Art:Molecular Sculpture: Difference between revisions

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[https://en.wikipedia.org/wiki/Dorothy_Hodgkin Dorothy Crowfoot Hodgkin] (1910-1994) was an eminent and ground-breaking crystallographer, who won the [[Nobel Prizes for 3D Molecular Structure|1964 Nobel Prize in Chemistry]] for solving the ~~structure~~ of vitamin B12 ~~in the~~ mid-1950's<ref name="crowfoot-v">PMID:13348621</ref>. In 1945, she solved the structure of penicillin. The structure had been controversial prior to her work, published in 1949<ref name="crowfoot-p">PMID:18134678</ref>. In 1971, she was a member of the team solving the structure of insulin<ref name="crowfoot-i">PMID:4932997</ref>.

<table align="right"

style="margin-left:8px;padding-left:5px;padding-right:5px;background-color:#e0e0e0;" width="610"><tr><td>

[[Image:Molecular model of Penicillin by Dorothy Hodgkin.jpg|600px]]

</td></tr><tr><td>

Molecular model of penicillin by Dorothy Crowfoot Hodgkin, ca. 1945. Behind the model are projections of the [[electron density map]].

By Science Museum London / [http://www.scienceandsociety.co.uk/ Science and Society Picture Library]. [https://creativecommons.org/licenses/by-sa/2.0 Creative Commons Attribution-Share Alike 2.0 License]. Source: [https://commons.wikimedia.org/w/index.php?curid=28024341 Wikimedia Commons].

</td></tr></table>

[https://en.wikipedia.org/wiki/Dorothy_Hodgkin Dorothy Crowfoot Hodgkin]<ref>''Dorothy Hodgkin, a life'' by Georgina Ferry, first published 1998 by Granta Books. 2014 edition by Bloomsbury Reader. 528 pages.</ref> (1910-1994) was an eminent and ground-breaking crystallographer, who won the [[Nobel Prizes for 3D Molecular Structure|1964 Nobel Prize in Chemistry]] for pioneering X-ray diffraction work that included solving the structures of penicillin (1949<ref name="crowfoot-p" />) and vitamin B12 (mid-1950's<ref name="crowfoot-v">PMID:13348621</ref>). She was 69th to win the Nobel in Chemistry, but only [https://en.wikipedia.org/wiki/List_of_Nobel_laureates_in_Chemistry the third woman to win it], after Marie Curie and her daughter Irène Joliot-Curie<ref>In 2018, only one additional woman has won the [https://en.wikipedia.org/wiki/List_of_Nobel_laureates_in_Chemistry Nobel Prize in Chemistry], making four out of 177: Ada Yonath.</ref>. In 1945, she solved the structure of penicillin. The structure had been controversial prior to her work, published in 1949<ref name="crowfoot-p">PMID:18134678</ref>. In 1971, she was a member of the team solving the structure of insulin<ref name="crowfoot-i">PMID:4932997</ref>. The insulin structure was solved at the time the [[Protein Data Bank]] was being founded, and was not deposited until 1980 as 1ins, superceded by [[4ins]] in 1989<ref>[http://History.Molviz.Org See <i>Earliest Solutions for Macromolecular Crystal Structures</i> at History.MolviZ.Org].</ref>.

An excellent 4.5 minute video by Huy Do Duc (Hochschule für Technik und Wirtschaft, Dresden) explains the science behind this model. The video is available at the [https://www.mhs.ox.ac.uk/backfromthedead/exhibition/the-structure-of-penicillin/ Museum of the History of Science] (Oxford, UK).

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When it comes to larger sculptures, Miramodus "Giant Models" make a striking impression: see the photo of the nylon monomer, above left.

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An example illustrating the importance of models from Byron's Bender occurred at a scientific meeting in the mid 1970's. At this time, less than two dozen protein structures had been solved. David Davies brought a Bender model of an immunoglobulin Fab fragment, and Jane and David Richardson brought a Bender model of superoxide dismutase. While comparing these physical models at the meeting, they realized that both proteins use a similar fold, despite having only about 9% sequence identity. This incident<ref name="benderig">PMID: 1271464</ref> was the first recognition of the occurrence of what is now recognized as the immunoglobulin superfamily domain in proteins that are apparently unrelated by sequence.

