My software notes

January 21, 2006

define the secondary structure by yourself (It can be different with the PDB file)

Filed under: pymol/ molmol — kpwu @ 4:37 am

1jlz.png

每一個從Protein Data Bank上抓到的pdb file應該都會包含一段header,內容是描述此protein的基本性質,二級結構分布,源自哪個物種,三度空間結構的定義等等,當pymol開啟pdb file時,會去找這段header,並依照pdf file的二級結構定義而產生helix/strands/loops.
若是home-made的pdb files,如用xplor,cns, cyana等軟體計算得到的pdb, pymol無法讀取hearders,所以其二級結構必定不同於正確值,這時可使用下列方法解決.

  1. 使用alter指令 (sample pdb: 1jc6.pdb)
  • OPEN File
    load 1j6c.pdb
  • Hide the DEFAULT presentations
    hide all
  • show cartoon
  • 原先的helix是從resiuse 4 to 9,改為b-strand (ss=’S’是strand, ss=’H’是helix, ss=’L’是loop’)
    alter 4-9/, ss=’S’
    alter 11-15/, ss=’L’
    alter 17-19/, ss=’H’
  • SHOW Cartoon AGAIN!!
    show cartoon
  • set bg_color and widow size, the final result picture is left one at top

    Last modified: 2004/04/27

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