{"id":493,"date":"2016-10-20T15:19:43","date_gmt":"2016-10-20T06:19:43","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=493"},"modified":"2017-01-11T18:12:17","modified_gmt":"2017-01-11T09:12:17","slug":"modeller%e3%81%ab%e3%82%88%e3%82%8bmissing-side-chain%e3%81%ae%e4%bb%98%e5%8a%a0","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2016\/10\/20\/modeller%e3%81%ab%e3%82%88%e3%82%8bmissing-side-chain%e3%81%ae%e4%bb%98%e5%8a%a0\/","title":{"rendered":"Modeller\u306b\u3088\u308bmissing side chain\u306e\u4ed8\u52a0"},"content":{"rendered":"

\u74b0\u5883: macOS Sierra 10.12, 3.3 GHz Intel Core i5, \u30e1\u30e2\u30ea8 GB\uff0e
\n\u53c2\u8003: bioinformatics > \u69cb\u9020\u4e88\u6e2c > MODELLER > \u7c21\u5358\u306a\u5b9f\u884c\u4f8b<\/a> (2015.05.03)<\/p>\n

PKC\u03b4 C1B\u30c9\u30e1\u30a4\u30f3\u306e\u7d50\u6676\u69cb\u90201ptr.pdb<\/a>\u306f\uff0cLYS234, ARG273, \u305d\u3057\u3066GLU274\u306e\u5074\u9396\u304c\u6b20\u3051\u3066\u3044\u307e\u3059\uff0e\u307e\u305f\uff0cMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306e\u305f\u3081\u306b\uff0cN\u672b\u7aef\u3068C\u672b\u7aef\u306bGLY\u6b8b\u57fa\u3092\u4ed8\u52a0\u3057\u305f\u3044\uff0e\u4ee5\u524d\u306f\uff0cSwiss-pdb viewer\u3067\u7c21\u5358\u306b\u51fa\u6765\u3066\u3044\u307e\u3057\u305f\u304c\uff0cmacOS Sierra\u3067\u8d77\u52d5\u3057\u306a\u304b\u3063\u305f\u306e\u3067\uff0cPymol\u3068Modeller\u3092\u4f7f\u3044\u307e\u3057\u305f\uff0e<\/p>\n

\u6700\u8fd1\u306f\u30db\u30e2\u30ed\u30b8\u30fc\u30e2\u30c7\u30ea\u30f3\u30b0\u30b5\u30fc\u30d0\u30fc\u304cWeb\u306b\u591a\u304f\u3042\u308a\u307e\u3059\u304c\uff0c\u30ed\u30fc\u30ab\u30eb\u3067\u3082\u30db\u30e2\u30ed\u30b8\u30fc\u30e2\u30c7\u30ea\u30f3\u30b0\u304c\u51fa\u6765\u308b\u3088\u3046\u306bMODELLER<\/a> (version 9.17) \u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u4f7f\u3044\u307e\u3059\uff0e<\/p>\n

$ brew tap salilab\/salilab\n$ brew install modeller<\/code><\/pre>\n
Edit \/usr\/local\/Cellar\/modeller\/9.17\/modlib\/modeller\/config.py
\nand replace XXXX with your Modeller license key<\/p>\n
Pymol\u30671PTR\u3092\u958b\u304d\uff0cN\u672b\u7aef\u306e\u30ab\u30eb\u30dc\u30cb\u30eb\u70ad\u7d20\u3092\u9078\u629e (control+\u4e2d\u30af\u30ea\u30c3\u30af or \u53f3\u30c0\u30d6\u30eb\u30af\u30ea\u30c3\u30af) \u3057\u3066\u304b\u3089\uff0cmenu > Build > Residue > Glycine\u3092\u9078\u629e\u3057\u3066GLY\u6b8b\u57fa\u3092\u4ed8\u52a0\uff0e\u540c\u69d8\u306b\uff0cN\u672b\u7aef\u306e\u7a92\u7d20\u539f\u5b50\u3092\u9078\u629e\u3057\u3066\uff0cGLY\u6b8b\u57fa\u3092\u4ed8\u52a0\u3057\u307e\u3059 (\u672c\u5f53\u306e\u30b7\u30fc\u30af\u30a8\u30f3\u30b9\u3067\u306fPRO\u3067\u3059)\uff0eN\u672b\u7aef\u306b\u4ed8\u52a0\u3057\u305fGLY\u6b8b\u57fa\u304c\u5468\u56f2\u3068\u3076\u3064\u304b\u3063\u3066\u3044\u308b\u306e\u3067\uff0c\u624b\u52d5\u3067\u9003\u304c\u3057\u3066\u3042\u3052\u307e\u3059\uff0e<\/p>\n
Mouse Mode\u30923-Button Editing\u306b\u5207\u308a\u66ff\u3048\u3066\u304b\u3089\uff0ccontrol+\u53f3\u30af\u30ea\u30c3\u30af\u3067\u7d50\u5408\u3092\u9078\u629e\u3057\u307e\u3059\uff0e\u8868\u793a\u3055\u308c\u305f\u30db\u30a4\u30fc\u30eb\u3092\u30c9\u30e9\u30c3\u30b0\u3057\u3066\u4e8c\u9762\u89d2\u3092\u5909\u5316\u3055\u305b\u307e\u3057\u305f\uff0eFile > Save Molecule > OK > 1PTR_patch.pdb\u3068\u3057\u3066\u4fdd\u5b58\uff0e<\/p>\n
