I'll add another molecular replacement anecdote to the growing list: 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. Cheers, Dave ============================ David C. Briggs PhD Father, Structural Biologist and Sceptic ============================ University of Manchester E-mail: [email protected] ============================ http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB ============================ On 23 May 2010 20:42, Joyce, Gordon M. (NIH/NIAID) [F] <[email protected]> wrote: > I recently used an ensemble of many proteins with Phaser. A single model did > not find a solution but this ensemble of seven very similar molecules gave a > correct solution with a TFZ of ~9.0. I did not trim the side chains in this > ensemble (first try worked) but this introduced variation may be beneficial > in the search. > Also try FFAS03 to identify the closest models (not just sequence based) > http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl > > There are instructions in phaser manual (shown below) about how to generate a > single model based on these proteins. > > ------------------------------------------------------------------------------------------------------------------------------------------- > How can I obtain a "mixed model", as described by Schwarzenbacher et al. > (Acta Cryst. D60:1229-1236, 2004)? > > Use the FFAS server maintained by the Godzik lab. However, the procedure to > get a "mixed model" with the original conformation of conserved side chains > is not immediately obvious. > > * Enter your sequence, choose the PDB database, click Search, and when the > search is finished you'll be at the Results page. > * From that page, click on the link to the PDB database in the "Results > vs" column. > * For each model of interest, make a note of the percent sequence identity > (quite far to the right). You'll need this to give Phaser an idea of the > expected RMS error of the model. Then click on the "scwrl" link under > "Psi-Blast/align/model". This will open a page on the SCWRL server. > * Click the check box for "Retain original conformations of conserved > residues", then click "Submit query". > * Finally, when the result from this appears, right-click "Get mixed > model" and choose "Save Link As..." (or whatever the equivalent is on your > browser, e.g. click-hold on a Mac) to save the PDB file with the mixed model. > --------------------------------------------------------------------------------------------------------------------------------------------- > > Also I agree with Jürgen, Balbes can work great and very quickly. > > HTH, > Gordon > > M. Gordon Joyce, Ph.D. > > Intramural AIDS Research Fellow, > Structural Immunology Section, > Laboratory of Immunogenetics, > NIAID/NIH > Twinbrook II, Rm 108, > 12441 Parklawn Drive, > Rockville, > MD 20852, USA > > Office Phone: 301 594 0242 > Lab Phone: 301 496 3792 > --------------------------------------------------------------------------------------------------- > > -----Original Message----- > From: Miri Hirshberg [mailto:[email protected]] > Sent: Sunday, May 23, 2010 3:35 PM > To: [email protected] > Subject: Re: [ccp4bb] Finding best model for molecular replacement > > Sun., May 23rd 2010 > EBI > > Paul, > > 1. yes you can run your sequence against all PDB. > > 1. http://www.ebi.ac.uk/pdbe-srv/view/ > drop the one letter sequence in the sequence box and search > > 2. http://www.ebi.ac.uk/Tools/fasta33/index.html > > From the Databases protein you pick > Protein structure Sequence > > You drop your 1-letter code sequence in the sequence box and search You > > both 1&2 run the same search but the layout of the output is a bit different. > > 3. You can also try http://meta.bioinfo.pl/submit_wizard.pl > it will predict 3D structure using many methods. > > Miri > > On Sun, 23 May 2010, Paul Lindblom wrote: > >> >> Hi everybody, >> >> I just crystallized a new project protein. How can I find a possible >> model for using molecular replacement? I have the sequence of my >> protein. Is it enough to make a sequence search in the pdb? Or is there >> another approach I can use? >> >> Thanks a lot, >> >> Paul >> >> >> > > > ------------------------------------ > Dr Miri Hirshberg > European Bioinformatics Institute UK > PDBe - EBI -EMBL > http://www.ebi.ac.uk/pdbe > > Phone: +44 (0) 1223 492647 > FAX: +44 (0) 1223 494468 > ------------------------------------ >
