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。
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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 <距离值> of <选择>以及same <属性> as <选择>
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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