One of my friends (Jose Luis Lopez) from here at the University of Salamanca is currently building animations using Spartan. They are taking Spartan output and generating multiple .pdb files. They are then taking the .pdb files and converting them to a multi-frame .xyz file ... to play in Chime.
Some years ago I bought Spartan so I could construct simple peptides as PDB files. Then I found out that its PDB files lack residue (amino acid) identifiers and chain names! So it was useless for peptides and nucleotides. Possibly they have fixed that -- I haven't tried recent versions.
XYZ files also lack residue and chain info, which is why we've stuck with using PDB and MODEL/ENDMDL for macromolecular animations -- but it works fine. I have made many such animations playable in Protein Explorer at http://molvis.sdsc.edu/protexpl/morfdoc.htm
and also earlier ones in the Protein Morpher at
http://www.umass.edu/microbio/chime/morpher/index.htm
where I have also documented macromolecular morphing /animation methods at
http://www.umass.edu/microbio/chime/morpher/morphmtd.htm
Protein Explorer generates animations in Chime that can be saved as html files (scripts included), and then played outside of PE. Examples are at the first link above, e.g.
http://molvis.sdsc.edu/atlas/hivpi_m3.htm
-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532
http://www.umass.edu/molvis/martz
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