{"id":518,"date":"2013-04-21T07:01:00","date_gmt":"2013-04-21T06:01:00","guid":{"rendered":"http:\/\/blopig.com\/blog\/?p=518"},"modified":"2020-12-09T13:23:11","modified_gmt":"2020-12-09T13:23:11","slug":"making-small-molecules-look-good-in-pymol","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2013\/04\/making-small-molecules-look-good-in-pymol\/","title":{"rendered":"Making small molecules look good in PyMOL"},"content":{"rendered":"<p>Another largely&nbsp;plagiarized post for my &#8220;personal notes&#8221; (thanks <a title=\"original pretty small molecule post\" href=\"http:\/\/www.lorieau.com\/methods-and-reference\/molecular-viewers\/30-pymol--ball-and-stick-figures.html\" target=\"_blank\" rel=\"noopener\">Justin Lorieau<\/a>!) and following on from the <a title=\"make proteins look good\" href=\"http:\/\/blopig.com\/blog\/?p=418\">post<\/a> about pretty-fication of macromolecules. &nbsp;For my slowly-progressing confirmation report I needed some beautiful small molecule representation. &nbsp;Here is some PyMOL code:<\/p>\n<pre class=\"toolbar:1 show-plain:3 lang:default decode:true crayon-selected\">show sticks\r\nset ray_opaque_background, off\r\nset stick_radius, 0.1\r\nshow spheres\r\nset sphere_scale, 0.15, all\r\nset sphere_scale, 0.12, elem H\r\ncolor gray40, elem C\r\nset sphere_quality, 30\r\nset stick_quality, 30\r\nset sphere_transparency, 0.0\r\nset stick_transparency, 0.0\r\nset ray_shadow, off\r\nset orthoscopic, 1\r\nset antialias, 2\r\nray 1024,768<\/pre>\n<p>And the result:<\/p>\n<p><a href=\"https:\/\/i0.wp.com\/blopig.com\/blog\/wp-content\/uploads\/2013\/04\/ligand.png\"><img data-recalc-dims=\"1\" decoding=\"async\" loading=\"lazy\" class=\"alignnone size-medium wp-image-520\" src=\"https:\/\/i0.wp.com\/blopig.com\/blog\/wp-content\/uploads\/2013\/04\/ligand-300x225.png?resize=300%2C225\" alt=\"ligand\" width=\"300\" height=\"225\" srcset=\"https:\/\/i0.wp.com\/www.blopig.com\/blog\/wp-content\/uploads\/2013\/04\/ligand.png?resize=300%2C225&amp;ssl=1 300w, https:\/\/i0.wp.com\/www.blopig.com\/blog\/wp-content\/uploads\/2013\/04\/ligand.png?resize=624%2C468&amp;ssl=1 624w, https:\/\/i0.wp.com\/www.blopig.com\/blog\/wp-content\/uploads\/2013\/04\/ligand.png?w=1024&amp;ssl=1 1024w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/a><\/p>\n<p>Beautiful, no?<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Another largely&nbsp;plagiarized post for my &#8220;personal notes&#8221; (thanks Justin Lorieau!) and following on from the post about pretty-fication of macromolecules. &nbsp;For my slowly-progressing confirmation report I needed some beautiful small molecule representation. &nbsp;Here is some PyMOL code: show sticks set ray_opaque_background, off set stick_radius, 0.1 show spheres set sphere_scale, 0.15, all set sphere_scale, 0.12, elem [&hellip;]<\/p>\n","protected":false},"author":6,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[29,14,351,31,201,15],"tags":[133,132,134],"ppma_author":[483],"class_list":["post-518","post","type-post","status-publish","format-standard","hentry","category-code","category-howto","category-molecular-visualization","category-notes","category-small-molecules","category-technical","tag-molecular-graphics","tag-pymol","tag-small-molecules"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":483,"user_id":6,"is_guest":0,"slug":"jp","display_name":"JP Ebejer","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/0c2ee7f7a071e0ff6aebc09ddb6c7bdd90146efeb8dfac34f7724f0b04ceafe8?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/518","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=518"}],"version-history":[{"count":5,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/518\/revisions"}],"predecessor-version":[{"id":6343,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/518\/revisions\/6343"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=518"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=518"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=518"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=518"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}