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使用Pymol的Modevectors脚本绘画豪猪图

原文地址:点我查看   英文好的建议看原文,我的英文不是很好,以免有翻译错误或者翻译不准确的地方

脚本下载地址:modevectors

使用:

加载脚本使用run命令

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modevectors first_obj_frame, last_obj_frame [,first_state=1 [,last_state=1 [,outname=modevectors \
  [,head=1.0 [,tail=0.3 \[,head_length=1.5 [,headrgb=(1.0,1.0,1.0) [,tailrgb=(1.0,1.0,1.0) [,cutoff=4.0 
  [,skip=0 [,cut=0.5 [,atom=CA [,stat=show [,factor=1.0 [,notail=0]]]]]]]]]]]]]]

更多类型可以看pdf底部

当脚本完成object会显示"modevectors" 可以通过 outname=modevectors 修改

例子:

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modevectors 1E3M, 1W7A
modevectors 1E3M, 1W7A, outname="arrows"
modevectors 1E3M, 1W7A, atom="P"

复制/粘贴 如下代码查看modevectors。此使用多个蛋白且箭头联系首尾

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import modevectors
# fetch the PDBs from pdb.org
fetch 1c3y, finish=1, multiplex=0, async=0
# separate the first and last states of the NMR ensemble to individual objects
split_states 1c3y, 1, 1
split_states 1c3y, 23, 23
hide
# run the modevectors code
modevectors 1c3y_0001, 1c3y_0023
# just setup a nice representation
as cartoon, 1c3y_0001 or 1c3y_0023
show cgo, modevectors
color marine, 1c3y_0001
color purpleblue, 1c3y_0023

附样式图片(编号1-13): Mv_default   

Mv_fig2

Mv_fig3 

Mv_fig4

Mv_fig5

Mv_fig6

Mv_fig7

Mv_fig8

Mv_fig9

Mv_fig10

Mv_fig11

Mv_fig12

Mv_fig13

图片代码:

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reinitialize
import modevectors

fetch 1c3y, async=0

split_states 1c3y, 1, 1
split_states 1c3y, 23, 23
hide
 
#This is the default setting (Fig.1)
modevectors 1c3y_0001, 1c3y_0023
 
#This is shows that the direction of the arrows is drawn from the 1c3y_0001 towards 1c3y_0023 (Fig.2)
show cartoon, 1c3y_0023
color red, 1c3y_0023
 
#This controls the base radius of the cone/arrow head in angstroms (Fig.3)
modevectors 1c3y_0001, 1c3y_0023, head=2.5
 
#This controls the radius of the cylinders/arrow tails in angstroms (Fig.4)
modevectors 1c3y_0001, 1c3y_0023, tail=0.75
 
#This controls the length of the cone/arrow head in angstroms (Fig.5)
#Note that this option does NOT increase the vector length but simply changes the tail length
modevectors 1c3y_0001, 1c3y_0023, head_length=3.0
 
#This controls the colour of the cone/arrow head using RGB values (Fig.6)
modevectors 1c3y_0001, 1c3y_0023, headrgb=(1.0,0.0,0.0)
 
#This controls the colour of the cylinder/arrow tails using RGB values (Fig.7)
modevectors 1c3y_0001, 1c3y_0023, tailrgb=(1.0,0.0,0.0)
 
#This controls the which vectors to show based on a specific cutoff value in angstroms.  Vector lengths that are less 
#than the cutoff value will not be displayed (Fig.8)
modevectors 1c3y_0001, 1c3y_0023, cutoff=30.0
 
#This controls how many vectors to skip (integer value) and is useful when there are too many vectors showing.  
#Skip=1 will show every other arrow (Fig.9)
modevectors 1c3y_0001, 1c3y_0023, skip=1
 
#This controls how much to cut from each vector (in angstroms).  Note that arrows will point in the opposite directions 
#when too much is cutoff (resulting in a negative vector length) (Fig.10) and should be used with caution!
modevectors 1c3y_0001, 1c3y_0023, cut=15.0
 
#This controls which atom to draw a vector from (Fig.11).  Note that this is case-sensitive and is really only useful 
#when atom=CA or when atom=P (for DNA backbones)
modevectors 1c3y_0001, 1c3y_0023, atom=CB
 
#This controls how much to multiple the length of each vector by (percentage increase/decrease) (Fig.12)
#This example halves the length of each vector (50%)
modevectors 1c3y_0001, 1c3y_0023, factor=0.5
 
#This hides the statistics which count atoms skipped, atoms counted (number of arrows showing), and number of atoms 
#that did not meet the cutoff and are not shown
modevectors 1c3y_0001, 1c3y_0023, stat=hide
 
#This example shows multiple options being used (Fig.13)
modevectors 1c3y_0001, 1c3y_0023, head=2.0, tail=1.0, head_length=2.0, headrgb=(1.0,0.0,0.0), tailrgb=(0.0,0.0,1.0),
cutoff=0.0,skip=0,cut=0,atom=CA,factor=0.8
 
#Finally, this example hides all arrow tails and only uses arrow heads via the notail option(No Figure)
modevectors 1c3y_0001, 1c3y_0023, head=2.0, cutoff=0.0,skip=0,cut=0,atom=CA,factor=0.8, notail=1
Licensed under CC BY-NC-SA 4.0