I have run the flexible alignment tool and it overlays the molecules nicely however it doesn't update the Project Table. Therefore when you exclude one molecule you lose the alignment. Is there a fix for this?

This problem has been fixed in Suite 2009 Update 2. You should update your software to obtain the fix.

One workaround would be to create an entry from the Workspace, then use Entry → Split by molecule to create separate entries for each molecule in the alignment.

Keywords: align, flexible ligand alignment, project table update, Maestro

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