Can I apply distance, angle, or dihedral constraints on the sites when searching for matches to a hypothesis?
In Suite 2010, you can apply distance, angle, or dihedral constraints on the sites by creating a hypoID.cnst file. The file is described in the Phase User Manual, Appendix B, under Matching Constraints File. To set up this file, you can use the following procedure. 1. In the directory that contains your hypothesis, run the following command: $SCHRODINGER/run -FROM phase phase_constraints -setup hypoID This command creates the temporary subdirectory hypoID_constraints, where the files ref.mae, hypo.def, and hypo.xyz are written. hypo.xyz contains all the sites in hypoID.xyz, plus all the projected points associated with those sites. Projected sites are of type ‘Z’ rather than ‘Q’, because Maestro doesn’t display sites of type ‘Q’, and you need to be able to see them in order to define constraints. 2. Start Maestro in this temporary subdirectory (or change to it after starting Maestro. 3. Import the reference ligand ref.mae using the Import panel, then import the hypothesis hypo.xyz usin
