Dear developers, I have four questions concerning phenix.automr (I'm using version 1.6.4): a) is there a way to make the program try all permutations for the search order of my four search molecules, or do I have to write a script ? b) how can I completely switch off the search in the alternative spacegroups - I am under the impression that although the "effective parameters" are all_plausible_sg_list = None use_all_plausible_sg = False the search is not only done in the spacegroup I specified (#92=P41212) but also in #96=P43212 . I believe so because the output says: ... 2 alternative spacegroups SpaceGroup will be determined by highest LLG in search for FIRST ensemble Search order: P 43 21 2 P 41 21 2 ... (I would rather run a second search "manually" in the other spacegroup!) c) I have two occurrences of seq_file ("all.seq" and "all.dat"; the latter is symlinked to the former). Am I right that I could just leave out one of them? I did this after looking at http://www.phenix-online.org/documentation/automr.htm#anch70 but I wonder which of the specifications of sequences and masses overrides the other one? or is the first specification used for editing the search models, and the second for getting the likelihood terms right? d) what kind of editing is done? Is phenix.sculptor run internally? I find {a,b,c,d}_edited.pdb but are they actually used? thank you, Kay P.S. I run with "phenix.automr mr.eff" where mr.eff is automr { data = "m879_2_rg92.mtz" seq_file = all.dat ensemble { ensembleID = "mol1" copies_to_find = 1 coords = a.pdb identity = 80 } ensemble { ensembleID = "mol2" copies_to_find = 1 coords = b.pdb identity = 45 } ensemble { ensembleID = "mol3" copies_to_find = 1 coords = c.pdb identity = 45 } ensemble { ensembleID = "mol4" copies_to_find = 1 coords = d.pdb identity = 45 } component { component_type = *protein nucleic_acid seq_file = all.seq component_copies = 1 } autobuild_variables{ n_cycle_rebuild_max = 1 } }