{"id":903,"date":"2013-07-06T16:59:41","date_gmt":"2013-07-06T15:59:41","guid":{"rendered":"http:\/\/www.blopig.com\/blog\/?p=903"},"modified":"2020-12-09T13:27:34","modified_gmt":"2020-12-09T13:27:34","slug":"making-protein-protein-interfaces-look-decently-good","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2013\/07\/making-protein-protein-interfaces-look-decently-good\/","title":{"rendered":"Making Protein-Protein Interfaces Look (decently) Good"},"content":{"rendered":"<p>This is a little PyMOL script that I&#8217;ve used to draw antibody-antigen interfaces. If you&#8217;d like a commented version on what each and every line does, <a href=\"mailto:jinwoo.leem@st-annes.ox.ac.uk\">contact me<\/a>! This is a slight modification of what has been done in <a href=\"http:\/\/www.pymolwiki.org\/index.php\/Gallery\">PyMOL Wiki<\/a>.<\/p>\n<pre class=\"lang:default decode:true\">load FILENAME\nset_name FILENAME, complex\t\n\nset bg_rgb, [1,1,1]  \t\n\ncolor white \t     \t\t\n\nhide lines\nshow cartoon\n\nselect antibody, chain a\nselect antigen, chain b\n\nselect paratopeAtoms, antibody within 4.5 of antigen \nselect epitopeAtoms, antigen within 4.5 of antibody\n\nselect paratopeRes, byres paratopeAtoms\nselect epitopeRes, byres epitopeAtoms\n\ndistance interactions, paratopeAtoms, epitopeAtoms, 4.5, 0\n\ncolor red, interactions\nhide labels, interactions\n\nshow sticks, paratopeRes\nshow sticks, epitopeRes\n\nset cartoon_side_chain_helper, on\n\nset sphere_quality, 2\nset sphere_scale, 0.3\nshow spheres, paratopeAtoms\nshow spheres, epitopeAtoms\ncolor tv_blue, paratopeAtoms\ncolor tv_yellow, epitopeAtoms\n\nset ray_trace_mode, 3\nunset depth_cue\nset specular, 0.5<\/pre>\n<p>Once you orient it to where you&#8217;d like it and ray it, you should get something like this.<br \/>\n<a href=\"https:\/\/i0.wp.com\/www.blopig.com\/blog\/wp-content\/uploads\/2013\/07\/contacts.png?ssl=1\"><img data-recalc-dims=\"1\" decoding=\"async\" loading=\"lazy\" class=\"aligncenter size-large wp-image-905\" alt=\"contacts\" src=\"https:\/\/i0.wp.com\/www.blopig.com\/blog\/wp-content\/uploads\/2013\/07\/contacts.png?resize=625%2C283&#038;ssl=1\" width=\"625\" height=\"283\" srcset=\"https:\/\/i0.wp.com\/www.blopig.com\/blog\/wp-content\/uploads\/2013\/07\/contacts.png?resize=1024%2C465&amp;ssl=1 1024w, https:\/\/i0.wp.com\/www.blopig.com\/blog\/wp-content\/uploads\/2013\/07\/contacts.png?resize=300%2C136&amp;ssl=1 300w, https:\/\/i0.wp.com\/www.blopig.com\/blog\/wp-content\/uploads\/2013\/07\/contacts.png?resize=624%2C283&amp;ssl=1 624w, https:\/\/i0.wp.com\/www.blopig.com\/blog\/wp-content\/uploads\/2013\/07\/contacts.png?w=1205&amp;ssl=1 1205w\" sizes=\"auto, (max-width: 625px) 100vw, 625px\" \/><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>This is a little PyMOL script that I&#8217;ve used to draw antibody-antigen interfaces. If you&#8217;d like a commented version on what each and every line does, contact me! This is a slight modification of what has been done in PyMOL Wiki. load FILENAME set_name FILENAME, complex set bg_rgb, [1,1,1] color white hide lines show cartoon [&hellip;]<\/p>\n","protected":false},"author":22,"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],"tags":[],"ppma_author":[511],"class_list":["post-903","post","type-post","status-publish","format-standard","hentry","category-code","category-howto","category-molecular-visualization"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":511,"user_id":22,"is_guest":0,"slug":"jinwoo","display_name":"Jinwoo Leem","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/65d338dc0b03d3026aa9a98f5e43889ca6c9ac9d0f45fe65ea5931207597ce2d?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\/903","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\/22"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=903"}],"version-history":[{"count":5,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/903\/revisions"}],"predecessor-version":[{"id":6344,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/903\/revisions\/6344"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=903"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=903"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=903"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=903"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}