Phenix: Difference between revisions

621 bytes added ,  26 August 2020
→‎Tips and Tricks: regression tests
(→‎Special positions: Bond across symmetry axis)
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* Automatic detection of NCS groups:
* Automatic detection of NCS groups:
  phenix.refine data.hkl model.pdb main.ncs=True
  phenix.refine data.hkl model.pdb ncs=True ncs_search.enabled=True
* Manual specification of NCS groups:
* Manual specification of NCS groups:
  phenix.refine data.hkl model.pdb ncs_groups.params ncs_search.enabled=True
  phenix.refine data.hkl model.pdb ncs_groups.params  
where ncs_groups.params contains e.g.:
where ncs_groups.params contains e.g.:
  refinement.ncs.restraint_group {
  refinement.ncs.restraint_group {
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== Tips and Tricks ==
== Tips and Tricks ==
1) To check the syntax of a Phenix parameter file (for any program, not just phenix.refine), you
can run this command (replacing params.eff with the file of interest):
libtbx.phil params.eff
If it works, it will just print out the parameters - if not, the error message should give some indication where the error occurred.


A handy tip: to check the syntax of a Phenix parameter file (for any program, not just phenix.refine), you
2) To check the proper functioning of a Phenix program, e.g. phenix.auto_sharpen, with Phenix's regression tests, type this on the command line:
can run this command (replacing params.eff with the file of interest):
    phenix_regression.list auto_sharpen
This will then list the command(s) that you can run on your computer to test
phenix.auto_sharpen. On Tom Terwilliger's computer the output looks like:


  libtbx.phil params.eff
  libtbx.python "/net/anaconda/raid1/terwill/misc/PHENIX/modules/phenix_regression/segment_and_split_map/tst_auto_sharpen.py"


If it works, it will just print out the parameters - if not, the error message should give some indication where the error occurred.
Copy and paste the line with the regression test you are interested in, and make sure that it runs and
ends with "OK". (For phenix.refine, there are >300 regression tests!)


== Installation from source, and of Rosetta interface ==
== Installation from source, and of Rosetta interface ==
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