Thanks all! Actually I have tried different systems and did find that the "molecular envelop" map shows up at a resolution of 40A (50S ribsome).
Hailiang > 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, <[email protected]> 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 <[email protected]> >> 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 >> >> >> > >> >> >> >
