Molecular Sculpting

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Revision as of 13:25, 9 April 2010 by Inchoate (talk | contribs)
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What the heck is molecular sculpting?

Molecular sculpting works like a real-time energy minimizer, except that it isn't minimizing the energy. Instead, its just trying to return local atomic geometries (bonds, angles, chirality, planarity) to the configuration the molecules possess when they were first loaded into PyMOL.

To actually use this feature:

  1. Load a PDB file.
  2. Configure the mouse for editing (Mouse menu) or click in the mouse/key matrix box.
  3. Select "auto-sculpting" from the Sculpting menu.
  4. Select Sculpting from the Wizard menu.
  5. Ctrl-middle-click on any atom in your protein to activate sculpting
     the green part will be free to move
     the cyan part will be a fixed cushion to provide context
     the grey part will be excluded.
  6. Now perform any conformational editing operation in the green region such as:
     ctrl-left-click-and-drag on an atom
     ctrl-right-click on a bond, then ctrl-left-click-and-drag about that bond.

You can adjust the radius and cushion using the blue pop-up menus.

Right now I'm not sure the sculpting feature is more than entertainment, but my expectation is that it will become part of PyMOL's crystallographic model building system in the future.