1PTR_patch.pdb\u3092\u30c6\u30ad\u30b9\u30c8\u30a8\u30c7\u30a3\u30bf\u3067\u958b\u304d\uff0c\u4e9c\u925b (ZN) \u539f\u5b50\u3068\u30ea\u30ac\u30f3\u30c9 (PRB) \u306e\u884c\u3092\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u5f8c\u308d\u306b\u79fb\u52d5\u3055\u305b\u3066\u4fdd\u5b58\u3057\u307e\u3059\uff0e<\/p>\n
 <\/p>\n
\u6b21\u306bModeller\u306e\u305f\u3081\u306e\u30a2\u30e9\u30a4\u30f3\u30e1\u30f3\u30c8\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u6210\u3057\u307e\u3059\uff0e\u30db\u30e2\u30ed\u30b8\u30fc\u30e2\u30c7\u30ea\u30f3\u30b0\u3092\u884c\u3046\u6642\u306f\u30bf\u30f3\u30d1\u30af\u8cea\u914d\u5217\u306e\u30a2\u30e9\u30a4\u30f3\u30e1\u30f3\u30c8\u306fClustal Omega<\/a>\u306a\u3069\u306e\u30b5\u30fc\u30d3\u30b9\u3067\u884c\u3046\u3053\u3068\u304c\u3067\u304d\u307e\u3059\uff0e\u4eca\u56de\u306f\uff0c\u5074\u9396\u306e\u88dc\u5b8c\u306a\u306e\u3067\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u3057\u307e\u3057\u305f\uff0e\u30a2\u30e9\u30a4\u30f3\u30e1\u30f3\u30c8\u30d5\u30a1\u30a4\u30eb\u4e2d\u306edot (.) \u306ftemplate\u69cb\u9020\u3092\u30b3\u30d4\u30fc\u3057\u525b\u4f53\u3068\u3057\u3066\u6271\u3046\u3053\u3068\u3092\u610f\u5473\u3057\u307e\u3059\uff0e
\nalign.pir\u3092\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u4f5c\u308a\u307e\u3059.\u30db\u30e2\u30ed\u30b8\u30fc\u30e2\u30c7\u30ea\u30f3\u30b0\u3067\u4e9c\u925b\u30a4\u30aa\u30f3\u3092\u6271\u3044\u305f\u3044\u6642\u306f\uff0c\u8a18\u53f7\u306fz\u3067\u3059\uff0e<\/p>\n
>P1;TARGET\r\nsequence:TARGET::::::::\r\nG...K......................................RE......G...*\r\n>P1;1PTR_patch\r\nstructureX:1PTR_patch:230:A:284:A::::\r\nG...K......................................RE......G...*<\/pre>\n
\u8a08\u7b97\u3092\u5b9f\u884c\u3059\u308b\u305f\u3081\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u30d5\u30a1\u30a4\u30ebmodel.py\u3092\u4f5c\u308a\u307e\u3059\uff0e<\/p>\n
from modeller import *\r\nfrom modeller.automodel import *\r\n\r\nlog.verbose()\r\nenv = environ()\r\n\r\n# Read in HETATM records from template PDBs\r\nenv.io.hetatm = True\r\n\r\na = automodel(env,\r\n              alnfile  = 'align.pir',\r\n              knowns   = '1PTR_patch',\r\n              sequence = 'TARGET',\r\n              assess_methods=(assess.DOPE,\r\n                              #soap_protein_od.Scorer(),\r\n                              assess.GA341))\r\na.starting_model= 1\r\na.ending_model  =10\r\na.make()<\/pre>\n
MODELLER\u3092\u5b9f\u884c\u3057\u307e\u3059\uff0e<\/p>\n
$ mod9.17 model.py\n<\/code><\/pre>\n
\u4eca\u56de\u306f\u30e2\u30c7\u30eb\u309210\u500b\u751f\u6210\u3057\uff0c15\u79d2\u7a0b\u3067\u8a08\u7b97\u304c\u7d42\u308f\u308a\u307e\u3057\u305f\uff0emodel.log\u30d5\u30a1\u30a4\u30eb\u306e\u6700\u5f8c\u306b\u30e2\u30c7\u30eb\u306e\u8a55\u4fa1\u5024\u304c\u66f8\u304b\u308c\u3066\u3044\u307e\u3059\uff0e<\/p>\n
>> Summary of successfully produced models:\r\nFilename                          molpdf     DOPE score    GA341 score\r\n----------------------------------------------------------------------\r\nTARGET.B99990001.pdb          1105.60205    -3754.83594        1.00000\r\nTARGET.B99990002.pdb          1112.45032    -3754.93115        1.00000\r\nTARGET.B99990003.pdb          1102.25818    -3705.38794        1.00000\r\nTARGET.B99990004.pdb          1112.61877    -3740.67261        1.00000\r\nTARGET.B99990005.pdb          1100.41248    -3773.57837        1.00000\r\nTARGET.B99990006.pdb          1110.39478    -3751.47119        1.00000\r\nTARGET.B99990007.pdb          1108.92419    -3746.39502        1.00000\r\nTARGET.B99990008.pdb          1109.27356    -3732.12354        1.00000\r\nTARGET.B99990009.pdb          1099.53418    -3808.25830        1.00000\r\nTARGET.B99990010.pdb          1100.34485    -3785.94385        1.00000<\/pre>\n
