VMD用户指南：分子可视化与分析操作详解

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VMD用户指南是一份详尽的手册，专为运行和使用分子可视化与分析软件VMD而设计。该文档覆盖了图形用户界面（GUI）和文本控制台界面的全面操作指南，旨在帮助用户展示、操控分子，并个性化定制VMD的外观和行为，以满足不同用户的特定需求。在VMD的1.7.1版本中，作者P.Grayson、J.Gullingsrud、B.Isralewitz、D.Norris和J.Stone来自伊利诺伊大学和贝克曼研究所的理论生物物理组。指南的目的是为生物计算资源环境（BioCoRE）、MD工具包（MDTools）、NAMD（分子动力学模拟器）以及VMD本身提供深入理解，特别是对于那些初次接触或者希望提高VMD技能的人来说，它提供了入门级教程。第一部分，"Introduction"，包含了以下内容： 1.1 节介绍了VMD及其相关项目如BioCoRE和MDTools的更多信息，以帮助用户了解这些工具的背景和应用场景。 1.2 提供了联系作者的方式，以便用户在遇到问题或需要技术支持时能够获取帮助。 1.3 记录了程序的版权信息和引用要求，确保用户了解使用软件的规范。 1.4 明确了版权和免责声明，告知用户关于版权归属和责任划分。 1.5 鼓励用户注册VMD，这可能涉及到许可证管理和软件更新。 1.6 感谢语表达了作者对支持者和社区的感谢，并提及了未来的发展计划。接下来的章节深入到实际操作层面： 2.1 "Rapid Introduction to VMD" 是一个快速入门教程，帮助用户快速掌握VMD的基本功能和操作流程。 2.2 "Viewing a Molecule: Myoglobin" 教导用户如何查看和探索分子结构，例如展示肌红蛋白这个实例。 2.3 "Rendering an Image" 探讨图像渲染技术，让用户了解如何创建高质量的分子模型图。 2.4 "A Quick Animation" 展示如何制作简单动画，演示分子运动或结构变化。 2.5 "An Introduction to Atom Selection" 教授如何选择和筛选原子，这对于分析和操作特定部分至关重要。 2.6 "Comparing and Selecting Representations" 介绍了不同的分子表示方法，帮助用户根据需要选择合适的展示方式。这份用户指南不仅提供了丰富的操作步骤，还包含了许多实用技巧和定制选项，使得无论是科研人员还是学生都能从中受益。通过细致的学习和实践，用户将能够充分利用VMD的强大功能进行复杂的分子模拟和可视化分析工作。

Chapter 2

Tutorials

2.1 Rapid Introduction to VMD

For those of you who don’t like reading manuals, here is a quick introduction to VMD. To start it

type vmd on the command line of your shell (Unix), or start it by clicking the VMD icon in your

desktop or Start menu (Microsoft Windows). VMD should start up in a window titled vmd console,

a display window entitled OpenGL Display, and a button bar entitled main. Text commands are

typed in the console window, graphics are displayed and manipulated in the display window, and

most commands are available from the menu interface, accessible through the button bar. (The

menus are built on the Forms or FLTK library so all future references in the documentation will

refer to them as forms and not menus.) All the forms except the main form can be turned oﬀ by

pressing the button in the center top. There are two ways to perform almost all functions in VMD,

either use the forms or the text console. Some of the more sophisticated commands, such as Tcl

scripting, are only available in the text interface.

2.2 Viewing a molecule: Myoglobin

You have probably obtained VMD in order to visualize molecules, so we’ll load up one of the

provided molecular structures to demonstrate the capabilities of VMD. On the button bar, click on

the Mol button. This brings up the Molecules form [§4.4.3]. (As before, this form may be turned

oﬀ by clicking the button in the center top of the form, labeled Molecules). Select Load From Files

on the Molecules form to bring up the Files form [§4.4.5].

