visualizing docking output

There have a been a few recent posts regarding visualization of the
 output from docking calculations so thought I'd throw in my 0.02.
 While it is relatively easy to visualize a single protein ligand complex
 with
 any of a number of tools, most of us are not interested in looking at
 just one ligand.  Typically the user of a docking program will want to
 examine dozens or even hundreds of docked ligands.  To my knowledge
 there is currently no commercial or academic software which adequately
 addresses this problem.  Before software vendors get upset and start
 flaming me, let me specify what I think is necessary.  The program
 should be able to
 1. Read a protein as a PDB file.
 2. Read a multi-structure file containing a set of ligands in a file
    format appropriate for small molecules (SDF,mol2, not PDB).
 3. Allow facile creation and display of a protein surface colored by
 electrostatic
    potential.  It should also be easy to toggle the surface on and off.
 4. Be capable of displaying hydrogen bonds between the protein and
    ligand.
 5. Allow the user to easily scroll through the set of ligands,
 displaying
 each ligand in the active site of the protein.
 6. Provide adequate performance with macromolecular systems.
 It would also be nice to be able to
 7. Mark interesting compounds and save the marked compounds to a
    file.
 8. Display a 2D ligand structure along with the 3D structure.
 9. Display docking scores along with 3D strucutres.
 10. Filter structures - e.g. show me only those structure which make a
     hydrogen bond with ASP 87.
  11. Visualize close contacts.
 None of this is rocket science,  but I have yet to find a package which
 satisfies all the requirements.  Our solution was to write our own
 viewer. Unfortunately this viewer relies on Molecular Inventor which has
 been orphaned by SGI
 I'd be happy if anyone could prove me wrong and point me to software
 which fulfills the requirements above.  I'd also be interested in any
 toolkits,
 Active-X/COM/WhateverMicrosoftIsCallingItToday components for
 doing molecular graphics.  I'll gladly summarize for the list.
 Pat
 --
 W. Patrick Walters, Ph.D.
 Vertex Pharmaceuticals, Inc., 130 Waverley St., Cambridge, MA  02139
 Voice: (617)577-6242   FAX: (617)577-6400
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