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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 * 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>
-* [[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.
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 ==Why Morph?==
 <table align='right' border='0' width='285' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'>&nbsp;</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; reload this page to restart the toggling.)</td></tr></table>
+[[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.
 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===
 <table align='right' border='0' width='184' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'>&nbsp;</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; reload this page to restart this movie.)</td></tr></table>
+[[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.
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 ====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.''
-<!--''SADLY, AS OF 2020, THE YALE MORPH SERVER AND GALLERY OF MOLECULAR MOVEMENTS HAS BEEN OFFLINE FOR A NUMBER OF YEARS.''-->
 ''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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 ===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 ''Scene Authoring Tool''.
+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>
 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: