Задание №2. водородные связи

load 1lmp.pdb

remove solvent

extract ligands,het

as surface, 1lmp

set transparency,0.5

as sticks, ligands

show stick, byres(1lmp w. 4 of ligands)

center ligands

origin ligands

zoom ligands

h_add

ligands – action – find – polar contacts – to any excluding solvent

ligands – color – by elements – purpele

png pic1.png

Задание №3. мутация в белке.

Select 107Ala

mutation to THR

apply

mutant color green

save 2lmp.pdb

png pic2.png

Задание 4.

load 1lmp.pdb

load 2lmp.pdb

set matrix_mode, 1

set movie_panel, 1

set scene_buttons, 1

set cache_frames, 1

hide all

show cartoon, all

show sticks, resi 130-132

show sticks, resi 107

set movie_auto_interpolate, off

set matrix_mode, 1

set movie_panel, 1

set scene_buttons, 1

set cache_frames, 1

select target, resi 107

translate [150,0,0]

rotate y, 15, object=1

orient 2lmp or 1lmp

mset 1 x150

frame 1

mview store

mview store, object=1lmp

mview store, object=2lmp

frame 80

orient 1lmp and target

mview store

mview store, object=1lmp

mview store, object=2lmp

frame 120

orient 2lmp and target

mview store

mview store, object=1lmp

mview store, object=2lmp

frame 150

python

cmd.madd("1 x5"); cmd.frame(3000);

cmd.rotate("y", -15.5, object="1lmp")

cmd.mview("store", object="1lmp")

cmd.mview("store", object="2lmp")

cmd.mview("interpolate", object="1lmp")

cmd.mview("reinterpolate")

python end

super 2lmp, 1lmp

orient target

mview store

madd 1 x30

mview interpolate, object=1mp

mview interpolate, object=2lmp

mview reinterpolate

mplay

mpng mov

(ссылка на видео)

https://drive.google.com/file/d/0B43yozs610EXR2ZndV9SSnBGZXM/view

Задание №5. присоединение флуоресцентной метки.

Load Tamra.sdf

load 1lmp.pdb

select m, /Tamra///UNK`0/C

select s, /1lmp//A/SER*37/CB

fuse s, m

torsion 15

png pic4.png

Задание №6.

скрипт для построения политриптофановой цепи.

frag thr

python

for x in range(3,101):

cmd.edit("/thr///" + str(x-1) + "/C")

editor.attach_amino_acid("pk1","thr")

for x in range(2,99):

cmd.set_dihedral(

"/thr///" + str(x) + "/N", "/thr///" + str(x) + "/CA",

"/thr///" + str(x) + "/C", "/thr///" + str(x+1) + "/N", -47)

cmd.set_dihedral(

"/thr///" + str(x) + "/CA", "/thr///" + str(x) + "/C",

"/thr///" + str(x+1) + "/N", "/thr///" + str(x+1) + "/CA", 180)

cmd.set_dihedral(

"/thr///" + str(x) + "/C", "/thr///" + str(x+1) + "/N",

"/thr///" + str(x+1) + "/CA", "/thr///" + str(x+1) + "/C", -57)

python end