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Phenix: Difference between revisions
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→phenix.elbow - electronic Ligand Builder and Optimisation Workbench
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This can then be used in elbow as a chemical component. This option provides more information than the SMILES string. | This can then be used in elbow as a chemical component. This option provides more information than the SMILES string. | ||
phenix.elbow -- | phenix.elbow --chemical_component TA1 | ||
== Model building and completion == | == Model building and completion == | ||
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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. | |||
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 | 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. | libtbx.python "/net/anaconda/raid1/terwill/misc/PHENIX/modules/phenix_regression/segment_and_split_map/tst_auto_sharpen.py" | ||
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 == | ||