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/<http://www.sbg.bio.ic.ac.uk/%7Ephyre/>) >> >> 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 >
