Computer
Graphic Display ofMolecular Structures
Computer
Graphic Display ofThere are many programs that let you visualize and study molecules
in three dimensions.
We will use RasMol. Links to two other programs are given at
the end.
One powerful feature of Rasmol is that it allows the user to display different parts of the molecule in different formats, such as spacefilling, alpha-carbon backbone trace, or ribbons indicating alpha helix and beta sheet; an example is shown in the image at top left. In the program (but not in the image above), the user can rotate the image freely to view it from different directions; this gives a 3D appearance. One can also view in stereo mode, in which the image is split, allowing cross-eyed or wall-eyed viewing.
Learning to use the program requires some effort, but, once you learn it, your ability to visualize molecules and their interactions improves far beyond what you can perceive with static 2D images in a book or journal article.
There are several steps in learning the program.
1. Download a copy of the program to
your own computer.
2. Download the files, termed PDB files, that tell the program where
to put the atoms. PDB files and links are described here.
3. Learn the commands that tell the program what to do. Start
here .
4. Learn what "scripts" are and what they do, both so you can use
scripts developed for this class, and so you can learn to write your
own scripts. Start here.
Hardware: RasMol will run best on a reasonably modern Macintosh or a PC running Windows 95/98/2000/XP. Older computers can be used but tend to be slow.
RasMol is called RasWin for Windows, and RasMac for the Macintosh. The two programs are practically the same, with a few exceptions noted below. The version we will use is version 2.6.
On your computer, make a folder called "RasMol" (or "Raswin" or "Rasmac" if you prefer). Get the version of RasMol appropriate for your platform (PC or Mac) at Download RasMol . Note that the link for the Windows version talks about it being for Windows 95 or NT; however, the program will also run on Windows 98, 2000 or XP. When you download the program, place into your RasMol folder.
To draw molecules, RasMol must know the positions of all the atoms. These are experimentally determined by x-ray crystallography (sometimes by NMR), and are stored in special files of molecular coordinates called PDB files. More details:
What are PDB files?.
What can you see at various resolutions in
x-ray structures?
You can download PDB files and save them in a directory. You can get PDB files from the PDB data bank. If you already know the file name (such as 1lmb.pdb for lambda repressor:DNA complex) you can enter it in the box marked "Enter a PDB ID:"; otherwise, you can click on "SearchLite" to do a keyword search. On the resulting page, enter some information, such as the name of the protein, and the search engine will find all the relevant files. I have stored a number of PDB files of protein-DNA co-crystals locally for your convenience. Before downloading these, however, take a look at the directions for scripts below; these directions enable you to download several useful PDB files in an easy way.
When you download PDB files, you should save them using the SaveAs command of your browser into a RasMol folder (directory). For many purposes, it is most convenient to have them in the same directory as the RasMol program.
Warning: For some PDB files, not all the biologically relevant molecules are present. An example for this class is the PDB file for the leucine zipper protein GCN4. Link here to read more about this problem and learn how to cope with it. All the files at the above link are complete.
You can configure your Browser to run RasMol when you download the file. If you choose to do this, you see the molecule in RasMol as soon as it is downloaded; that is, you don't need to save it, load RasMol, and open the file to view it. The directions at the above link are only for Netscape 2.0 and 3.0.
I was able to do it for Netscape 4.0, 4.6 and 4.75, and for Internet Explorer 5.0, on the PC as described, but I haven't figured out how to do so for later versions of Netscape or IE on the Mac. If you figure this out, let me know (jlittle@u.arizona.edu) .
At least in Netscape 4.75 and Internet Explorer 5.0, when you click
on the file the browser gives you the choice of opening it in RasMol
or saving it to your hard drive. If your browser works differently,
perhaps you can save it using File/SaveAs , then naming the file and
telling it where to save the file.
I have adapted a tutorial, originally written by Profs. Bill Montfort and Michael Wells (Dept. of Biochemistry), for this class. This tutorial uses a high-resolution protein:DNA complex (the same one depicted at the top of the page) to introduce you to the commands used to examine molecules, and to make images like the one at the top of this page.
Another useful source is Eric Martz's Rasmol home page. You can link from there or with the next link to some additional tutorials. One of the difficult aspects of RasMol is knowing how to use the "Select" commands; here is a tutorial that is a big help.
Scripts are files that contain a series of commands like the ones you type in yourself in the RasMol Command Line window. Usually they contain pauses for you to study the image, and then you hit a key to proceed. One advantage of scripts is that you can view them without knowing the commands or anything about the molecule. The disadvantage is that you don't have much control over what is displayed.
Scripts can be used for two different purposes.
First, they are a powerful and easy way to show particular features of a molecule. You can learn to write them, although it takes some time. This involves using the commands that you learn in the tutorial described above. Additional help is in another tutorial about writing scripts.
