That's not what I suggested. you have a tetramer and you have found two ligands within the protein and two ligands outside your protein - right ? Now if you merge those 4 found ligands with your protein and then turn on symmetry mates you will find that the two ligands which were shown outside your protein surprisingly also show up inside your protein but in a symmetry related position. Now you can safe in Coot the symmetry related chains do some manual editing vie your favourite text editing tool for coordinates and only retain those symmetry related ligands. Next you open your set of coordinates and only import those ligands which are in the right position. You will end up with your tetramer and 4 ligands sitting in the right position. If not then I misunderstood your original post.
Jürgen On Oct 24, 2012, at 11:12 AM, Uma Ratu wrote: 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<mailto: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<tel:%2B1-410-614-4742> Lab: +1-410-614-4894<tel:%2B1-410-614-4894> Fax: +1-410-955-2926<tel:%2B1-410-955-2926> http://lupo.jhsph.edu<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> ...................... 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
