[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

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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