2012, at 10:16 AM, Uma Ratu wrote: > > Hello, > > I have problems to find the ligand using WinCoot. > > The protein was purified with NADH, and crystallized. Data diffraction is > bellow 2A. > Structure is solved using molecular replacement. > The protein is homo-tetramer. > > I then exam the model. I can identify two ligand positions inside two of > the monomers. > When I take a close look at the other two monomer, it is very clear that > there are big molecular there. > But Coot failed to find them. > > Here is how I did: > > Method 1: Load NAD. Then "Calculator - Other Modelling Tools - Find Ligand" > Coot find 4 ligands. Two inside the tetramer, two outside the tetramer. > > Method 2: Validate - Unmodelled blobs > Coot returns 4 blobs, two inside the tetramer, two outside the tetramer > > Both methods failed to identify the other two ligands inside the tetramer. > > Attached is the electronic density map of one of the questioned ligands. > > I use WinCoot - 0.7 - pre-1 > > Thank you for advice > > Uma > <blob-1.jpg> > > > > >
