[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
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
}
}
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