Is it possible within Phase to work with pre-aligned ligands?

You can keep the conformation and the alignment of a set of ligands but to do that you need to set the environment variable:
export SCHRODINGER_PHASE_SCORE_IN_PLACE=1 (bash)
or
setenv SCHRODINGER_PHASE_SCORE_IN_PLACE 1 ([t]csh)
and then start Maestro and work as usual with the workflow.

This will silently turn off alignment in all parts of the Develop Pharmacophore Model workflow after Find Common Pharmacophores. It will also silently affect Find Matches to Hypothesis when searching a database (although you probably don't want this to happen). If you're searching a file or Project Table entries, there's already a score-in-place option, so there's no need to define the variable for those purposes.

And, after quitting Maestro, be sure to unset the variable before running any other Phase software from that shell:

unset SCHRODINGER_PHASE_SCORE_IN_PLACE

Keywords: Phase, score in place, external hypothesis, aligned structures, Maestro

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