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Dear Pete,
Coot offers using secondary structure restraints, i.e. this does not
refer to refinement but to model building where your calculations do not
apply.
It helps a great deal if you are looking at a patch of density at, say,
3.5A resolution which you recognise as alpha-helix or beta-strand and
simply ask your model building program of choice to "place a helix here"
which you can incorporate into your model or at least use as a guideline
for correcting yours.
Tim
On 09/22/2011 10:18 PM, Pete Meyer wrote:
> I've noticed that people seem to be using or recommending secondary
> structure restraints for low resolution refinement lately, but I'm
> somewhat confused about the logic underlying their use.
>
> Using ballpark figures from a system I'm familiar with: 30000 atoms
> (90000 positional parameters), 4500 residues, 100000 reflections and
> 95000 geometric (bond and angle) restraints.
> n_ref / n_param ~= 1.11
> (n_ref + n_geom) / n_param ~= 2.16
>
> Assuming all residues are localized, and each residue provides 2
> secondary structure restraints (best-case scenario), this changes the
> effective observation to parameter ratio to:
>
> (n_ref + n_geom + n_ss ) / n_param ~= 2.26
>
> In short, the effective observation to parameter ratio improves by ~4%.
> This seems like a relatively small improvement, especially if the
> trade-off is that Ramachandran statistics can't be used for validation
> anymore. It also seems like the improvement would decrease with larger
> proteins (the number of additional parameters from adding a residues
> increase faster than the number of secondary structure restraints that
> residue could provide).
>
> Does anyone have any suggestions that could help clear things up?
>
> Thanks,
>
> Pete
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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