[phenixbb] phenix.automr questions

Thomas C. Terwilliger terwilliger at lanl.gov
Sat Aug 28 08:07:08 PDT 2010


Hi Kay,

I'll answer what I can; perhaps Randy the others may have more comments.

>> 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 ?

It would be a good idea for me to put that in. For now, yes, you have to
make a script to do that.

>>
>> 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!)

Yes, it runs the inverse hand even if you say
"use_all_plausible_sg=False".  However it should not run all the other
space groups (all_plausible_sg_list : ['P 4 2 2', 'P 4 21 2', 'P 41 2 2',
'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2']).  I'll see
if we can put in a flag so it doesn't run the inverse hand if you don't
want it to.


>>
>> 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?

Looking at your parameters file, I see what you mean.   If you supply two
different files, then yes, the one you specified at the top of your file
with "seq_file=all.dat" is going to be used for editing the file for
autobuild, and the one you specified in the scope "component" is going to
be used for getting the likelihood terms right.

Normally (always?) these should be the same. So normally, just supply the
first one "input_seq_file=seq.dat") and it will be used for both purposes.

Or if you have several components, only specify them in the "component"
scopes, and all of them will be put together into a single file and used
as the input to autobuild.


>>
>> 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?

Only basic editing to make the model compatible with autobuild is done. No
sculpting is done inside automr for now.

All the best,
Tom T


>>
>> 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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>>




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