Thank you all very much for your help. I am a thousand miles farther than I was at the time I sent out my question(s)!!
--- Paul Emsley <[EMAIL PROTECTED]> wrote: > Thanks Juegen, > > > On Wed, May 09, 2007 at 08:45:16AM -0700, Juergen > Bosch wrote: > > Hi James, > > > > start Coot, and read in your cif file plus a > coordinate file containing > > your ligand. Read in your structure and read in > your mtz file as Auto, > > then you end up with two maps FWTxPHWT and > DELFWTxPHDELWT. > > Next go to Calculate / Other Modelling Tools and > select Fit Ligand. > > Since you should have some nice extra density in > you difference map > > select this map to search your ligand in that map. > Let Coot do the rest. > > You can also select flexible ligand docking etc. > > I would also add that for a difference map, I'd > notch up the signigicance > level to 3 sigmas or so. And that should reduce > spurious hits. > > > Should work as advertised. Once your ligand is in > the position you > > expect it to be you can run real space refinement > using the difference > > density map at this point. Then go to > Calculate/Merge Molecules and > > select which one you want to merge, save the new > coordinates including > > your found ligand. > > > > Good luck, > > > > Juergen > > > > P.S. this is assuming Coot 0.31, and there's also > a Coot BB :-) > > 0.3.1 (and not to be > confused with 0.0.31) > > > > > James Pauff wrote: > > > > >Good day all, > > > > > >I have what may be a very simple question. I am > > >trying to insert a substrate/ligand into the > active > > >site of my enzyme using COOT, into electron > density > > >that I have already utilized in "O" for this > purpose. > > >I've created the substrate library file (*.cif) > using > > >a pdb file from PRODRG in the ccp4 sketcher. In > COOT, > > >I went to File->Get Monomer..., but when I type > the 3 > > >letter code, I get nothing. > > OK, Coot should be more informative about what kind > of nothing > you get. > > > >Further, I have imported the substrate as a > separate > > >pdb file, and can move it close to the active > site, > > >but I have no idea how to orient/manipulate the > ligand > > >into the electron density. If I can eventually > get > > >the ligand as a monomer into the screen, I still > don't > > >know how to manipulate its orientation prior to > > >writing it into the enzyme's pdb, so I guess that > I'm > > >just generally stuck here. > > If all else fails, there's alway Rotate/Translate > Zone > (in the Model/Fit/Refine dialog). Using that you can > drag > and rotate the fragment. > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
