Morphs: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Eran Hodis, Wayne Decatur, David Canner, Joel L. Sussman, Karsten Theis, Angel Herraez

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 ====MS-DOS morph2.exe====
-A very simple program, named '''morph2.exe''', performs linear interpolation and has been freely available since the late 1990's in the ''PDBTools'' package by Eric Martz.<ref>[http://www.umass.edu/microbio/rasmol/pdbtools.htm PDBTools] by Eric Martz include a simple linear interpolation morphing program. This program operates only in MS-DOS (under MS Windows), but the C source code is included. Available within ''Protein Explorer'' are [http://www.umass.edu/microbio/chime/morpher/morphmtd.htm step by step instructions] for making linear interpolation morphs.</ref>. This program, which was used for most of the morphs made by Martz (including the one on this page), requires that the two starting PDB files contain exactly the same atoms in exactly the same order. (Achieving this usually requires some hand editing of the PDB files.) Its advantages include that it is straightforward to include ligand in the morph, or at the end of the morph, and to include multiple protein and nucleic acid chains. [http://www.umass.edu/microbio/chime/morpher/morphmtd.htm Step by step instructions] are available within ''Protein Explorer''. While these instructions were written for Chime, rather than Jmol, everything there applies equally to Jmol except the last section on ''Playback Scripts''. Caution: check the results -- morph2.exe appears to fail with very large PDB files but its limits have not been defined.
+A very simple program, named '''morph2.exe''', performs linear interpolation and has been freely available since the late 1990's in the ''PDBTools'' package by Eric Martz.<ref>[http://www.umass.edu/microbio/rasmol/pdbtools.htm PDBTools] by Eric Martz include a simple linear interpolation morphing program. This program operates only in MS-DOS (under MS Windows), but the C source code is included. Available within ''Protein Explorer'' are [http://www.umass.edu/microbio/chime/morpher/morphmtd.htm step by step instructions] for making linear interpolation morphs.</ref>. This program, which was used for most of the morphs made by Martz (including the Lac repressor morph near the top of this page), requires that the two starting PDB files contain exactly the same atoms in exactly the same order. (Achieving this usually requires some hand editing of the PDB files.) Its advantages include that it is straightforward to include ligand in the morph, or at the end of the morph, and to include multiple protein and nucleic acid chains. [http://www.umass.edu/microbio/chime/morpher/morphmtd.htm Step by step instructions] are available within ''Protein Explorer''. While these instructions were written for Chime, rather than Jmol, everything there applies equally to Jmol except the last section on ''Playback Scripts''. Caution: check the results -- morph2.exe appears to fail with very large PDB files but its limits have not been defined.
 ===Animating Morph PDB Files===