Article ID: 1348 - Last Modified: May 2, 2012
Can I apply distance, angle, or dihedral constraints on the sites when searching for matches to a hypothesis?
From Suite 2011 on, you can set up distance, angle, or dihedral constrainst from the Advanced Matching Options dialog box, by clicking Constraints, and then setting up the desired constraints.
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
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 using the Manage Hypotheses panel.
hypo.xyz in the Workspace, then add
ref.mae to the Workspace. The order of inclusion is necessary to get the correct numbering of sites when you define constraints, and so that picking picks the sites of the hypothesis rather than the atoms of the reference ligand.
5. Use Tools → Measurements to define the constraints, by picking the sites for each constraint.
6. If you have defined distances, click Write in the Distances tab and write the file
distances.csv to the temporary subdirectory, then close the dialog box.
7. If you have defined angles, click Write in the Angles tab and write the file
angles.csv to the temporary subdirectory, then close the dialog box.
8. If you have defined dihedrals, click Write in the Dihedrals tab and write the file
dihedrals.csv to the temporary subdirectory, then close the dialog box.
Each type of constraint must be written from its own tab.
9. Run the following command:
$SCHRODINGER/run -FROM phase phase_constraints -cleanup hypoID
If there are no errors (e.g., you accidentally clicked an atom on the reference ligand rather than a site), the file hypoID.cnst is created, and the directory hypoID_constraints is removed. You can then run a Find Matches job with the constraints that you selected.
From the command line you can run
pharm_align_mol to set up a database or file search with the constraints. If you want to run the seacrh without the constraints, use
-useConstraints false with these programs.
Keywords: Phase, Maestro
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