PyMOL コマンドリファレンス
PyMOLのコマンド集（メモ用）
角度または2面角の測定
get_dihedral [atom1], [atom2], [atom3], [atom4]
get_angle [atom1], [atom2], [atom3]
コマンドのログを画面に表示する
set overlay, 1 #1: on; 0: off
きれいな図
set ray_shadow, off #影を消す
set depth_cue, 0 #奥行のもやを消す
turn and rotate
turn x, 180 #camera turns
rotate x, 180 #coordinates of objects rotate
set valence #double bond etc.
set valence, 1
stickモデルで、builderモード等で二重結合に表示を変えたいとき
set valence_mode, 1 #bonds inside
SHOW COORDINATES OF SPECIFIC ATOMS
iterate_state 1, idx 99, print name, x, y, z # show the coordinates of the atom (the internal num. of 99)
ある原子の座標を知りたいとき
RAY_TRACE_MODE
set ray_trace_mode, 1 # trace mode on
set ray_trace_gain, 1 # change thickness
set ray_trace_color, black # change color
きれいな図
set cartoon_loop_radius, 0.3
cartoon表示の大きさ変更
RAY SETTING
set ray_opaque_background, 0 # create the transparent backgrounds
背景を透明にする
LABEL
label 1igt & n. ca, resn + resi # show residue name and residue number
set label_color, black #ラベルの色を変える
label sele & n. ca, “%.2f” %b # show temperature factor to two decimal place
書式付きでラベルを作れる
COLOR
spectrum b, blue_white_red, 0_17AB,27.3,28.5 # color by B-column
B因子（温度因子）により色を変えて表示する
B因子の列に表示したい任意の値に置き換えることでいろいろ使える
BOND DASH REPRESENTATION
set dash_radius, 0.1 # change the thickness of dash line such as hydrogen bonds
結合を示す線の太さを変える
SELECTION
select loop, A/94-103/ # equivalent to “c. a & i. 94-103”
select srr, byres loop around 4 #select residues, 4 angstroum around loop
CREATE ASYMMETRIC UNITS
symexp zzz, 08_4M7K, h3, 15
結晶構造単位を表示する
zzz: new object name, 08_4M7K: pdb object including information, h3: selection name, 15: cutoff length from selection
MOVIE ムービーの操作
set movie_delay, 1000 # How ms (m sec) per 1 frame; 1000 → 1 frame / s; 500 → 2 frame / s
mplay #play movie
frame 100 #move to 100 step
CHANGE SECONDARY STRUCTURE
alter 4M61Fv & c. b & i. 97-109, ss='L' # helix: ss='H', strand: ss='S'
rebuild
指定した領域の二次構造を変更する
SHOW DISTANCEs
distance hbonds, i. 210-222 & (n. o+n), all & (n. o+n), 3.5, mode=2
二原子間の距離を測る
hbonds: selection name
3.5: show distance within 3.5A between "i. 210-222 & (n. o+n)" and "all & (n. o+n)"
きれい
set_color oxygen, [1.0,0.4,0.4]
set_color nitrogen, [0.5,0.5,1.0]
remove solvent
as spheres
util.cbaw
bg white
set light_count,10
set spec_count,1
set shininess, 10
set specular, 0.25
set ambient,0
set direct,0
set reflect,1.5
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 2
unset depth_cue
viewport 400,400
