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* [[Hexokinase#Conformational_change_associated_with_substrate_binding]] | * [[Hexokinase#Conformational_change_associated_with_substrate_binding]] | ||
* [[Calmodulin#Calmodulin_in_Motion]] | * [[Calmodulin#Calmodulin_in_Motion]] | ||
* [[Human lactoferrin]] | |||
===Morphs Elsewhere=== | ===Morphs Elsewhere=== | ||
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* 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: | * 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> | 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> | ||
* [[Protein Explorer]] developed by [[User:Eric Martz|Eric Martz]] at the University of Massachusetts, Amherst, USA.<ref name='pe'>Protein Explorer: easy yet powerful macromolecular visualization. Martz, E., Trends Biochem Sci. 27:107-9. 2002. [http://www.ncbi.nlm.nih.gov/pubmed/11852249 PubMed 11852249] developed by [[User:Eric Martz|Eric Martz]] at the University of Massachusetts, Amherst, USA.</ref> | * [[Protein Explorer]] developed by [[User:Eric Martz|Eric Martz]] at the University of Massachusetts, Amherst, USA.<ref name='pe'>Protein Explorer: easy yet powerful macromolecular visualization. Martz, E., Trends Biochem Sci. 27:107-9. 2002. [http://www.ncbi.nlm.nih.gov/pubmed/11852249 PubMed 11852249] developed by [[User:Eric Martz|Eric Martz]] at the University of Massachusetts, Amherst, USA.</ref> Note that Protein Explorer went out of service in the early 2000's because it was built around [[Chime]]. Chime was not open source, and its owners ceased to maintain it. | ||
* Database of the Morphit Pro server [http://morphit-pro.cmp.uea.ac.uk/MorphItPro/faces/faces/listMorphs.xhtml?faces-redirect=true]. and associated DynDom software [http://dyndom.cmp.uea.ac.uk/dyndom/dyndomDatabases.jsp#NRD] by Steven Hayward and coworkers at the University of East Anglia, UK. | * Database of the Morphit Pro server [http://morphit-pro.cmp.uea.ac.uk/MorphItPro/faces/faces/listMorphs.xhtml?faces-redirect=true]. and associated DynDom software [http://dyndom.cmp.uea.ac.uk/dyndom/dyndomDatabases.jsp#NRD] by Steven Hayward and coworkers at the University of East Anglia, UK. | ||
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==Why Morph?== | ==Why Morph?== | ||
<table align='right' border='0' width='285' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'> | <table align='right' border='0' width='285' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'> | ||
[[Image:Mage_hb.gif]]</td></tr><tr><td bgcolor='#e8e8e8'>Toggling between the carbonmonoxy and deoxy conformations of heme in hemoglobin. (This is NOT a morph.) Convergent stereo snapshots from a Kinemage. (Stops after 25 cycles; | [[Image:Mage_hb.gif]]</td></tr><tr><td bgcolor='#e8e8e8'>Toggling between the carbonmonoxy and deoxy conformations of heme in hemoglobin. (This is NOT a morph.) Convergent stereo snapshots from a Kinemage. (Stops after 25 cycles; Shift-Reload this page to restart the toggling.)</td></tr></table> | ||
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. | 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. | In contrast, predicting the actual trajectory through which a conformational change occurs is rarely, if ever, the goal of a morph. | ||
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===True Movies=== | ===True Movies=== | ||
<table align='right' border='0' width='184' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'> | <table align='right' border='0' width='184' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'> | ||
[[Image:Lacrep_anim_small.gif]]</td></tr><tr><td bgcolor='#e8e8e8'>True movie of the morph shown in Jmol elsewhere near the top of this page. (Stops after 100 cycles; | [[Image:Lacrep_anim_small.gif]]</td></tr><tr><td bgcolor='#e8e8e8'>True movie of the morph shown in Jmol elsewhere near the top of this page. (Stops after 100 cycles; Shift-Reload this page to restart this movie.)</td></tr></table> | ||
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. | 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. | ||
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====Proteopedia PyMOL Morpher==== | ====Proteopedia PyMOL Morpher==== | ||
