#分子模拟#可视化软件VMD原子选择详解

生信杂谈 · 公众号 · · 2017-06-19 23:59

正文

VMD是一个非常优秀的分子模拟可视化软件，与Pymol，UCSF Chimera齐名，个人还是最喜欢使用VMD，唯一不好的一点是其主要支持的脚本语言为没落的TCL语言。但是VMD在分子模拟轨迹分析中占有非常重要的作用。可谓不可不学习呀。VMD的快速入门网上已经有中文教程，这里不做过多讲解，若没有一点基础，可以先看网上的教程。

今天和大家分享VMD的原子选择方面的内容。

VMD官方教程使用的原子为肌红蛋白PDB，mbco.pdb，该结构文件可以在此下载或者官网下载。

概览

原子的选择最基本的参数莫过于一些基本参数，在Graphical Representations中的Singlewords可以查看。

基本参数例如：protein，not protein，nucleic backbone
原子名称例如：atom C
残基名称例如：resname HEM

当然一个参数也可以包含多个参数，例如：
name C CA N O将会选择骨架原子，这与protein backbone实际上是一样的。

VMD甚至强大的可以使用正则表达式，例如：
name “C.*”,注意的是正则表达式需要用双引号进行包裹，该选择表示的是所有名字起始为C的原子。

VMD同样可以用布尔操作符and，or以及not，例如：
resname HEM and not name "N.*"将会选择肌红蛋白的除去氮原子的血红素

当然VMD还可以操作一些计算，例如x>5会选择x坐标大于5的原子，mass>12 and mass<14选择12到14之间原子质量单元。

当然也可以用计算来进行一些高级操作，例如sqrt( sqr(x) +sqr(y) + sqr(z) ) < 10会选择中心点内10埃的球体内原子。同样常用的还有within of 以及same as

原子选择关键字与功能

Keyword	Arg	Description	描述中文
all	bool	everything	所有
none	bool	nothing	空
name	str	atom name	原子名称
type	str	atom type	原子类型
index	num	the atom number, starting at 0	原子序号，0开始
serial	num	the atom number, starting at 1	原子序号，1开始
atomicnumber	num	atomic number (0 if undefined)	原子数（如果未定义则为0）
element	str	atomic element symbol string (‘X’ if undefined)	原子元素符号字符串（如果未定义则为X）
altloc	str	alternate location/conformation identifier	替代位置/构像标识符
chain	str	the one-character chain identifier	特征链
residue	num	a set of connected atoms with the same residue number	一组具有相同残基数的连接原子
protein	bool	a residue with atoms named C, N, CA, and O	蛋白
nucleic	bool	a residue with atoms named P, O1P, O2P and either	核酸
		O3’, C3’, C4’, C5’, O5’ or O3, C3, C4, C5, O5*.
		This definition assumes that the base is phosphorylated,
		an assumption which will be corrected in the future.
backbone	bool	the C, N, CA, and O atoms of a protein	骨架
		and the equivalent atoms in a nucleic acid.
sidechain	bool	non-backbone atoms and bonds	侧链
water,	bool	all atoms with the resname H2O, HH0, OHH, HOH,	水
waters		OH2, SOL, WAT, TIP, TIP2, TIP3 or TIP4
fragment	num	a set of connected residues	联系残基
pfrag	num	a set of connected protein residues	联系蛋白残基
nfrag	num	a set of connected nucleic residues
sequence	str	a sequence given by one letter names	单字符序列
numbonds	num	number of bonds	成键数
resname	str	residue name	残基名
resid	num	residue id	残基id
segname	str	segment name	片段名
x, y, z	float	x, y, or z coordinates	坐标
radius	float	atomic radius	原子半径
mass	float	atomic mass	原子质量
charge	float	atomic charge	原子电荷
beta	float	temperature factor	温度因子
occupancy	float	occupancy	占有率
user	float	time-varying user-specified value
at	bool	residues named ADA A THY T
acidic	bool	residues named ASP GLU
acyclic	bool	``protein and not cyclic’’
aliphatic	bool	residues named ALA GLY ILE LEU VAL
alpha	bool	atom’s residue is an alpha helix
amino	bool	a residue with atoms named C, N, CA, and O
aromatic	bool	residues named HIS PHE TRP TYR
basic	bool	residues named ARG HIS LYS
bonded	bool	atoms for which numbonds > 0
buried	bool	residues named ALA LEU VAL ILE PHE CYS MET TRP
cg	bool	residues named CYT C GUA G
charged	bool	``basic or acidic’’
cyclic	bool	residues named HIS PHE PRO TRP TYR
hetero	bool	``not (protein or nucleic)’’	非蛋白或核酸
hydrogen	bool	name “[0-9]?H.*”	氢
large	bool	``protein and not (small or medium)’’
medium	bool	residues named VAL THR ASP ASN PRO CYS
		ASX PCA HYP
neutral	bool	residues named VAL PHE GLN TYR HIS CYS
		MET TRP ASX GLX PCA HYP
polar	bool	``protein and not hydrophobic’’	极性氨基酸
purine	bool	residues named ADE A GUA G
pyrimidine	bool	residues named CYT C THY T URI U
small	bool	residues named ALA GLY SER
surface	bool	``protein and not buried’’	蛋白表面氨基酸
rasmol	str	translates Rasmol selection string to VMD	将Rasmol选择字符串转换为VMD
alpha_helix	bool	atom’s residue is in an alpha helix
pi_helix	bool	atom’s residue is in a pi helix
helix_3_10	bool	atom’s residue is in a 3-10 helix
helix	bool	atom’s residue is in an alpha or pi or 3-10 helix
extended_beta	bool	atom’s residue is a beta sheet
bridge_beta	bool	atom’s residue is a beta sheet
sheet	bool	atom’s residue is a beta sheet
turn	bool	atom’s residue is in a turn conformation
coil	bool	atom’s residue is in a coil conformation
structure	str	single letter name for the secondary structure	二级结构单字符
phi, psi	float	backbone conformational angles	骨架构像角度
within	str	selects atoms within a specified distance of	特别包含距离
		a selection (i.e within 5 of name FE).
exwithin	str	exclusive within, equivalent to (within 3 of X) and not X.
same	str	selects atoms which have the same keyword as	具有相同关键字
		the atoms in a given selection (i.e. same segname as resid 35)
ufx, ufy, ufz	num	force to apply in the x, y, or z coordinates	强制应用于x，y或z坐标

当然还有一些计算函数，这个比较简单，就不翻译了

Function	Description
sqr(x)	square of x
sqrt(x)	square root of x
abs(x)	absolute value of x
floor(x)	largest integer not greater than x
ceil(x)	smallest integer not less than x
sin(x)	sine of x
cos(x)	cosine of x
tan(x)	tangent of x
atan(x)	arctangent of x
asin(x)	arcsin of x
acos(x)	arccos of x
sinh(x)	hyperbolic sine of x
cosh(x)	hyperbolic cosine of x
tanh(x)	hyperbolic tangent of x
exp(x)	``e to the power x’’
log(x)	natural log of x
log10(x)	log base 10 of x

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