Morphs: Difference between revisions

* [[User:Luis E Ramirez-Tapia/T7 RNA polymerase|T7 RNA Polymerase]]

* [[Lipase lid morph]]

===Morphs Elsewhere===

* Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis, [http://molmovdb.org molmovdb.org], developed by Mark Gerstein and coworkers at Yale University, USA.<ref name='flores'>The Database of Macromolecular Motions:

new features added at the decade mark. Flores, S. ''et al.'', Nucleic Acids Res., .34 (Database issue) D1–D6. 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16381870 PubMed 16381870], [http://papers.gersteinlab.org/e-print/molmovdb-update-nar/preprint.pdf PDF].</ref><ref>Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis, [http://molmovdb.org molmovdb.org], developed by Mark Gerstein and coworkers at Yale University, USA.</ref>

===Non-Morph Animations===

==Why Morph?==

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The purpose of molecular morphing is to smooth the visual transition between two molecular conformations, making it easier to see and understand the structural differences between them.

In contrast, predicting the actual trajectory through which a conformational change occurs is rarely, if ever, the goal of a morph.

When the differences are small, simply toggling an image between the two states is adequate. [http://kinemage.biochem.duke.edu/ David Richardson's MAGE]<ref>[http://kinemage.biochem.duke.edu/ Kinemages] by David and Jane Richardson, Duke University, USA.</ref>, first available in 1992<ref name='history'>[http://history.molviz.org History of Macromolecular Visualization]</ref> supports visual toggling between macromolecular conformations. Hundreds of interactive molecular structure tutorials called kinemages take advantage of this capability. At the right are snapshots of hemoglobin toggled in MAGE. (MAGE is available in java applet form, and is an option for molecular displays in Proteopedia<ref>For sample pages that use the MAGE applet in Proteopedia, see [[Hemoglobin]] and [[Ribulose-1,5-bisphosphate carboxylase/oxygenase]]</ref>.)

===True Movies===

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A true movie is a series of static snaphots displayed sequentially in rapid succession. An example of a true movie of a morph is shown at right. Note that you '''cannot rotate the molecule with the mouse''', so you can view the morph from only the single perspective chosen by the author of the movie. Also, a separate movie must be provided for each change in rendering or coloring, while the rendering and coloring in Jmol can be easily be changed with script commands while displaying the same morph PDB file.

==Morphing Methods==

Before making a new morph from published PDB files, search the [http://molmovdb.org/cgi-bin/movie.cgi Gallery of Morphs] where you will find thousands of morphs from jobs previously submitted to the [http://molmovdb.org Yale Morph Server] (see below). It is quite possible that your morph has already been made, and is already available there!

====Proteopedia PyMOL Morpher====

Advantages:

The [http://fatcat.godziklab.org FATCAT Structural Alignment Server] also produces "chemically possible" morphs. After an optionally flexible alignment (permitting twists at hinge points determined by FATCAT), a linear interpolation is done between the aligned models. Then "the intermediate structures are optimized by energy gradient minimization employing a reduced representation force field."

====Biomolecular Morphing by Kleywegt at Uppsala====

====Yale Morph Server====

===Linear Interpolation===

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.

====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 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===

<blockquote>

<pre>

anim mode palindrome;