Can I generate a hypothesis in Phase from a prealigned set of ligands?
Yes. To suppress all alignment of ligands in Phase, set the environment variable SCHRODINGER_PHASE_SCORE_IN_PLACE to any value before you start Maestro. You can then import your prealigned conformer sets into the Develop Pharmacophore Model workflow and use them to generate hypotheses without performing any alignment. Likewise, if you are creating the hypothesis from the command line, set SCHRODINGER_PHASE_SCORE_IN_PLACE to any value before you start the jobs. There is no command option to suppress alignment. This environment variable turns off alignment for all Phase jobs, whether run from Maestro or from the command line, including findng matches to a hypothesis. If you want to align ligands, you must unset this environment variable and restart Maestro or run the command-line jobs. Alternatively, you can start the jobs (or Maestro) from a shell in which this environment variable is not set.
