My software notes

January 21, 2006

select specifc residue/ribose and give hydrogen bonds, showing with surface and sphere.(Use hybrid DNA as example)

Filed under: pymol/ molmol — kpwu @ 4:32 am

1l3m.png

  • 從程式集開啟PyMOL
    Open PyMol
  • 載入pdb files, 可用指令模式或用工具列啟動
    load 1L3M ( Use PyMOL Tcl/Tk GUI, File -> open -> /your_path/1L3M.pdb)
  • 消去預先顯示的畫面
    hide all
  • 順著Z軸翻轉180度
    rotate z, 180
  • 設定背景顏色為白色
    bg_color white
  • 此1L3M.pdb為雙股螺旋DNA,每一股helix定義為一個chain,下兩個步驟為分別選擇chain A, chain B的方式
    select chain-a, chain a
    select chain-b, chain b
  • chain a, chain b都用sticks表示,而且把bond的半徑縮小
    show sticks, chain-a
    show sticks, chain-b
    set stick_radius = 0.13
  • 定義chain a為藍色,chain b為綠色
    color green, chain-b
    color blue, chain-a
  • 細分chain a的residues兩部份, 1-5 & 6-12,選擇方式如下,a15 & a612分別是選擇的object的名稱
    select a15, resi 1-5
    select a612,resi 6-12
  • a15部分畫surface圖,a612部分畫sphere圖
    show surface, a15
    show sphere, a612
  • a15的surface顏色為yellow, a612的sphere也是yellow
    set surface_color,yellow, a15
    set sphere_color,yellow, a612
  • a15的透明度是0.33, a612的透明度是0.76
    set transparency, 0.33, a15
    set sphere_transparency,0.76,a612
  • 手動增加兩個氫鍵,使用dist指令;其中///A/6/1H6的意思是/object/segment/chain/residues/atom的分類方式,在1L3M.pdb檔案中,只有一個object,一個segment,兩個chain(a/b),並選取residue 6的1H6,其餘三個選擇亦是如此;
    dist hb1, ///A/6/1H6, ///B/19/O4
    dist hb2, ///A/6/N1, ///B/19/H3
  • 在這裡你會看到這個dist的指令其實是量距離的工具,但只要把label拿掉就像是一個hydrogen bond
    hide labels
  • 兩hbond的顏色分別定義為red for hb1, and orange for hb2
    color red, hb1
    color orange, hb2
  • 最後把剛剛做出的兩組hbond修改一下,定義dash的radius是0.11(both for hb1,hb2),hb1的lenght是2,hb2沒有gap,你可以明顯看出hb1,hb2的差別.
    set dash_radius, 0.11
    set dash_length, 2,hb1
    set dash_gap, 0, hb2
  • 以chain B上的residue 18為中心放大,scale為-8
    zoom ///B/18,-8
  • 在輸入ray之前你看到hbond是細細的,ray指令執行後,會是類似stick的效果,可以自行比較.

你也可以在Tcl/Tk GUI視窗的command input area把上述的所有指令一次輸入,類似macro的功能(把下列指令全選,一次貼上即可)
load 1L3M.pdb
hide all
rotate z, 180
bg_color white
select chain-a, chain a
show sticks, chain-a
set stick_radius = 0.13
select chain-b, chain b
show sticks, chain-b
color green, chain-b
color blue, chain-a
select a15, resi 1-5
select a612,resi 6-12
show surface, a15
show sphere, a612
set surface_color,yellow, a15
set sphere_color,yellow, a612
set transparency, 0.33, a15
set sphere_transparency,0.76,a612
dist dist1, ///A/6/1H6, ///B/19/O4
dist dist2, ///A/6/N1, ///B/19/H3
hide labels
color red, dist1
color orange, dist2
set dash_length, 2,dist1
set dash_gap, 0, dist2
set dash_radius, 0.11
zoom ///B/18,-8
rayLast modified: 2004/04/27

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1 Comment »

  1. 您好,
    我是pymol的初學者,找到您的blog覺得非常感動。。。
    不知道能不能跟您請教pymol上使用的問題呢?
    我的問題其實都很簡單,
    如果您不方便回答也沒關係,我還是會定期參考您的blog,
    希望您能繼續多分享pymol的使用note

    Comment by shinnan — March 12, 2007 @ 5:14 pm | Reply


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