'''<font color="magenta">Recommended</font>'''. Proteopedia provides a page http://proteopedia.org/cgi-bin/morph that sends a morph request to the [https://pymol.org/2/ PyMOL program] and automatically uploads the resulting multi-model file to proteopedia. An example of a morph made by the server is [http://proteopedia.org/wiki/index.php/Image:Morph_semet_apo-chaind.pdb_zn_complex-chaina.pdb_u4043.pdb here], and it is shown on this [http://proteopedia.org/wiki/index.php/User:Kristian_Koski/P4H#flexible_loops page]. | '''<font color="magenta">Recommended</font>'''. Proteopedia provides a page http://proteopedia.org/cgi-bin/morph that sends a morph request to the [https://pymol.org/2/ PyMOL program] and automatically uploads the resulting multi-model file to proteopedia. An example of a morph made by the server is [http://proteopedia.org/wiki/index.php/Image:Morph_semet_apo-chaind.pdb_zn_complex-chaina.pdb_u4043.pdb here], and it is shown when you click the green links on this [http://proteopedia.org/wiki/index.php/User:Kristian_Koski/P4H#flexible_loops page]. | ||
Advantages: | Advantages: | ||
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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." | 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." | ||
Limitations: FATCAT does only one chain from each model. | Limitations: FATCAT does only one chain from each model. Chains are re-numbered so it is time consuming to relate the new numbers to the original sequence numbers. In the resulting morph, it appears that some changes may be made to at least one model even when a "rigid" alignment is specified. | ||
====Biomolecular Morphing by Kleywegt at Uppsala==== | ====Biomolecular Morphing by Kleywegt at Uppsala==== | ||
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====Yale Morph Server==== | ====Yale Morph Server==== | ||
<!--''SADLY, AS OF 2020, THE YALE MORPH SERVER AND GALLERY OF MOLECULAR MOVEMENTS HAS BEEN OFFLINE FOR A NUMBER OF YEARS.''--> | |||
''NOT WORKING AGAIN in January 2023. STILL NOT WORKING November 2024.'' | |||
''WORKING AGAIN in February, 2021. Their animation player doesn't work because it still requires Java, but you can download the morph PDB file and animate it in Proteopedia or Jmol. See [[#Animating Morph PDB Files|instructions below]].'' | ''WORKING AGAIN in February, 2021. Their animation player doesn't work because it still requires Java, but you can download the morph PDB file and animate it in Proteopedia or Jmol. See [[#Animating Morph PDB Files|instructions below]].'' | ||
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===Combination of rigid body movement and linear interpolation=== | ===Combination of rigid body movement and linear interpolation=== | ||
To explore conformational changes on the fly within Jmol, the storymorph suite | To explore conformational changes on the fly within Jmol, the storymorph suite defines several Jmol functions to superimpose and morph related structures. The method is described in detail at [[Jmol/Storymorph]], together with some demonstrations and interactive examples. | ||
===Animating Morph PDB Files=== | ===Animating Morph PDB Files=== | ||
If you upload your multiple-model morph PDB file to Proteopedia, animating it is as simple as checking that option in Proteopedia's | If you upload your multiple-model morph PDB file to Proteopedia, animating it is as simple as checking that option in Proteopedia's [[Scene authoring tools]]. | ||
<blockquote> | <blockquote> | ||
For those who wish to make their own animation scripts in [[Jmol/Application|Jmol]] outside of Proteopedia (e.g. in the [http://bioinformatics.org/jmol-tutorials Jmol Tutorial-Authoring Template]), the script required to animate a multiple-model PDB file in Jmol is much simpler than what was needed in Chime. Here are the commands needed in Jmol: | For those who wish to make their own animation scripts in [[Jmol/Application|Jmol]] outside of Proteopedia (e.g. in the [http://bioinformatics.org/jmol-tutorials Jmol Tutorial-Authoring Template]), the script required to animate a multiple-model PDB file in Jmol is much simpler than what was needed in Chime. Here are the commands needed in Jmol: | ||