Examples of Links to the Protein Explorer (PE) with Prespecified Molecules.

Details on how such links work, and rules for their formats.
Construction of Hyperlinks to Protein Explorer

I. Demonstration links using various sources for PDB files:
(All these sources are available from Molecules Galore at the Macromolecular Visualization Freeware (RasMol) Home Page).

Hemoglobin, oxygenated, 206 kb
(alpha1beta1 dimer; 1hho.pdb from the Protein Data Bank).
Hemoglobin, oxygenated, 412 kb (alpha2beta2 tetramer, full "Biomolecule"; 1hho.mmol from EBI-PQS)
Hemoglobin, oxy, 618 kb, in Comparator, both dimer and tetramer (same as above two links, but side by side).

Complete IgG1 antibody molecule, 708 kb
(H2L2 including hinge region, theoretical model courtesy Eduardo Padlan; from UMass server)
Eduardo A. Padlan, Anatomy of the Antibody Molecule, Mol. Immunol. 31:169-217, 1994.

Large Noncovalent Assemblies
Lipid bilayers with water, in crystalline (260 kb) or fluid (280 kb) conformations, or both in Comparator (530 kb).
(theoretical models, courtesy Helmut Heller, M. Schaefer, Klaus Schulten, "Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases", J. Phys. Chem. 97:8343-60, 1993.)
Lipid bilayer slice containing gramicidin channel, 316 kb
(phosphatidyl ethanolamine, theoretical model courtesy Serge Crouzy, from a UMass FTP Server).
Serge Crouzy, Thomas B. Woolf, and Benoit Roux, "A molecular dynamics study of gating in dioxolane-linked gramicidin A" channels", Biophys. J. 67:1370-86, 1994.
Rhinovirus capsid (870 kb)
(alpha carbons only, 48,000 atoms) courtesy Robert M. Bock Laboratory, U Wisconsin, Madison, Virus Visualization site.)

ATP, 4 kb
(from the micromolecule database at KLOTHO).
Olestra-like molecule, 25 kb
(from the Molecular Models database of Dave Woodcock, Okanagan University College, Canada).
NaCl crystal, 1 kb
(from R. Benjamin Young and Michael Mehl's Crystal Lattice Structures site).
Penicillamine, molecular dynamics animation, 104 kb
(from Akira Dobashi's 3D Molecular Modeling Homepage in Tokyo, Japan).
After the molecule loads, click on MDL, then click Animation on Chime's menu to start the animation.

Animations & Morphs
After the molecule loads, click on Explore, Advanced Explorer, then NMR Model Selection, then Auto to play these movies (ensembles of models in PDB NMR format). (Or, as soon as the molecule appears, enter .n in the command input slot to jump directly to the NMR Model Selection page.)

EF hand morphed (gaining calcium), 300 kb
(from recoverin, at the Protein Morpher).
Ribose-binding protein (1urp -> 1dri).
From Sweden: a morph (binding ribose) produced by Gerard Kleywegt with his LSQMAN software available at the Uppsala Software Factory Biomolecular Morphing site.