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>
