{"id":592,"date":"2013-04-24T10:24:59","date_gmt":"2013-04-24T10:24:59","guid":{"rendered":"http:\/\/blopig.com\/blog\/?p=592"},"modified":"2013-04-24T13:33:30","modified_gmt":"2013-04-24T12:33:30","slug":"constrain-a-pdb-to-particular-chains","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2013\/04\/constrain-a-pdb-to-particular-chains\/","title":{"rendered":"Constrain a PDB to particular chains"},"content":{"rendered":"<p>In many applications you need to constrain PDB files to certain chains. You can do it using this <a title=\"PDB_constrain\" href=\"http:\/\/www.stats.ox.ac.uk\/~krawczyk\/pdb_constrain.tgz\">program<\/a>.<\/p>\n<p><strong>A. What does it do?<\/strong><\/p>\n<p>Given a pdb file, write out the ATOM and HETATM entries for the supplied chain(s).<\/p>\n<p>PDB_constrain needs three arguments:<\/p>\n<ol>\n<li><span style=\"line-height: 1.714285714;font-size: 1rem\">PDB file to constrain.<\/span><\/li>\n<li><span style=\"line-height: 1.714285714;font-size: 1rem\">Chains from the pdb file to constrain.<\/span><\/li>\n<li><span style=\"line-height: 1.714285714;font-size: 1rem\">Output file.<\/span><\/li>\n<\/ol>\n<p><strong>B. Requirements: <\/strong><\/p>\n<p>Biopython &#8211; should be installed on your machines but in case you want to use it locally, download the <a title=\"Biopython\" href=\"http:\/\/biopython.org\/wiki\/Download\">latest version<\/a> into the PDB_constrain.py&#8217;s directory (don&#8217;t need to build).<\/p>\n<p><strong>C. Example use:<\/strong><\/p>\n<p>C.1 Constrain 1A2Y.pdb to chains A and B &#8211; write results in constr.pdb<\/p>\n<pre class=\"lang:sh decode:true\">python PDB_constrain.py -f 1A2Y.pdb -c AB -o const.pdb<\/pre>\n<p>&nbsp;<\/p>\n<p>C.2 Constrain 1ACY to chain L, write results in const.pdb &#8211; this example shows that the constrainer works well with &#8216;insertion&#8217; residue numbering as in antibodies where you have 27A, 27B etc.<em><br \/>\n<\/em><\/p>\n<pre class=\"lang:sh decode:true\">python PDB_constrain.py -f 1ACY.pdb -c L -o const.pdb<\/pre>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>In many applications you need to constrain PDB files to certain chains. You can do it using this program. A. What does it do? Given a pdb file, write out the ATOM and HETATM entries for the supplied chain(s). PDB_constrain needs three arguments: PDB file to constrain. Chains from the pdb file to constrain. Output [&hellip;]<\/p>\n","protected":false},"author":4,"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":[14,15],"tags":[],"ppma_author":[482],"class_list":["post-592","post","type-post","status-publish","format-standard","hentry","category-howto","category-technical"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":482,"user_id":4,"is_guest":0,"slug":"konrad","display_name":"Konrad Krawczyk","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/fdb224fe7b0775e3c9a6956ae2a5ffd7c35ab8ce3ff99c5f6e0a51d45557cdd6?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\/592","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\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=592"}],"version-history":[{"count":8,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/592\/revisions"}],"predecessor-version":[{"id":616,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/592\/revisions\/616"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=592"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=592"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=592"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=592"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}