[phenixbb] can mr_rosetta include twin_law?

Terwilliger, Thomas Charles terwilliger at lanl.gov
Fri Mar 27 11:17:40 PDT 2015

Hi Fenyun,

I'm sorry for the trouble with mr_rosetta and your refinement_params file!  I am not sure what is wrong,  I tried a test using the test data available in phenix.  You can get the test data with:

  phenix_regression.wizards.test_command_line_rosetta_quick test_refine_after_mr

I tried the following command in the directory test_refine_after_mr that is created if you issue the command above:

  phenix.mr_rosetta seq_file=seq.dat search_models=coords1.pdb start=place_model stop=place_model data=fobs.mtz is_sub_process=True already_placed=true place_model.denmod_after_refine=False debug=True max_wait_time=1 refinement_params=twin.eff

and the refinement did successfully use twin.ff, looking at  WORK_2/coords1_ref_001.log:

============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 25 25 25 90 100 90
    space_group = "P 1 21 1"

  twinning {
    twin_law = "h,-h-k,-l"
#phil __OFF__

If you would like to send me all the input files and full log file I'll be happy to try and figure out what is happening.

All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Ni, Fengyun [fni at bcm.edu]
Sent: Friday, March 27, 2015 11:02 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] can mr_rosetta include twin_law?

Hi everyone,

When I run phenix.mr_rosetta, I use the following file (twin.eff) to add the twin_law with the keyword: refinement_params=twin.eff. I checked the output that the phenix.refine stage could recognize this file. But the autobuild step can not read this file and give the error information as follows,

refinement.twinning {
  twin_law = "h,-h-k,-l"

Unable to read the parameters file twin.eff.

Is there anyway to overcome this issue? Thank you very much in advance!

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