{"id":148,"date":"2008-06-15T11:52:23","date_gmt":"2008-06-15T11:52:23","guid":{"rendered":"http:\/\/occamstypewriter.org\/rpg\/2008\/06\/15\/all_i_see_is_you\/"},"modified":"2008-06-15T11:52:23","modified_gmt":"2008-06-15T11:52:23","slug":"all_i_see_is_you","status":"publish","type":"post","link":"https:\/\/occamstypewriter.org\/rpg\/2008\/06\/15\/all_i_see_is_you\/","title":{"rendered":"All I see is you"},"content":{"rendered":"<p>You know those stereo images so belov\u00e9d of structural-type people?  The ones you get in journals where you&#8217;re supposed to be able to squint somehow and see it in 3-D?<\/p>\n<p>\nI&#8217;ve never been able to pull off that trick.  Never been able to see those silly &#8216;Magic Eye&#8217; things either.  Must be something to do with being a predator \u2014 evolutionarily it&#8217;s good to see what&#8217;s really there, rather than some abstract shape that may or may not be lunch, or in the worst case, something with sharper teeth and bigger claws than me.<\/p>\n<p>\nWhich, if structural biology is in the genes, probably puts my children at an evolutionary disadvantage, but hey. <\/p>\n<p>\nThree-dimensional visualization of protein structures is not to be dismissed lightly.  You cannot truly grok a protein structure until you have seen it in 3-D, run your fingers lightly over its crevasses and curves, felt its binding pockets and smelled its van der Waals radii. <\/p>\n<p>\n(Maybe that latter was a bit <em>too<\/em> poetic).<\/p>\n<p>\nI tend to do all that on a screen, with 3-D glasses. The first time a lysine side-chain brushes your nose you&#8217;ll never want to go back to 2-D. But it&#8217;s (a) quite expensive to get 3-D on LCD screens and (b) everyone prints the figures out anyway. So structural biologists are wont to print stereo diagrams in their papers.  My previous boss, who must have suffered from the same sort of evolutionary history, kept a set of viewers in his drawer.  These are two glass lenses in a metal frame, with swinging metal legs so that you could place the things over a picture, peer down and see in stereo.  Very useful, simple to operate, and almost impossible to replace if <del>stolen<\/del> lost or broken.<\/p>\n<p>\nSo for the last couple of years I&#8217;ve been reduced to either squinting (and looking out for larger predators) or giving up in disgust, going to the <a href=\"http:\/\/www.rcsb.org\/pdb\/home\/home.do\">PDB<\/a>, downloading the files and trying to imagine it in 3-D by rotating the thing on my screen.<\/p>\n<p>\nBut a couple of weeks ago in the office I came across a veritable wonder of modern technology.  Ladles and gentlespoons, I present the Stereopticon 707:<\/p>\n<p>\n<a href=\"http:\/\/www.flickr.com\/photos\/pommiebastards\/2579564539\/\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/farm4.static.flickr.com\/3036\/2579564539_2a37882ec6.jpg\" alt=\"\" width=\"462\" height=\"500\" \/><\/a><\/p>\n<p>\nThis flimsy bit of card with two plastic lenses actually folds flat, and what&#8217;s more, does exactly what it claims to.  It is so simple, so easy to use and <a href=\"http:\/\/www.stereopticon.com\/\">cheap<\/a> that I can&#8217;t help thinking it should come with every undergraduate textbook.<\/p>\n<p>\n<a href=\"http:\/\/www.flickr.com\/photos\/pommiebastards\/2579564231\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/farm4.static.flickr.com\/3176\/2579564231_2cd8e813f7.jpg\" alt=\"\" width=\"494\" height=\"500\" \/><\/a><br \/>\n<em>Side elevation<\/em><\/p>\n<p>\nIsn&#8217;t she just wonderful?<\/p>\n<p>\n<a href=\"http:\/\/www.flickr.com\/photos\/pommiebastards\/2579563719\/\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/farm4.static.flickr.com\/3050\/2579563719_84cfe8f58e.jpg\" alt=\"\" width=\"500\" height=\"443\" \/><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>You know those stereo images so belov\u00e9d of structural-type people? The ones you get in journals where you&#8217;re supposed to be able to squint somehow and see it in 3-D? I&#8217;ve never been able to pull off that trick. Never &hellip; <a href=\"https:\/\/occamstypewriter.org\/rpg\/2008\/06\/15\/all_i_see_is_you\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-148","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/occamstypewriter.org\/rpg\/wp-json\/wp\/v2\/posts\/148","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/occamstypewriter.org\/rpg\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/occamstypewriter.org\/rpg\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/rpg\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/rpg\/wp-json\/wp\/v2\/comments?post=148"}],"version-history":[{"count":0,"href":"https:\/\/occamstypewriter.org\/rpg\/wp-json\/wp\/v2\/posts\/148\/revisions"}],"wp:attachment":[{"href":"https:\/\/occamstypewriter.org\/rpg\/wp-json\/wp\/v2\/media?parent=148"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/occamstypewriter.org\/rpg\/wp-json\/wp\/v2\/categories?post=148"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/occamstypewriter.org\/rpg\/wp-json\/wp\/v2\/tags?post=148"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}