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, <[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
>> >>
>> >
>>
>>
>>
>
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