[phenixbb] phenix.automr questions

Kay Diederichs kay.diederichs at uni-konstanz.de
Sat Aug 28 07:39:40 PDT 2010

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 
    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,


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
     n_cycle_rebuild_max = 1

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