Byron's Bender remained available through the 1990's. Tim Herman, then of the Medical College of Wisconsin (later he founded<ref name="3dmd" /><ref name="cbm" />) was one of its last avid users. Tim brought the Bender into local high schools and taught teachers and groups of students how to construct models.

Byron's Bender remained available through the 1990's. [[#Tim_Herman|Tim Herman]], then of the Medical College of Wisconsin (later he founded<ref name="3dmd" /><ref name="cbm" />) was one of its last avid users. Tim brought the Bender into local high schools and taught teachers and groups of students how to construct models.

Aside from the importance of the tactile as well as visual input these models provide, another of their great strengths is that they jiggle and vibrate when handled, thereby simulating thermal motion. Too often users of computer models lose sight of the fact that protein molecules in living systems are constantly flexing due to thermal motion.

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Shortly after conceiving the idea for his [[#Byron's Bender|Bender]], crystallographer Byron Rubin realized that the machine used in Midas Muffler shops to customize automobile tailpipes operated on a similar principle, but at larger scale. He collaborated with the local shop to construct a backbone sculpture of rubredoxin about 5 feet high from stainless steel tailpipe. Rubin's rubredoxin sculpture ~~(not shown<ref>We have been unable to obtain a photograph of this sculpture. If you can provide one, please send it to {{Contact}}.</ref>)~~ won the Chandler competetion at the University of North Carolina in 1973. It stood in the lobby of the Paul M. Gross Chemistry Building at Duke University, Durham NC USA from 1973-2008. Since 2008 it has been in the atrium of the French Family Science Center at Duke.

Shortly after conceiving the idea for his [[#Byron's Bender|Bender]], crystallographer Byron Rubin realized that the machine used in Midas Muffler shops to customize automobile tailpipes operated on a similar principle, but at larger scale. He collaborated with the local shop to construct a backbone sculpture of rubredoxin about 5 feet high from stainless steel tailpipe. Rubin's rubredoxin sculpture won the Chandler competetion at the University of North Carolina in 1973. It stood in the lobby of the Paul M. Gross Chemistry Building at Duke University, Durham NC USA from 1973-2008. Since 2008 it has been in the atrium of the French Family Science Center at Duke.

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Jane S. Richardson's hand drawn ribbon representation of triose phosphate isomerase, published in 1980<ref name="jsr80" />. Image from [https://commons.wikimedia.org/wiki/File:TIM-end_ribbon_shaded.png Wikimedia Commons], under the [https://creativecommons.org/licenses/by/4.0/deed.en Creative Commons Attribution 4.0 International] license.

For photos of Jane Richardson and more examples of her beautiful drawings, see ''[https://stories.duke.edu/sciences-mother-of-ribbon-diagrams-celebrates-50-years-at-duke Science’s ‘Mother of Ribbon Diagrams’ celebrates 50 years at Duke]''.

</td></tr></table>

Crystallographer Jane Richardson is not known for protein molecular sculpture, aside from her involvement with wire models made with [[#Byron's Bender|Byron's Bender]]<ref name="bender72" /><ref name="benderig" />. However, she made an indelible impact on protein sculptors by introducing and popularizing simplified and beautiful drawings of protein backbones starting in 1980, notably schematic ribbon diagrams<ref name="jsr80">PMID:19431356</ref><ref>PMID:7020376</ref><ref>PMID:4079792</ref><ref>PMID:3853075</ref><ref>PMID:1477272</ref>.

Crystallographer Jane Richardson is not known for protein molecular sculpture, aside from her involvement with wire models made with [[#Byron's Bender|Byron's Bender]]<ref name="bender72" /><ref name="benderig" />. However, she made an indelible impact on protein sculptors by introducing and popularizing simplified and beautiful drawings of protein backbones starting in 1980, notably schematic ribbon diagrams<ref name="jsr80">PMID:19431356</ref><ref>PMID:7020376</ref><ref>PMID:4079792</ref><ref>PMID:3853075</ref><ref>PMID:1477272</ref><ref>PMID:10932243</ref>.

