Tom, The WORK_1 folder only contains "imported_fp_sigfp_freer.mtz". I ran the regression test this is the result: ~ heather$ /Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/build/mac-intel-osx-x86_64/bin/phenix_regression.wizards.test_command_line_rosetta_quick test_hhr Skipping phenix rosetta tests: rosetta build not available. ~ heather$ The rosetta build is indeed available and I have gotten other MR_rosetta runs to begin as long as I supply my own models. Also there were a few other regression tests with similar names that I tried as well. ~ heather$ /Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/build/mac-intel-osx-x86_64/bin/phenix_regression.wizards.test_command_line_rosetta ; exit; Running all command_line tests Number of tests to run: 7 ================================================================= Running test_mr_rescoring x coord_mr.1.pdb x coord_mr.1_data.mtz x cycle_best_2.mtz x cycle_best_2_nf.map x edited_align.ali x fobs.mtz x mr_rescoring.eff x mr_rescoring.pkl x perfect.mtz x seq.dat x test_mr_rescoring.com x test_mr_rescoring.log FAILED TO RUN: test_mr_rescoring ***************************************************** Error: test_command_line_rosetta failed ***************************************************** logout [Process completed] I don't know what is going on here, but any more ideas are greatly appreciated. ~Heather | On Fri, 15 Jun 2012 19:29:49 +0000 | "Terwilliger, Thomas C" wrote: | Hi again Heather, | | One other idea: try this regression test: | | phenix_regression.wizards.test_command_line_rosetta_quick test_hhr | | It should take a second or two and will say "OK" if everything is all right and it can start from an hhr file. If that works...then you can look at the commands in | | test_hhr/test_hhr.com | | which should look like: | | phenix.mr_rosetta data=1dfn.mtz seq_file=1dfn.seq hhr_files=1dfn.hhr number_of_models=1 \ | number_of_models_to_skip=2 start_point=place_model stop_point=place_model \ | run_place_model=False | | and run this command directly, gradually changing all the inputs in it until they match yours...and somewhere along the way it should fail, giving you a clue what needs to be fixed. | | All the best, | Tom T | | | ________________________________________ | From: Terwilliger, Thomas C | Sent: Friday, June 15, 2012 1:17 PM | To: PHENIX user mailing list | Cc: Terwilliger, Thomas C | Subject: RE: [phenixbb] MR_Rosetta | | Hi Heather, | | This should work from an hhr file as you tried to do...I just tried an example to make sure. I am guessing that something happened in the downloading of the PDB file. Can you look in your file: | | WORK_1/*/mr_model_preparation.log | | to see if there is an error listed there? | | If that doesn't help, let me know. | All the best, | Tom T | | ________________________________________ | From: [email protected] [[email protected]] on behalf of Heather Condurso [[email protected]: Friday, June 15, 2012 12:58 PM | | To: [email protected] | Subject: [phenixbb] MR_Rosetta | | Hello all, | | I am working on a structure for which a good molecular replacement model doesn't really exist ( highest sequence similarity is 24% for a protein with completely different function and even worse for proteins with a more similar function). As I try and solve the phase with Se-Met derived protein, I thought I would try and use MR_rosetta and see what happens. I have also tried to use pyrosetta to generate better models, but the structure alignments suggest my protein to be primarily composed of beta sheets so the models from ab initio methods aren't great. I am using the GUI and have given my sca file, a sequence file, the 3 and 9 fragment files, and both the global and local alignment hhr files. I thought that phenix would use the hhr alignments to pull models directly from the pdb, but without giving a model pdb, MR_rosetta fails. So my question is how do I input the models? Should I download each of the pdbs and clean them up a bit? How many should I include? I ! unde! | rstand the more I include the more computing time this will take. Can you give any recommendations as to other parameters to change keep the computing time down initially to identify the best model before extensive time is used? | | I appreciate any help you may be able to provide, | Heather Condurso | UF-Department of Chemistry | [email protected] | _______________________________________________ | phenixbb mailing list | [email protected] | http://phenix-online.org/mailman/listinfo/phenixbb

Randy, I have tried this method with blast results, but not with the hhpred results. How many structures do you suggest I use in ensembler? I am willing to try anything. THanks, Heather | On Fri, 15 Jun 2012 21:04:37 +0100 | Randy Read wrote: | Dear Heather, | | MR_Rosetta can do amazing things, but it might also be worth trying something more manual that has worked for us for several structures with models in the 20% range (e.g. angiotensinogen). Get a number of models from the HHpred search, use the HHpred alignment to superimpose them with phenix.ensembler and turn on the trim option (Ensemble generation settings -> Trim residues deviating more than threshold). This prunes the ensemble back to the conserved core, which (with any luck) should also be preserved in your target structure. Pruning off things that are wrong turns out to be very good for improving the signal-to-noise. After ensembler, run phenix.sculptor (using your HHpred alignment) to trim off the non-conserved side chains from the trimmed ensemble) and then try to solve it in Phaser with the resulting sculpted ensemble. | | Good luck! | | Randy | | ----- | 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: [email protected] | Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk | | On 15 Jun 2012, at 19:58, Heather Condurso wrote: | | > Hello all, | > | > I am working on a structure for which a good molecular replacement model doesn't really exist ( highest sequence similarity is 24% for a protein with completely different function and even worse for proteins with a more similar function). As I try and solve the phase with Se-Met derived protein, I thought I would try and use MR_rosetta and see what happens. I have also tried to use pyrosetta to generate better models, but the structure alignments suggest my protein to be primarily composed of beta sheets so the models from ab initio methods aren't great. I am using the GUI and have given my sca file, a sequence file, the 3 and 9 fragment files, and both the global and local alignment hhr files. I thought that phenix would use the hhr alignments to pull models directly from the pdb, but without giving a model pdb, MR_rosetta fails. So my question is how do I input the models? Should I download each of the pdbs and clean them up a bit? How many should I include? ! I un! | de! | > rstand the more I include the more computing time this will take. Can you give any recommendations as to other parameters to change keep the computing time down initially to identify the best model before extensive time is used? | > | > I appreciate any help you may be able to provide, | > Heather Condurso | > UF-Department of Chemistry | > [email protected] | > _______________________________________________ | > phenixbb mailing list | > [email protected] | > http://phenix-online.org/mailman/listinfo/phenixbb | | _______________________________________________ | phenixbb mailing list | [email protected] | http://phenix-online.org/mailman/listinfo/phenixbb