Phenix: Difference between revisions

Phenix (edit)

625 bytes added , 26 August 2020

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 == Tips and Tricks ==
+) 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
+) 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 ==