By simplifying protein models from imponderable masses of atoms to elegant ribbon diagrams, she facilitated scientists' understanding of protein folds and their families and superfamilies. Her influence can be seen ~~in the work of~~ [[#Mara G. Haseltine|Mara G. Haseltine]] and in the later sculptures of [[#MolecularSculpture.Com|Byron Rubin]].

By simplifying protein models from imponderable masses of atoms to elegant ribbon diagrams, she facilitated scientists' understanding of protein folds and their families and superfamilies. Her influence can be seen some sculptures by [[#Mara G. Haseltine|Mara G. Haseltine]], glass blocks by [[#Patrick Goldsmith|Patrick Goldsmith]], and in the later sculptures of [[#MolecularSculpture.Com|Byron Rubin]].

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==Arthur Olson==

[http://mgl.scripps.edu/ Molecular Graphics Laboratory]

Arthur Olson founded the [http://mgl.scripps.edu/ Molecular Graphics Laboratory] in 1981 at The Scripps Research Institute. Jon Huntoon joined around 2005 to set up a 3D printing service, the [http://models.scripps.edu Scripps Physical Model Service], which ran until 2017. The Olson group pioneered ''Augmented Reality'', where a hand-held physical model is rendered via camera on a computer, with additional structures or properties represented, responding to manual manipulation in real time<ref>PMID:15794144</ref><ref>PMID:15766549</ref>. Olson participated in David Goodsell's Molecular Graphics Art Shows in [http://mgl.scripps.edu/people/goodsell/mgs_art/mgs_art.html 1994] and [http://mgl.scripps.edu/people/goodsell/mgs_art/mgs_art2/index.html 1998].

(Awaiting permission to reproduce an image here.)

==Stephen Darling==

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[http://luminorum.com Luminorum.Com], founded in 2005 by father and son Patrick and Alex Goldsmith, sculpts laser-etched protein molecules and other objects into optical-quality glass blocks.

{| align="left" width="210" style="background-color:e0e0e0;margin:10px;"

|-

|

Image:Luninorum-penicillin-in-glass.png|200px

default [https://www.facebook.com/patrick.goldsmith.96/videos/10201822796030051/]

</imagemap>

|-

| Penicillin molecular model in glass, rendered by Luminorum. Click to play video.

|}

Luminorum has rendered in glass [[#Dorothy Crowfoot Hodgkin|Dorothy Crowfoot Hodgkin]]'s 1945 structure of penicillin. [https://www.facebook.com/patrick.goldsmith.96/videos/10201822796030051/ A video is available] through [https://www.facebook.com/Luminorum-Ltd-424298224307551/ Luminorum's Facebook page].

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:Homologous Hope is a delicate work of art that floats like a cloud above the atrium. Patients and their families entering the building look up and see hope on the horizon, hope inspired by the generosity of the Grays, by the creative environment of University, and by the efforts of the dedicated doctors and scientists.

In 2016, Hasentine installed [https://www.clotmag.com/oped/a-sculpture-for-the-age-of-corona-virus-dancing-on-the-line-between-art-and-scientific-discovery-by-mara-g-haseltine ''SARS Inhibited'' in a reflecting pool in Singapore's Biopolis]. Twelve meters wide, it represents a backbone trace of an X-ray structure of the main SARS protease [[1p9s]].

==Eckhardt, Karim & Rehbein==

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==See Also==

*[[Byron's Bender]]

*[[:Category:PDB Art]]

*[[History of Macromolecular Visualization]]

*[[Molecular modeling and visualization software]]

*{{Template:Francoeur-2011-Talk}}

==Notes & References==

[[Category: PDB Art]]

