unambiguous space group ? Jürgen
On May 23, 2010, at 4:52 PM, Paul Lindblom wrote: > Thank you all for your quick answers. I already tried the phyre server but > could not find a appropriate model. Balbes found a structure with 29% > identity, but no solution. Now I am running molrep with the model balbes > found... > > 2010/5/23 Nathaniel Echols <[email protected]> > On Sun, May 23, 2010 at 12:57 PM, David Briggs <[email protected]> > wrote: > I like to generate some models using the "Phyre" server > > ( http://www.sbg.bio.ic.ac.uk/~phyre/ ) > > Feed the best .pdbs into Mr Bump. > > Go and get coffee. Come back and find a solution with post-refmac > R/Rfree in the mid-30s. > > IMHO, Phyre models are often pretty good, and Phyre is worth running > on any sequence you are messing with - the output is nice and > informative. > > My experience has been exactly the opposite; I've seen many people waste a > lot of time this way. Phyre is a fold-recognition server - it is not > intended to generate optimal, physically accurate models. It's possible that > they've improved the output since I last used it, but I've seen plenty of > models with overlapping sidechains and completely unrealistic packing. Use > Modeller or Rosetta (both also available as web servers) if you want as > accurate a homology model as possible. Even so, if you can find homologs in > the PDB with better than 30% sequence identity, you'll probably have at least > as much success using those as search models, after judicious pruning (which > I think MrBUMP can do automatically). > > This is not to say that homology modelling isn't occasionally useful for MR, > but it is not the first thing I'd try unless I had put a great deal of > thought into the pipeline and had a large cluster to run it on. I know the > JCSG has had some luck with this approach, but they have full-time > programmers and something like 400 CPUs. > > -Nat > - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
