[phenixbb] omit map with twinning?

Nathaniel Echols NEchols at lbl.gov
Thu Feb 18 10:06:33 PST 2010

On Feb 18, 2010, at 9:55 AM, Kelly Daughtry wrote:
> 1) Generate a refinement..eff file which includes the twin law.
> When I run from the gui, I do not believe that phenix is actually
> including the twin law. It is not shown as being read in the log file
> (but the log file show that the refinement.eff was an input). And the
> maps look the same as without the twin law. So, either I am doing
> something wrong, or it is not reading the twin law.

Several questions: did you try to start the omit map GUI with refinement.eff as a command-line argument, or did you add it to the list of input files along with the model and data?  If the latter, did you make sure to change the file type to "Refine config"?  If so, could you please send me (not the list) the file autobuild.eff in the output directory?

> From the command line:
> phenix.autobuild twin_law="-k,-h,-l" data.mtz model.pdb omit.eff
> (generated from omit_map autobuild.eff)

This will definitely not work - the twin law parameter is only for phenix.refine, but AutoBuild only processes its own set of parameters.  You need to set the parameter that tells AutoBuild to pass refinement.eff to phenix.refine, i.e.:

phenix.autobuild data.mtz model.pdb omit.eff input_files.refine_eff_file_list=/path/to/refinement.eff

or edit omit.eff and change the parameter there:

autobuild {
  input_files {
    refine_eff_file_list = "/path/to/refinement.eff"

But I still think it should work in the GUI - at least in 1.6.  Tom, would it be straightforward to add the twin law to the AutoBuild parameters so it can be specified directly as done for simulated annealing, instead of using extra config files?  (Even better would be an option to set the twin law automatically as required after AutoBuild runs xtriage.)


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

More information about the phenixbb mailing list