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 </td></tr></table>
-[https://en.wikipedia.org/wiki/Dorothy_Hodgkin Dorothy Crowfoot Hodgkin] (1910-1994) was an eminent and ground-breaking crystallographer, who won the [[Nobel Prizes for 3D Molecular Structure|1964 Nobel Prize in Chemistry]] for solving the structure of vitamin B12 in the mid-1950's<ref name="crowfoot-v">PMID:13348621</ref>. In 1945, she solved the structure of penicillin. The structure had been controversial prior to her work, published in 1949<ref name="crowfoot-p">PMID:18134678</ref>. In 1971, she was a member of the team solving the structure of insulin<ref name="crowfoot-i">PMID:4932997</ref>.
+<table align="right"
+style="margin-left:8px;padding-left:5px;padding-right:5px;background-color:#e0e0e0;" width="610"><tr><td>
+[[Image:Molecular model of Penicillin by Dorothy Hodgkin.jpg|600px]]
+</td></tr><tr><td>
+Molecular model of penicillin by Dorothy Crowfoot Hodgkin, ca. 1945. Behind the model are projections of the [[electron density map]].
+By Science Museum London / [http://www.scienceandsociety.co.uk/ Science and Society Picture Library]. [https://creativecommons.org/licenses/by-sa/2.0 Creative Commons Attribution-Share Alike 2.0 License]. Source: [https://commons.wikimedia.org/w/index.php?curid=28024341 Wikimedia Commons].
+</td></tr></table>
+[https://en.wikipedia.org/wiki/Dorothy_Hodgkin Dorothy Crowfoot Hodgkin]<ref>''Dorothy Hodgkin, a life'' by Georgina Ferry, first published 1998 by Granta Books. 2014 edition by Bloomsbury Reader. 528 pages.</ref> (1910-1994) was an eminent and ground-breaking crystallographer, who won the [[Nobel Prizes for 3D Molecular Structure|1964 Nobel Prize in Chemistry]] for pioneering X-ray diffraction work that included solving the structures of penicillin (1949<ref name="crowfoot-p" />) and vitamin B12 (mid-1950's<ref name="crowfoot-v">PMID:13348621</ref>). She was 69th to win the Nobel in Chemistry, but only [https://en.wikipedia.org/wiki/List_of_Nobel_laureates_in_Chemistry the third woman to win it], after Marie Curie and her daughter Irène Joliot-Curie<ref>In 2018, only one additional woman has won the [https://en.wikipedia.org/wiki/List_of_Nobel_laureates_in_Chemistry Nobel Prize in Chemistry], making four out of 177: Ada Yonath.</ref>. In 1945, she solved the structure of penicillin. The structure had been controversial prior to her work, published in 1949<ref name="crowfoot-p">PMID:18134678</ref>. In 1971, she was a member of the team solving the structure of insulin<ref name="crowfoot-i">PMID:4932997</ref>. The insulin structure was solved at the time the [[Protein Data Bank]] was being founded, and was not deposited until 1980 as 1ins, superceded by [[4ins]] in 1989<ref>[http://History.Molviz.Org See <i>Earliest Solutions for Macromolecular Crystal Structures</i> at History.MolviZ.Org].</ref>.
+An excellent 4.5 minute video by Huy Do Duc (Hochschule für Technik und Wirtschaft, Dresden) explains the science behind this model. The video is available at the [https://www.mhs.ox.ac.uk/backfromthedead/exhibition/the-structure-of-penicillin/ Museum of the History of Science] (Oxford, UK).
 {{Clear}}
@@ Line 55: / Line 65: @@
 When it comes to larger sculptures, Miramodus &quot;Giant Models&quot; make a striking impression: see the photo of the nylon monomer, above left.
+{{Template:Francoeur-2011-Talk}}
 {{Clear}}
@@ Line 76: / Line 88: @@
 An example illustrating the importance of models from Byron's Bender occurred at a scientific meeting in the mid 1970's. At this time, less than two dozen protein structures had been solved. David Davies brought a Bender model of an immunoglobulin Fab fragment, and Jane and David Richardson brought a Bender model of superoxide dismutase. While comparing these physical models at the meeting, they realized that both proteins use a similar fold, despite having only about 9% sequence identity. This incident<ref name="benderig">PMID: 1271464</ref> was the first recognition of the occurrence of what is now recognized as the immunoglobulin superfamily domain in proteins that are apparently unrelated by sequence.
