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Hi Hailiang, may be your expectations did not match the reality? I did exactly this for teaching purposes a few weeks ago and it worked for me quite well. Try different models with different molecule/solvent ratio, try adding solvent: phenix.fmodel model.pdb high_res=10 k_sol=0.35 b_sol=50 Yes, Ethan is right of course, you can choose the resolutions in Coot -:) Pavel. On Wed, Jun 1, 2011 at 4:55 PM, <[log in to unmask]> wrote: > Hi Pavel: > > I tried phenix.fmodel at different resolutions up to 20A, and never got > any big envelop covering the whole molecule. > > ...anyway, thanks... > > Hailiang > > > > Hi Hailiang, > > > > to get feeling about how maps may look like at different resolutions do > > the > > following learning exercise: download a structure from PDB and compute > > Fcalc > > maps at different resolutions: > > > > phenix.fmodel model.pdb high_res=1 > > phenix.fmodel model.pdb high_res=2 > > phenix.fmodel model.pdb high_res=3 > > phenix.fmodel model.pdb high_res=4 > > phenix.fmodel model.pdb high_res=5 > > ... > > phenix.fmodel model.pdb high_res=10 > > phenix.fmodel model.pdb high_res=20 > > > > then load them in Coot and you will get your answer. > > > > Pavel. > > > > > > On Wed, Jun 1, 2011 at 4:35 PM, Hailiang Zhang <[log in to unmask]> wrote: > > > >> Hi there, > >> > >> I have a preliminary question. For very low resolution data, say 10A or > >> even lower, is the density map supposed to be more like a big envelop > >> covering the whole molecule, or more like a collection of isolated small > >> envelops covering small motifs (eg helix as cylinder envelop)? I got the > >> later one but need to make sure and persuade others I didn't do things > >> wrong. > >> > >> Any references will also be appreciated! > >> > >> Thanks! > >> > >> Hailiang > >> > > > > >