Morphs: Difference between revisions

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The presence of obvious artifacts of linear interpolation, such as objects passing through each other, can be useful because it reminds viewers that the morph's value is only to help visualize the details of the conformational change -- and is not intended to suggest the actual trajectory of change. An example is the morph of [[Recoverin, a calcium-activated myristoyl switch|Recoverin]], in which the N-linked myristoyl group passes through a protein chain.

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''.

====Linear Morph Server====

[[User:Karsten Theis]] has provided a server for linear interpolation between two PDB files: [http://www.bioinformatics.org/pdbtools/morph2 Linear morph between two PDB files]. Use with caution as it has not yet been tested thoroughly.

====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''.

===Animating Morph PDB Files===

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 The presence of obvious artifacts of linear interpolation, such as objects passing through each other, can be useful because it reminds viewers that the morph's value is only to help visualize the details of the conformational change -- and is not intended to suggest the actual trajectory of change. An example is the morph of [[Recoverin, a calcium-activated myristoyl switch|Recoverin]], in which the N-linked myristoyl group passes through a protein chain.
-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''.
+====Linear Morph Server====
+[[User:Karsten Theis]] has provided a server for linear interpolation between two PDB files: [http://www.bioinformatics.org/pdbtools/morph2 Linear morph between two PDB files]. Use with caution as it has not yet been tested thoroughly.
+====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''.
 ===Animating Morph PDB Files===