Second, in class we will use several scripts I have written; in these scripts, I have included various stopping points at which you can rotate the molecule at will, and then hit a key to restore the previous view. These scripts will be especially helpful in understanding the various DNA-binding motifs commonly found in specific DNA-binding proteins. I encourage you to download these scripts to your own computer and use them. Directions for downloading and running these scripts are given here. You can get them from a link given below. The way to do this differs somewhat for the Macintosh and the PC, as described separately for each.
1. Make a folder dedicated to this exercise. Let's call it "motifs", but it can have a different name if you like, and it doesn't have to be under the RasMol folder. Copy (don't move) RasMol into that folder; its name is 'RasMac v 2.6' (you need a copy of RasMol in the same folder, so that the program will be able to find the files). If you want access to the help file (rasmol.hlp), copy it to this folder as well.
2. You now want to download the files to run the scripts. There are two ways. The first (2a) is easier, but I'm not sure it will work on all computers. If it doesn't, try method 2b.
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2a. Click motifs.sea.hqx . If you are using Netscape, it will open the file, which looks like gibberish. Click on File/SaveAs, and save it in your "motifs" folder. |
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1. Make a folder dedicated to this exercise. Let's call it "motifs", but it can have a different name if you like, and it doesn't have to be under the RasMol folder. Copy (don't move) RasMol into that folder; its name is 'RasWin v 2.6' or perhaps rw32b2a.exe (you need a copy of RasMol in the same folder, so that the program will be able to find the files). If you want access to the help file (rasmol.hlp), copy it to this folder as well.
2. You now want to download the files to run the scripts. There
are two ways. The first (2a) is easier, but I'm not sure it will work
on all PC's. If it doesn't, try method 2b.
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2a. Click motifs.zip. This file contains many files in a "zipped" or "packed" format, just to make it easier to transfer them as a group. To unzip them, you need to have a program like WinZip installed on your computer. You can get a free evaluation version of WinZip at WinZip . Once it is installed, click on the motifs.zip file and tell it to put the files in the "motifs" folder you made above. A freeware program Freezip is another option. If you use FreeZip, I think that you should download the motifs.zip file (at the above link) then put it into your "motifs" folder before you click on it to unzip the files; the version of FreeZip that I have does not ask you where to put the files. |
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The scripts used in class, and downloaded above, focus on two different topics: DNA-binding motifs (motifs.txt), and detailed contacts between a particular protein and its binding site (contacts.txt).
Caution about using these scripts: They have various points at which the script pauses, usually for you to hit a key. If you rotate the structure at one of these pauses, in many cases it will not be oriented correctly for the next part of the program. The exceptions are indicated by phrases similar to "Rotate the structure as you like then hit a key to restore the view"; in these cases, it is fine to rotate it. If you have rotated it inappropriately (as described above), at this point the proper view I intended will be restored.
To run the scripts, you have to run the copy of RasMol that is in your "motifs" folder. If you run a different copy of RasMol, it won't be able to find these files.
The scripts describing DNA-binding motifs are all contained in a big script called "motifs.txt". To run this script in RasMol, you enter at the Command Line
script motifs.txt
and it should execute.
Eventually you will probably want to look at portions of this without going through the entire script. This is easy to do, because this script is a so-called "master script". It consists of a series of scripts about individual proteins. These individual scripts and their names are described here. Then, if you want to run one of them (for example gcn4.txt), you would enter at the command line
script gcn4.txt
and RasMol will run just that script.
In addition to "motifs.txt", there is another script called "contacts.txt", which describes and illustrates the detailed contacts between DNA and glucocorticoid receptor. To run it, enter
script contacts.txt
Several other excellent programs are available that you may want to consider using instead of or in addition to RasMol. I do not have much experience with these; let me know how you like them if you try them.
A spin-off of RasMol is called Chime. It allows you to view RasMol images directly on a web page. However, be warned that, if you install Chime in your browser (as a so-called Plug-in), it prevents you from using RasMol as a helper (see above), except during a single session; that is, if Chime is installed, PDB files will be shown in Chime not RasMol. See this link for more details on this problem.
Here is a link to Chime. Once installed, it will run pre-made scripts directly. With these, you need to indicate which images you want by clicking buttons in a frame.
Please note that the Chime pages argue strongly that RasMol is outmoded! This argument has some force is one is talking about developing teaching materials; however, for this graduate course the main purpose is to empower you to run the program on your own so that you can look at structures, both in this course and for pursuing your own interests later on. See here for a comparison.
These programs were developed by Prof. Richard Hallick (Department
of Biochemistry). They have excellent graphics and an easy interface
with pull-down menus; a link is MacMolecule.
Otherwise known as Swiss PDB viewer, this program allows one to superimpose structures, change particular amino acids to simulate the effect of mutations on the structure, and other features not offered by RasMol. In my very limited experience, it is harder to learn than RasMol.
This program is being used in Biochem 565. I don't know enough about it to compare its features to those of the other programs. Apparently it is more powerful than RasMol but a lot harder to learn. If you know more, please tell me!