Dear Patrick, Apologies for a partly non-CCP4 answer! You can use the HHPRED alignments in some of the software available in Phenix. One option is to provide the .hhr file to MRage, which will fetch the PDB entries, run Sculptor to modify the templates with one or more protocols, based on that alignment, and then test all the models that have been generated. That's fully automated and will often work. If it doesn't, an alternative is to run phenix.mr_model_preparation, which again will fetch the PDB entries and run the single best Sculptor protocol on all of them. I tend to prefer this option myself, because then you can look at whether it would be sensible to combine various alternative models as ensembles. One of the most powerful approaches is to run Ensembler (available in both CCP4 and Phenix, as is Sculptor) to make an ensemble, with the "trim=True" option turned on to trim any bits that don't agree among the structures in the ensemble. Cutting back to a conserved core has allowed a number of very recalcitrant structures to be solved with collections of models around the 20% sequence identity range.
Best wishes, Randy > On 20 Jul 2017, at 23:13, Patrick Loll <pjl...@gmail.com> wrote: > > I’m intrigued by the prospect of using AMPLE to test multiple distant > homologs in a MR problem. I’ve used HHPRED to identify about 20 > high-probability homologs of known structure, each of which has about 20-25% > identity with the unknown protein. However, it’s not clear to me from the > documentation whether the program will use the alignments from HHPRED, and, > if so, how I should provide that information. > > Or does AMPLE perform its own alignment? I.e., do I simply point the program > to a directory containing 20 different PDB files and stand back? > > Thanks for any insights. > > Cheers, > > Pat > --------------------------------------------------------------------------------------- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pjl...@gmail.com > pj...@drexel.edu ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
