-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOfEamUxlJ7aRr7hoRAiIuAJ9g6X38mWhX7oMAGSX8+qQt0Es7cQCgq4+p WMegXgDLxuS2E5494O/EiE8= =ENms -----END PGP SIGNATURE-----
