[phenixbb] A couple of questions regarding twinning

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Jun 3 07:15:47 PDT 2010


Hi Pietro,

I can answer part of this; hopefully others can cover the rest.

The output structure factor amplitudes from autobuild (i.e.,
exptl_fobs_hl_coeffs_freeR_flags.mtz) should be the same as the input ones
(e.g., from "data=....")

The maps are not detwinned unless you specify (as might be a good idea)
"two_fofc_in_rebuild" in which case with your refinement parameters file
you would get 2mFo-DFc maps from phenix.refine that are using detwinned
data.

There is currently no way to detwin the data in autobuild and use the
detwinned data in density modification (this would be a useful thing to
have, yes).  You would have to put in detwinned data to start with as
"data" to do this.


All the best,
Tom T

>> 1. The structure I work with has multiple twinning domains
>> (4 to be exact, with pseudo-orthorhombic 222 symmetry
>> induced by twinning in P1). I feed the autobuild script the
>> operators using a keyord:
>>
>> input_files.refine_eff_file_list=mytwinrefinement.eff
>>
>> (see attached file) but only the last one seems to be used.
>> Do I guess correctly that there is only provision for two domains
>> adn therefore the last twinning definition overrides any
>> previously defined one?
>>
>> If so, is there a way of specifying and using multiple
>> twinning domains/operators?
>>
>> 2. Output structure factor amplitudes: are they
>> detwinned? Are they detwinned before the density modification
>> in resolve? and during it?
>>
>> Thanks for any clarification/suggestions
>>
>> Regards
>>
>> Pietro
>>
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