Thank you for correcting me. The other two ligand inside the tetramer are fited manully now. Because their geomtry are significantly differed from the NAD PDB file that I used.
Thank all of you for your comments. Uma On Wed, Oct 24, 2012 at 11:23 AM, Bosch, Juergen <jubo...@jhsph.edu> wrote: > 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>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> >> >> >> >> >> > > ...................... > 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 > > > > >
