[phenixbb] phenix.automr questions
Kay Diederichs
kay.diederichs at uni-konstanz.de
Sun Aug 29 10:57:41 PDT 2010
Hi Tom,
thanks for answering my questions! Yes, it would be good to have a flag
to turn off the inverse hand because
a) having the possibility to look at each spacegroup offers a very
effective way of parallelization
b) if I "grep" the spacegroup name in the logfile I find:
dikay at turn10:-2010/phenix.automr% grep "P 4" mf92.log
Space group: P 41 21 2 (No. 92)
LIST OF ALL PLAUSIBLE SG: ['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']
Space group: P 41 21 2 (No. 92)
NEW dictDATA {'raw_data': [' P 4abw 2nw', (101.71700286865234,
101.71700286865234, 344.74798583984375, 90.0, 90.0, 90.0),
<scitbx_array_family_flex_ext.double object at 0xe554a10>,
<scitbx_array_family_flex_ext.double object at 0xe554bd0>,
<cctbx_array_family_flex_ext.miller_index object at 0xe4716c0>]}
space_group : P 41 21 2
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']
dictDATA: {'raw_data': [' P 4abw 2nw', (101.71700286865234,
101.71700286865234, 344.74798583984375, 90.0, 90.0, 90.0),
<scitbx_array_family_flex_ext.double object at 0xe554a10>,
<scitbx_array_family_flex_ext.double object at 0xe554bd0>,
<cctbx_array_family_flex_ext.miller_index object at 0xe4716c0>]}
HALL: P 4abw 2nw
P 43 21 2
P 41 21 2
Space-Group Name (Number): P 41 21 2 (92)
Space-Group Name: P 41 21 2
Space-Group Name (Number): P 41 21 2 (92)
P 43 21 2 *
P 41 21 2
Space-Group Name (Number): P 43 21 2 (96)
Fast Translation Function Table: Space Group P 43 21 2
Space Group Name (Number): P 43 21 2 (96)
Packing Table: Space Group P 43 21 2
Space-Group Name (Number): P 43 21 2 (96)
Refinement Table (Unsorted): Space Group P 43 21 2
Refinement Table (Sorted): Space Group P 43 21 2
Best Space Group: P 43 21 2
P 43 21 2
P 41 21 2 *
Space-Group Name (Number): P 41 21 2 (92)
Fast Translation Function Table: Space Group P 41 21 2
Best Space Group so far: P 43 21 2
Space Group Name (Number): P 41 21 2 (92)
Packing Table: Space Group P 41 21 2
Space-Group Name (Number): P 41 21 2 (92)
Refinement Table (Unsorted): Space Group P 41 21 2
Refinement Table (Sorted): Space Group P 41 21 2
Space-Group Name (Number): P 43 21 2 (96)
Best spacegroup from search with first component in permutation: P
43 21 2
Space-Group Name (Number): P 43 21 2 (96)
Fast Translation Function Table: Space Group P 43 21 2
Space Group Name (Number): P 43 21 2 (96)
Packing Table: Space Group P 43 21 2
Space-Group Name (Number): P 43 21 2 (96)
Refinement Table (Unsorted): Space Group P 43 21 2
Refinement Table (Sorted): Space Group P 43 21 2
Best Space Group: P 43 21 2
Space-Group Name (Number): P 43 21 2 (96)
Best spacegroup from search with first component in permutation: P
43 21 2
Space-Group Name (Number): P 43 21 2 (96)
Fast Translation Function Table: Space Group P 43 21 2
Space Group Name (Number): P 43 21 2 (96)
Packing Table: Space Group P 43 21 2
Space-Group Name (Number): P 43 21 2 (96)
Refinement Table (Unsorted): Space Group P 43 21 2
Refinement Table (Sorted): Space Group P 43 21 2
Best Space Group: P 43 21 2
Space-Group Name (Number): P 43 21 2 (96)
which shows that at a certain point the MTZ file's spacegroup is
abandoned and the calculation finishes in the enantiomorph spacegroup,
which has the drawback that I cannot really compare the best (complete)
results of both enantiomorphs. And with one good and three bad search
models I don't know if abandoning the given spacegroup early is
definitively the right decision (but it's hard for me to tell exactly
what criterion the decision was based upon - it may have been after an
exhaustive search in #92 in which case my worry would not be justified).
thanks,
Kay
> Message: 2
> Date: Sat, 28 Aug 2010 09:07:08 -0600 (MDT)
> From: "Thomas C. Terwilliger"<terwilliger at lanl.gov>
> To: "PHENIX user mailing list"<phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] phenix.automr questions
> Message-ID:<14563.128.165.0.81.1283008028.squirrel at webmail.lanl.gov>
> Content-Type: text/plain;charset=iso-8859-1
>
> 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
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