-Byron's Bender remained available through the 1990's. Tim Herman, then of the Medical College of Wisconsin (later he founded<ref name="3dmd" /><ref name="cbm" />) was one of its last avid users. Tim brought the Bender into local high schools and taught teachers and groups of students how to construct models.
+Byron's Bender remained available through the 1990's. [[#Tim_Herman|Tim Herman]], then of the Medical College of Wisconsin (later he founded<ref name="3dmd" /><ref name="cbm" />) was one of its last avid users. Tim brought the Bender into local high schools and taught teachers and groups of students how to construct models.
 Aside from the importance of the tactile as well as visual input these models provide, another of their great strengths is that they jiggle and vibrate when handled, thereby simulating thermal motion. Too often users of computer models lose sight of the fact that protein molecules in living systems are constantly flexing due to thermal motion.
@@ Line 89: / Line 101: @@
 </td></tr></table>
-Shortly after conceiving the idea for his [[#Byron's Bender|Bender]], crystallographer Byron Rubin realized that the machine used in Midas Muffler shops to customize automobile tailpipes operated on a similar principle, but at larger scale. He collaborated with the local shop to construct a backbone sculpture of rubredoxin about 5 feet high from stainless steel tailpipe. Rubin's rubredoxin sculpture (not shown<ref>We have been unable to obtain a photograph of this sculpture. If you can provide one, please send it to {{Contact}}.</ref>) won the Chandler competetion at the University of North Carolina in 1973. It stood in the lobby of the Paul M. Gross Chemistry Building at Duke University, Durham NC USA from 1973-2008. Since 2008 it has been in the atrium of the French Family Science Center at Duke.
+Shortly after conceiving the idea for his [[#Byron's Bender|Bender]], crystallographer Byron Rubin realized that the machine used in Midas Muffler shops to customize automobile tailpipes operated on a similar principle, but at larger scale. He collaborated with the local shop to construct a backbone sculpture of rubredoxin about 5 feet high from stainless steel tailpipe. Rubin's rubredoxin sculpture won the Chandler competetion at the University of North Carolina in 1973. It stood in the lobby of the Paul M. Gross Chemistry Building at Duke University, Durham NC USA from 1973-2008. Since 2008 it has been in the atrium of the French Family Science Center at Duke.
 {{Clear}}
@@ Line 139: / Line 151: @@
 </td><td>
 Jane S. Richardson's hand drawn ribbon representation of triose phosphate isomerase, published in 1980<ref name="jsr80" />. Image from [https://commons.wikimedia.org/wiki/File:TIM-end_ribbon_shaded.png Wikimedia Commons], under the [https://creativecommons.org/licenses/by/4.0/deed.en  Creative Commons Attribution 4.0 International] license.
+<br><br>
+For photos of Jane Richardson and more examples of her beautiful drawings, see ''[https://stories.duke.edu/sciences-mother-of-ribbon-diagrams-celebrates-50-years-at-duke Science’s ‘Mother of Ribbon Diagrams’ celebrates 50 years at Duke]''.
 </td></tr></table>
-Crystallographer Jane Richardson is not known for protein molecular sculpture, aside from her involvement with wire models made with [[#Byron's Bender|Byron's Bender]]<ref name="bender72" /><ref name="benderig" />. However, she made an indelible impact on protein sculptors by introducing and popularizing simplified and beautiful drawings of protein backbones starting in 1980, notably schematic ribbon diagrams<ref name="jsr80">PMID:19431356</ref><ref>PMID:7020376</ref><ref>PMID:4079792</ref><ref>PMID:3853075</ref><ref>PMID:1477272</ref>.
