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PHENIX Examples
Where can I find sample data?You can find sample data in the directories located in: $PHENIX/examples. Additionally there is sample MR data in $PHENIX/phaser/tutorial. Can I easily run a Wizard with some sample data?You can run sample data with a Wizard with a simple command. To run p9-sad sample data with the AutoSol wizard, you type: phenix.run_example p9-sad This command copies the $PHENIX/examples/p9-sad directory to your working directory and executes the commands in the file run.csh. What sample data are available to run automatically?You can see which sample data are set up to run automatically by typing: phenix.run_example --help This command lists all the directories in $PHENIX/examples/ that have a command file run.csh ready to use. For example: phenix.run_example --help PHENIX run_example script. Fri Jul 6 12:07:08 MDT 2007 Use: phenix.run_example example_name [--all] [--overwrite] Data will be copied from PHENIX examples into subdirectories of this working directory If --all is set then all examples will be run (takes a long time!) If --overwrite is set then the script will overwrite subdirectories List of available examples: 1J4R-ligand a2u-globulin-mr gene-5-mad p9-build p9-sad Are any of the sample datasets annotated?The PHENIX tutorials listed on the main PHENIX web page will walk you through sample datasets, telling you what to look for in the output files. For example, the Tutorial 1: Solving a structure using SAD data tutorial uses the p9-sad dataset as example. It tells you how to run this example data in AutoSol and how to interpret the results. | |