We will load a PDB (Protein Data Bank) ﬁle containing the coordinates of the atoms in myo-

globin (compliments of Joel Berendzen from the Biophysics Group at Los Alamos National Labora-

tory). In the browser on the left, select the line that says pdb only then click on the button labeled

Select pdb. Use the ﬁle browser that appears to go to the subdirectory proteins/ of the VMD distri-

bution (you may have to ask where this is located; On Unix systems try /usr/local/lib/vmd.On

Microsoft Windows systems, try C:/Program Files/University of Illinois/VMD. Once there,

select the ﬁle mbco.pdb. Once the PDB ﬁle is selected, click on the Load Molecule buttoninthe

center of the Files form. You have loaded a myoglobin structure. Figure 2.1 shows an example of

VMD displaying this protein.

You can use the mouse to manipulate the structure in the display window. There are three

basic mouse modes [§4.1.1]: rotation[§4.1.1], translation [§4.1.1], scaling[§4.1.1]. The mode can be

changed from the Mouse form, or by pressing r, t,ors on the keyboard. Experiment with these

Figure 2.1: Sample VMD session displaying myoglobin.

modes, and note how the cursor changes to indicate the current mode. In rotation mode, the left

mouse button controls rotation about axes parallel to the screen, and the middle button controls

rotation about the axis perpendicular to the screen. In translation mode, the left mouse button

controls translation parallel to the screen, while the middle button controls translation in and out

of the screen. Finally, in scaling mode, both the left and middle buttons control global scaling

when the mouse is moved left or right, but the middle button causes larger changes.

By default the myoglobin bonds are represented as lines and non-bonded atoms as points, with

the color in both cases representing the atom type. This representation is easy for the computer

to draw but is not always informative, especially when there are a large number of atoms. VMD

allows you to display many of the common molecular representations. To access these, open the

Graphics form [§4.4.6] using the button bar.

Suppose you would like to view the myoglobin structure with its protein backbone represented

as a tube, the heme represented as licorice, the SO

ion and CO molecule represented as van der

Waals spheres, and histidines 64 and 93 represented as CPK models. First, type backbone in the

atom selection text entry area and press ’enter’ to select the myoglobin backbone. All of the

protein except for the backbone will disappear. Choose drawing method ‘Tube’ from the drawing

method chooser to render the backbone as a tube, and chose coloring method ‘Backbone’ from the

coloring method chooser to color the tube with the predeﬁned backbone color. Click on the Create

New button. This causes a new line to appear on the browser identical to the ﬁrst line. The new

line can be changed without aﬀecting the ﬁrst one, so clear the atom selection text area and then

enter resname HEM to select the heme. At this point the heme isn’t visible because it cannot be

drawn as a tube, so choose the ‘Licorice’ drawing method to make it appear. Click on Create

New again to make a new view, and enter resname SO4 CO to select the SO

ion and the CO

molecule, and choose the drawing method ‘VDW’ to render them as Van der Waal spheres. Once

again, press the Create New button and enter resid 93 64 to select the two histidines, and render

them as ‘CPK’. If you followed all that, then congratulations, you have made a beautiful image of

myoglobin! Many more ways to represent atoms are possible. Please experiment with the options

available in the Graphics form.

2.3 Rendering an Image

This tutorial assumes Raster3D is installed on your system and the executable render is in your

path.

Find an interesting view of the molecule from the previous tutorial. Suppose you want to publish

this view in a journal and want a high quality image, or you want to make a large poster. Taking

the image from a screen capture results in a rather grainy image as the size of the pixels becomes

apparent, so you want something with more resolution. There are several programs available which

can render a high-quality raster image, based on an input script. VMD has the option to create

input scripts for many of these image processing programs, which may then be processed to create

a higher quality image of the scene displayed by VMD at the time the script was created. See the

section on rendering [§ 6] for a further description of how this works.