+Crystallographer Jane Richardson is not known for protein molecular sculpture, aside from her involvement with wire models made with [[#Byron's Bender|Byron's Bender]]<ref name="bender72" /><ref name="benderig" />. However, she made an indelible impact on protein sculptors by introducing and popularizing simplified and beautiful drawings of protein backbones starting in 1980, notably schematic ribbon diagrams<ref name="jsr80">PMID:19431356</ref><ref>PMID:7020376</ref><ref>PMID:4079792</ref><ref>PMID:3853075</ref><ref>PMID:1477272</ref><ref>PMID:10932243</ref>.
-By simplifying protein models from imponderable masses of atoms to elegant ribbon diagrams, she facilitated scientists' understanding of protein folds and their families and superfamilies. Her influence can be seen in the work of [[#Mara G. Haseltine|Mara G. Haseltine]] and in the later sculptures of [[#MolecularSculpture.Com|Byron Rubin]].
+By simplifying protein models from imponderable masses of atoms to elegant ribbon diagrams, she facilitated scientists' understanding of protein folds and their families and superfamilies. Her influence can be seen some sculptures by [[#Mara G. Haseltine|Mara G. Haseltine]], glass blocks by [[#Patrick Goldsmith|Patrick Goldsmith]], and in the later sculptures of [[#MolecularSculpture.Com|Byron Rubin]].
 {{Clear}}
@@ Line 171: / Line 185: @@
 ==Arthur Olson==
-[http://mgl.scripps.edu/ Molecular Graphics Laboratory]
+Arthur Olson founded the [http://mgl.scripps.edu/ Molecular Graphics Laboratory] in 1981 at The Scripps Research Institute. Jon Huntoon joined around 2005 to set up a 3D printing service, the [http://models.scripps.edu Scripps Physical Model Service], which ran until 2017. The Olson group pioneered ''Augmented Reality'', where a hand-held physical model is rendered via camera on a computer, with additional structures or properties represented, responding to manual manipulation in real time<ref>PMID:15794144</ref><ref>PMID:15766549</ref>. Olson participated in David Goodsell's Molecular Graphics Art Shows in [http://mgl.scripps.edu/people/goodsell/mgs_art/mgs_art.html 1994] and [http://mgl.scripps.edu/people/goodsell/mgs_art/mgs_art2/index.html 1998].
+(Awaiting permission to reproduce an image here.)
 ==Stephen Darling==
@@ Line 241: / Line 257: @@
 [http://luminorum.com Luminorum.Com], founded in 2005 by father and son Patrick and Alex Goldsmith, sculpts laser-etched protein molecules and other objects into optical-quality glass blocks.
+{| align="left" width="210" style="background-color:e0e0e0;margin:10px;"
+|-
+|
+<imagemap>
+Image:Luninorum-penicillin-in-glass.png|200px
+default [https://www.facebook.com/patrick.goldsmith.96/videos/10201822796030051/]
+</imagemap>
+|-
+| Penicillin molecular model in glass, rendered by Luminorum. Click to play video.
+|}
+Luminorum has rendered in glass [[#Dorothy Crowfoot Hodgkin|Dorothy Crowfoot Hodgkin]]'s 1945 structure of penicillin. [https://www.facebook.com/patrick.goldsmith.96/videos/10201822796030051/ A video is available] through [https://www.facebook.com/Luminorum-Ltd-424298224307551/ Luminorum's Facebook page].
 {{Clear}}
@@ Line 312: / Line 340: @@
 :Homologous Hope is a delicate work of art that floats like a cloud above the atrium. Patients and their families entering the building look up and see hope on the horizon, hope inspired by the generosity of the Grays, by the creative environment of University, and by the efforts of the dedicated doctors and scientists.
+In 2016, Hasentine installed [https://www.clotmag.com/oped/a-sculpture-for-the-age-of-corona-virus-dancing-on-the-line-between-art-and-scientific-discovery-by-mara-g-haseltine ''SARS Inhibited'' in a reflecting pool in Singapore's Biopolis]. Twelve meters wide, it represents a backbone trace of an X-ray structure of the main SARS protease [[1p9s]].
 ==Eckhardt, Karim & Rehbein==
@@ Line 356: / Line 386: @@
 ==See Also==
 *[[Byron's Bender]]
+*[[:Category:PDB Art]]
 *[[History of Macromolecular Visualization]]
 *[[Molecular modeling and visualization software]]
+*{{Template:Francoeur-2011-Talk}}
 ==Notes & References==
 <references />
 [[Category: PDB Art]]