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1. Jmol/Cavities pockets and tunnels (22,245 bytes)
   2: ... An alternative method for finding and displaying cavities is [[PACUPP]]. Several other methods are summariz...
   7: ==How To Show Cavities In Proteopedia==
   8: ...o consider an alternative method which represents cavities with pseudoatoms, [[PACUPP]].
   11: ...l uses two "rolling" spherical probes to identify cavities.
   12: *The smaller ''cavity probe'' detects the cavities. Its default radius is 1.2 Å. For comparison, th...
2. Image:1IH5 cavities xfine small 2 5 20 24.pdb (83 bytes)
3. User:Eric Martz/Cavities tests (2,280 bytes)
   10: ...ace "http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl";
   12: <text>Load isosurface cavities</text>
   15: ...mages/6/67/6zgi-cavities.jvxl -- see [[Image:6zgi-cavities.jvxl]])
   21: ...oad "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
   26: ...iki/index.php/Image:6zgi-cavities.pngj Image:6zgi-cavities.png])
4. Image:2j1n cavities fine small 3 5 20 24.pdb (133 bytes)
   2: ...orin structure 2j1n with pseudo-atoms filling the cavities, generated by PACUPP.
5. Image:Cavities and leucine plug abcg2.png (0 bytes)
6. Image:2j1n cavities vfine small 2.4 5 20 24.pdb (0 bytes)
7. Image:6zgi-cavities.jvxl (0 bytes)
8. Image:6zgi-cavities.pngj (0 bytes)
9. PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins (8,083 bytes)
   2: ...ith pseudoatoms. PACUPP provides tools to isolate cavities of interest and display their contents, their lin...
   13: ...ve 2-4 pseudoatoms each. By default, PACUPP hides cavities with <5 pseudoatoms.</ref>. All but one of these ...
   17: ...e when the <scene name='86/869942/Pacupp_depth/1'>cavities are colored by PACUPP's "depth" color scheme</sce...
   23: ...ings" off of clusters of pseudoatoms representing cavities. These methods are demonstrated in the YouTube vi...
   29: ...ws menu also offers a view suitable for measuring cavities. <scene name='86/869942/Dimensions/1'>Here are tw...
10. Image:Jmol-cavities-6zgi.png (0 bytes)
11. Image:Jmol-cavities-6zgi-2.5-10.png (0 bytes)
12. Image:Jmol-cavities-6zgi-1.4-10.png (0 bytes)

Page text matches

1. 1rrl (4,805 bytes)
   24: ...ciprocal lattice. (ii) The volume of the internal cavities can ;shrink' by several percent upon freezing eve...
2. 1rrh (4,819 bytes)
   24: ...ciprocal lattice. (ii) The volume of the internal cavities can ;shrink' by several percent upon freezing eve...
3. 2j21 (9,742 bytes)
   26: ...water-accessible crevices or hydrophobic internal cavities with no other structural changes but with a large...
4. 2j20 (9,816 bytes)
   26: ...water-accessible crevices or hydrophobic internal cavities with no other structural changes but with a large...
5. 1gwg (4,412 bytes)
   24: ... surface and in intramolecular and intermolecular cavities. In three cases, the structures could be automati...
6. 1gw9 (4,281 bytes)
   24: ... surface and in intramolecular and intermolecular cavities. In three cases, the structures could be automati...
7. 1aeq (5,642 bytes)
   24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
   26: Artificial protein cavities as specific ligand-binding templates: characteriz...
8. 1aed (5,651 bytes)
   24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
   26: Artificial protein cavities as specific ligand-binding templates: characteriz...
9. 1aes (3,996 bytes)
   24: ...ow small molecule penetration into buried protein cavities.
10. 1aej (5,637 bytes)
    24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
    26: Artificial protein cavities as specific ligand-binding templates: characteriz...
11. 1aek (5,621 bytes)
    24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
    26: Artificial protein cavities as specific ligand-binding templates: characteriz...
12. 1aeo (5,656 bytes)
    24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
    26: Artificial protein cavities as specific ligand-binding templates: characteriz...
13. 1aev (6,008 bytes)
    24: ...e specific binding behavior of artificial protein cavities can be harnessed and redirected toward the oxidat...
14. 1aee (5,619 bytes)
    24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
    26: Artificial protein cavities as specific ligand-binding templates: characteriz...
15. 1aet (4,017 bytes)
    24: ...ow small molecule penetration into buried protein cavities.
16. 1aeb (5,643 bytes)
    24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
    26: Artificial protein cavities as specific ligand-binding templates: characteriz...
17. 1aeu (3,986 bytes)
    24: ...ow small molecule penetration into buried protein cavities.
18. 1aeg (5,635 bytes)
    24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
    26: Artificial protein cavities as specific ligand-binding templates: characteriz...
19. 1aeh (5,653 bytes)
    24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
    26: Artificial protein cavities as specific ligand-binding templates: characteriz...
20. 1aem (5,649 bytes)
    24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
    26: Artificial protein cavities as specific ligand-binding templates: characteriz...

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