Open the Render form [§ 4.4.13] and click on the ‘Raster3D’ Output Format.Bothofthe

text boxes will ﬁll with default values and do not need to be changed. Press the Go button. If

everything works correctly, a message starting with:

Info 1) Rendering current scene to ’plot.r3d’ ...

Info 1) Raster3D file generation finished

Info 1) Executing post-render cmd ’ render < %s -sgi %s.rgb; ipaste %s.rgb’ ...

Raster3D V2.4j

will appear in the text console. After a few moments, a window should open with an image similar

to the one in the VMD display. This image is in the RGB graphics format and can be read by

many programs (such as xv and ipaste).

2.4 A Quick Animation

Another strength of VMD lies in its ability to playback trajectories resulting from molecular dynam-

ics simulations. A sample trajectory, alanin.DCD is provided in the proteins directory included

with VMD. To load it, click on the Mol button of the button bar to bring up the Molecules form

[§4.4.3]. Next click on the Load From Files button and select the psf and dcd option under the

Molecule File Types listing. Select alanin.psf for the psf ﬁle and alanin.DCD for the DCD by

clicking on the Select psf and Select dcd buttons respectively. After this, you need only click the

Load Molecule button in order to begin reading the trajectory. In the display window you should

see a simulation of an alanin residue in vacuo. It isn’t particularly informative, but you can easily

see that the structure is quite unstable in an isolated environment. After the DCD ﬁle has loaded,

it will by default stop. To see it again or to ﬁne- tune playback, open the Animate form [§4.4.7]

by clicking on the appropriate button in the button bar. Press the button that looks like >> to

play the animation. Use the slider at the bottom of the form to change the speed of playback. By

rotating the molecule around, etc. you should get an idea about how the system destabilizes over

the course of the simulation.

2.5 An Introduction to Atom Selection

In this section it is assumed that you have the myoglobin structure mbco.pdb loaded and the views

discussed in 2.2 created. If this is not true, go back to 2.2 and repeat the process described there.

VMD has a powerful atom selection method which is very helpful when generating attractive,

informative, and complex graphics. In the previous section you used a few of these atom selection

tools. This tutorial assumes that you have already loaded the myoglobin molecule, but it isn’t

necessary to recreate all the graphical representations.

To change which atoms are used to display each representation of the molecule shown in the

display window, open the Graphics form [§ 4.4.6] and select the representation you want to change.

You can then either edit the diﬀerent ﬁelds (selection, coloring method, or drawing method) or use

the Delete button to delete the view entirely. Try changing or deleting some of the views. When

ﬁnished, delete all representations for the myoglobin structure. To get the basic line drawing view

back, clear the atom selection text entry area (press Esc), enter all and press the Create New

button.

Atoms may be selected on the basis of a property, i.e. protein or not protein, water,or

nucleic backbone. They may also be selected by atom name, such as atom C, by residue name,

such as resname HEM, or by many other identiﬁers. Multiple atoms may be speciﬁed with one key-

word. For example, the selection name C CA N O will select the backbone atoms. (A similar eﬀect

may be obtained with the command protein backbone.) VMD can handle regular expressions,

so that name "C.*" will select all atoms with names starting with C. VMD also understands the

boolean operators and, or,andnot, so the selection resname HEM and not name "N.*" selects all

non-nitrogen atoms in the heme group of myoglobin.

Several more abstract selection criteria are available. For instance, the selection x > 5 ﬁnds all

atoms with an x coordinate greater than 5, while mass >12 and mass < 14 selects all atoms with

mass greater than 12 and less than 14 atomic mass units. Many math functions are also provided, so

the selection sqrt( sqr(x) + sqr(y) + sqr(z) ) < 10 will select atoms in a spherical region

of radius 10

A centered about the origin of the coordinate space. You can pick atoms nearby

a selection with the phrase “within <distance> of <selection>” and all residues with the same

property as a given selection as “same <property> as <selection>”.

See section § 5.3 for a full description of the selection command.