molpdf\u3082DOPE score\u3082\u5024\u304c\u4f4e\u3044\u7a0b\u8a55\u4fa1\u304c\u9ad8\u3044\u3053\u3068\u3092\u610f\u5473\u3057\u307e\u3059\uff0e\u4eca\u56de\u306f9\u756a\u76ee\u306e\u30e2\u30c7\u30eb\u304c\u3069\u3061\u3089\u306e\u8a55\u4fa1\u3067\u3082\u6700\u4f4e\u5024\u3067\u3057\u305f\uff0e
\n\"modeller1\"<\/a>Pymol\u3067TARGET.B99990009.pdb\u3068\u92f3\u578b\u306e1PTR_patch.pdb\u3092\u958b\u3044\u3066\u69cb\u9020\u3092\u78ba\u8a8d\u3057\u307e\u3059 (\u92f3\u578b\u3092stick\u8868\u793a\uff0c\u30e2\u30c7\u30eb\u3092line\u8868\u793a)\uff0eLYS234, ARG273, \u305d\u3057\u3066GLU274\u306e\u5074\u9396\u304c\u4ed8\u52a0\u3055\u308c\uff0cN\u672b\u7aef\u304a\u3088\u3073C\u672b\u7aef\u306b\u4ed8\u52a0\u3057\u305fGLY\u6b8b\u57fa\u3082\u308f\u305a\u304b\u306b\u6700\u9069\u5316\u3055\u308c\u3066\u3044\u307e\u3057\u305f\uff0e<\/p>\n
(\u4e86)<\/p>\n","protected":false},"excerpt":{"rendered":"
\u74b0\u5883: macOS Sierra 10.12, 3 …<\/p>\n","protected":false},"author":1,"featured_media":507,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"om_disable_all_campaigns":false,"_uag_custom_page_level_css":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"_locale":"","_original_post":"","footnotes":""},"categories":[5],"tags":[],"class_list":["post-493","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-5","ja"],"aioseo_notices":[],"uagb_featured_image_src":{"full":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/modeller1.png",320,480,false],"thumbnail":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/modeller1-150x150.png",150,150,true],"medium":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/modeller1-200x300.png",200,300,true],"medium_large":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/modeller1.png",320,480,false],"large":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/modeller1.png",320,480,false],"1536x1536":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/modeller1.png",320,480,false],"2048x2048":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/modeller1.png",320,480,false],"onepress-blog-small":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/modeller1.png",100,150,false],"onepress-small":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/modeller1.png",200,300,false],"onepress-medium":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/modeller1.png",267,400,false]},"uagb_author_info":{"display_name":"RCY","author_link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/author\/charlesy\/"},"uagb_comment_info":0,"uagb_excerpt":"\u74b0\u5883: macOS Sierra 10.12, 3 ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/493","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/comments?post=493"}],"version-history":[{"count":12,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/493\/revisions"}],"predecessor-version":[{"id":970,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/493\/revisions\/970"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media\/507"}],"wp:attachment":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media?parent=493"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/categories?post=493"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/tags?post=493"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}