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如何用Pymol做出那些美呆的结构图(晋级篇)

上一次的文章,我们介绍了Pymol的一些基础界面操作,点这里。今天我们主要了解一下Pymol的一些基本命令操作。就像Linux一样,要想更好的操作Pymol,掌握一些常用的命令是必不可少的。 Pymol中输入命令行的位置是外部GUI窗口,如图1中空白区域:

图1

201610271

Pymol是区分大小写的,不过目前为止Pymol还是只用小写,所以记住,所有的命令都是使用小写字母的。下面我们先来了解一下Pymol的语法。

Pymol命令的语法

Pymol的命令都是由关键词(keyword)加上一些变量(argument)组成,格式如下:

Pymol> keyword argument

无变量命令

每个命令关键词(keyword)是必须的,而变量则不是必须的,比如退出命令quit就不需要附加变量:

Pymol> quit

单变量命令

当然更多的命令通常是需要加变量的,比如放大命令zoom,但是你会发现即使你不加任何变量该命令也可以被执行,这是因为Pymol的许多命令有一个默认变量,下面两个命令的作用是一样的,其中的目标选择all就是zoom的默认变量:

Pymol> zoom

Pymol> zoom all

多变量命令

还有些命令可以带多个变量,比如加色命令color,它的用法如下:

Pymol> color color-name

虽然在描述上只带一个变量”color-name”,但其实它包含了第二个默认变量all,所以它的作用是把整个结构变成”color-name”的颜色。所以当你输入如图2命令color red时,所有的原子都变成了红色。

图2

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如果我们不想把全部区域上成红色,那么就要写出除“color-name”外的第二个变量,书写格式如下:

Pymol> color red, selection-expression
和“color red”的区别就是把默认的目标选择变量“all”变成了”selection-expression”,也就是说只有被这个变量选中的部分才会被变成”red”定义的颜色。要注意的是,如果一个命令带多个变量,则这些变量之间必须用逗号”,”隔开。”selection-expression”,所谓的”选择表达”,可以很简单,也可以非常地复杂。这个对Pymol命令的使用非常重要,下面我们详细了解下。

选择目标

在Pymol选择目标命令即select命令,非常常见,其标准表达格式是这样的:

Pymol> select selection-name, selection-expression

其中 selection-name是我们自己起的名字,selection-expression即为选择表达。选择表达(selection-expression)表示的是被选中的部分,它们可以是一些个原子,一些个Helix,一些个Beta sheet,或者它们的混合物。你可以给你的选择表达起个名字,以便可以多次使用它们。

选择表达由所谓的”selector”加上”identifier”组成,其中”selector”定义了某类属性,而”identifier”则在该类属性下需要被选择的部分。

举个栗子

Pymol> select test, resi 142+185-192+282

其中”resi”就是一个selector,它表示在pdb文件中氨基酸的编号;”142+185-192+282″则是对应的indentifier,它表示我们要选择蛋白质结构中的第142位,185-192之间的以及282位置的氨基酸。

整个语句的作用就是选择上述的氨基酸并命名为”test”。我们以图2红色结构为例子输入栗子命令便得到图3结构。可以发现在我输入上述的命令后,一共有142个原子被选择了。这些原子在Viewer中标识出来,同时一个叫作test的selection产生了。

图3

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下表列出了一些常见的selector:

2016102710

在选择表达中,selector还可以配合逻辑操作子(logical operator)使用,这样我们可以表达更加复杂的选择。这些操作子被列于下表中:

2016102711

这些逻辑选择还可以组合使用。比如你想选择chain b,但是不选择其中的residue 88:

Pymol> select chain b and (not resi 88)

在使用多重逻辑选择时,为了让Pymol正确处理顺序,请使用括号,这样最里层括号里面的内容将会被最先处理,以此类推。在Identifier中用到的原子以及氨基酸的命名规则可以在下面的网址中找到:http://www.wwpdb.org/docs.html

因此通过select的命令,我们可以选择蛋白质中几乎任何目标,大到一条链,小到一个原子。获得目标后我们便可以对其进行zoom,改变颜色,改变显示方式,进行标记等操作了。

对选择对象进项操作

对选择对象的操作可以包括显示(show),隐藏(hide),标记(label),删除(delete),缩放(zoom),ray等。功能非常多,我们只给出一些例子,其余的就靠小伙伴们自己挖掘了。

显示与隐藏

Pymol> show representation

Pymol> hide representation

其中representation可以为:cartoon, ribbon, dots, spheres, surface和mesh。使用这2个命令可以让Pymol以不同的方式显示蛋白质结构。

还记得我们上篇文章中,刚刚打开一个PDB文件,Pymol显示出来的结构是杂乱无章的。如果我们输入这个命令

Pymol> show cartoon

便得到图4

图4

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然后我们输入

Pymol> hide lines

将得到图5

图5

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移除溶剂分子

可以发现上图中还有一些红色的小点点,其实这是水分子,我们可以通过这个命令来移除结构中的溶剂分子得到图6。

Pymol> remove solvent

图6

201610276

改变目标颜色

上面我们已经介绍了如何给目标改变颜色。我们运行下列的命令,你能猜到图像变成什么样的了吗?

Pymol> color red, ss h

Pymol> color yellow, ss s

Pymol> color green, ss l+

其中“ss”代表secondary structure,“h”代表Helix,“s”代表Beta sheet,l+代表Loop和所以其他结构。这3句的作用分别是把所有的Helix变成红色;把所有的Beta sheet变成黄色;把所有的Loop以及其他部分变成绿色,于是我们得到图7

图7

201610277

改变背景颜色

为了得到能用来发表的图片,我们需要将背景变为白色,上次我们知道可以通过菜单栏进行设置,那怎么用命令行来进行呢?输入这个命令:
Pymol> bg_color white

图8

201610278

Ray

如果觉得当前显示窗口里面显示的结构图像已经满足你的要求了,我们就可以将它保存为图片。在这之前我们可以使用ray命令来优化图像,它可以使图像具有三维的反射及阴影特效,直接使用这个命令: Pymol> ray,即可得到图9

图9

201610279

对Pymol的介绍在这里要告一段落了,小编相信聪明的大家看过这两篇文章后,只要经过简单的练习,人人都可以做出美呆的蛋白质结构图的。


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