2.6 Comparing Two Structures

Let’s start from scratch by deleting everything: open the Mol form [§ 4.4.3], select every line in the

browser (there should be only one), and press the Delete button.

Start by loading the mbco.pdb structure with the Files form. Turn on just the heme, CO, and

histidines by using the selection commands resname HEM CO or resid 64 93. The dot (probably

green) in the middle is the iron and you can verify that by picking it with the mouse. Do this by

changing the “Object Mode” pull-down to “Pick”, and selecting “Atoms” for the pick mode in the

Mouse form. The label HEM154:FE should appear both on the display and in the text console.

Change the pick mode in the Mouse form to “Bonds”. To get the distance between the iron and

the oxygen of the CO, click with the left mouse button ﬁrst on the iron and then on the oxygen.

The ﬁrst click turned the FE label on and the second turned the O label on and drew a line

between the two atoms with the distance drawn in the middle and a bit to the right. The distance

between the two atoms is 2.94

A, as compared to 2.93

A in the paper; not bad. However, picking

the distance between the FE and the C of the CO reveals a distance of 1.91

A as compared to

1.85

A in the paper. The diﬀerence is that the structures in the VMD distribution are actually

preliminary structures obtained before the ﬁnal coordinates were determined.

In order to experiment with more complex picking modes, consider the angle made by the O

of the CO with the FE of the heme and the NE2 of residue 93 (you can click on the atoms to ﬁnd

which ones are which). Using the Mouse form, change the pick mode to “Angles”. This should

cause the cursor to become a red crosshair. Click on each of the three atoms using the left mouse

button. After the third pick, a shallow angle will appear indicating an 8.71 degree angle between

the three atoms.

Now load the intermediate star.pdb ﬁle which can also be found in the proteins directory of

your distribution. Again use the Files form to do this. Both of the molecules will be loaded side by

side. Go to the Graphics form and change the selection so it the same as the ﬁrst, i.e. resname HEM

CO or resid 64 93. The two molecules are almost atop each other, making it hard to distinguish

the two, so change the colors to simplify things.

First, in the Graphics form, change the Coloring method to ‘Molecule’. Use the Selected Molecule

chooser to change the mbco.pdb Coloring method to ‘Molecule’ as well. Open the Color form [§4.4.11]

and scroll the Category browser down until the line ‘Molecule’ is visible. Click on it then click

on the line which says mbco.pdb.(Theremaybetwombco lines if the ﬁle had been loaded before

in this session.) Scroll the Colors browser up to click on ‘blue’. This should change one of the

molecules in the display to blue.

Next, click on the last line in the Names chooser, which says star.pdb. This time, choose ‘red’

from the Colors chooser. The display should be much easier to understand. The myoglobin with

the bound CO is in blue and the intermediate state is in red. At this point it is easy to measure

the change in position between the two diﬀerent states by using the middle mouse button to pick

the same atom in the two conformations.

Once that is done, it is easy to point out one interesting aspect of the way VMD handles the

graphics. Go to the Mol form, select one of the two molecules, and press Toggle Fixed.Enter

translation mode and move the other molecule around. Notice that the number which lists the

distance between the two atoms never changes. That’s because the mouse only aﬀects the way the

coordinates are translated to the screen image. It does not aﬀect the real coordinates at all. It is

possible to change the coordinates in a molecule using the text command interface, or by using the

atom move pick modes [§4.1.2]).

By the way, unﬁx the molecules and do a ‘Reset View’ from the right pull-down menu to reset

everything. Load up the third structure, deoxy.pdb and give it the same selection as the other two

molecules. However, color this one green. Pull out Nature v. 371, Oct. 27, 1994 and turn to page

740. With a bit of manipulation you should be able to recreate the image that appears there.

2.7 Some Nice Represenations

The following views are quite nice for displaying proteins and nucleic acids:

selection: all

drawing method: tube

coloring method: segname (or chain)

why? This show the backbone of the protein and nucleic acid strands

selection: protein and (name CA or not backbone)

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