RASMOL Tutorial - Creating and Running Scripts

Created by: Angela M. Amoia 08/14/03
Adapted from a lesson by: William R. Montfort 09/12/00
Last Updated/Modified by: Angela M. Amoia 08/30/04
Lesson Date: 09/15/04 - W

A Bit About RASMOL Scripts

What is a script? A script is a text file that contains a number of RASMOL commands and allows a series of representations (views) to be predefined and executed sequentially by RASMOL. (To clarify, a text file is created using a text editor such as TextPad, wordpad or notepad, uses ascii format and has the file extension '.txt'.) A script is usually created to illustrate an interesting feature(s) of a protein. For our purposes, a script is highly annotated and should act as a stand-alone lesson. It is useful to describe each view you are showing (using the 'echo' command), just as a figure legend, so the viewer can understand what you are trying to point out. The script as a whole, should flow as if you are telling a story to your viewer. The user should be able to walk away having learned something about the protein without having the creator present to talk you through it.

Scripting Commands: We have seen several scripts in lecture and you will prepare scripts for your class presentations. Some scripting commands will be introduced through this tutorial however not all can be visited. For a complete list and description of commands please refer to the RasMol Manual (for version 2.6) http://www.umass.edu/microbio/rasmol/distrib/rasman.htm (Roger Sayle, Glaxo). A hard copy can be found in the computer lab in the class binder. Please DO NOT REMOVE this from the lab. I will NOT REPLACE IT!

Tips:

• READ THE MANUAL!

• PRACTICE! Writing scripts is fairly easy, however, sometimes the scripting language can become a bit cumbersome. But remember, the more scripts you write and the more mistakes you make, the more practice you will get and the better you will become! Don't get frustrated! You can't become an expert overnight!

• Print out a paper version of the scripts used in the tutorials (I have done this for you already) in order to see how the commands used relate to the display and annotations seen. I find this very helpful and it is a good way to take notes.

• Write your scipts using a text editor (TextPad preferably, wordpad or notepad can be used also). I suggest NOT using a program like Word. However, if you do make sure you save it as text with line breaks.

• When first learning how to create your own script I suggest making it step by step. By that I mean having a text editor open and immediately typing in commands that you used to create a view that you like. By doing this you will create a rough "master script" that contains all the views of interest. Check periodically if it is working to your expectations by executing it in RASMOL. This way you can pinpoint when a problem occurs before it becomes to far long. Once you have the entire script the way you want it and know it works by executing it in RasMol, you can go back and polish it up by adding your detailed figure descriptions using the 'echo' command.

Tutorial Exercise

This exercise is designed to teach you how to create and run scripts using the molecular graphics program RASMOL. If you have any questions, please ask!

Tutorial Exercise Objectives:

• Recall what a script is
• Run a pre-made script
• Create and run a SHORT novel script

Note: Next week in class (09/24/03) you will be asked to run your SHORT novel script. In two weeks (10/01/03) you will turn in the beginning of your RASMOL script for your project. In three weeks (10/08/03) you will turn in a printout of your RASMOL script that recreates one of the detailed figures in your cornerstone paper. For more details on these assignments, please see the computer section packet.

• Obtain TextPad. TextPad is a text editor similar to wordpad or notepad. It creates files using ascii format and files have the file extension '.txt'. TextPad should already be downloaded on the lab computers. If you would like to obtain a copy for your personal computer you can do the following: (1) Go to the UA's CCIT (Center for Computing & Information Technology) website (http://computing.arizona.edu); (2) Click on 'Site-licencensed Software', then Shareware/Freeware, then 'shareware.com'; (3) Search "TextPad" (no quotes, capitalize, no spaces); (4) Click 'Download Now' and follow the directions. Note where the program was placed so you can access it at a later time. You can make a shortcut on your desktop if you would like (recommended). (C:\Program Files\TextPad4\txpeng462.exe)

• Obtain the PDB file '1MBN.pdb' and the script 'ras_intro.txt' and put them into your Rasmol folder. (You should already have '1MBN.pdb' in your folder). The script 'ras_intro.txt' can be found locally at U:\shared\Read_Only\Rasmol or on the course website under Computer Section/Shared PDB's and RASMOL Scripts. Save the script as 'ras_intro.txt' (without quotes).

• Open 'ras_intro.txt' in TextPad (or a text editor such as notepad or wordpad). (1) Double click on the TextPad icon on the desk top; (2) File, Open, Navigate to 'ras_intro.txt'. If it doesn't appear right away, make sure your file type is set to Text Document (*.txt);(3) Minimize the window. Note: if you use Word (I don't suggest doing so), be sure to save the file as 'Text with line breaks'.

• Start RASMOL (rw32b2a.exe) from your Rasmol folder.

• Type 'source ras_intro.txt' (without quotes) in the command window to start the script. A wireframe of myoglobin and script commands should appear in the display and command window respectively. Note: To run any script, simply type 'source filename' where 'filename' refers to a script file.

• Maximize the text editor window or refer to the printed 'ras_intro.txt' to follow along as you step through the script. This will give you an understanding of how the commands are related to the display.

• Step through the different displays (paying attention to the annotation in the command window) by hitting any key, and change the view with the mouse at anytime; Press 'ctrl z' to exit at any time during the script.

PART II. Create and run a SHORT novel Script. In this part, we will create a short script together using the protein NP4 (1KOI.pdb). NP4 is a nitric oxide (NO) transport protein. It is similar to myoglobin in respect that it contains a heme cofactor that binds ligands. We will load the PDB file, highlight one interesting feature of the protein, vaguely annotate with "echo" comments, and use the "reset" and "pause" commands at least once.

I have created three versions of this script in advance. I strongly recommend you go back and practice at your own pace. You can find these on the course website under Computer Section /Computer Section Weekly Handouts:

Version 1: 'ras_introscripts_np4raw.txt '. This version contains the least amount of annotation and no side notes describing the commands used. Its purpose is to illustrate the bare bones of a script. Together we will recreate this script step-by-step from scratch. We will go as far as we can and then you can finish at your will.

Version 2: 'ras_introscripts_np4notes.txt'. This version contains fully annotated views (i.e. with detailed figure descriptions) and side notes describing the commands used. Its purpose is to familiarize you on how scripting commands relate to the display. This will be useful when going back on your own. Note: THIS SCRIPT WILL NOT EXECUTE IN RASMOL! IT IS A PAPER VERSION ONLY FOR LEARNING PURPOSES. YOU CAN EITHER PRINT IT OR HAVE IT OPEN IN A TEXT EDITOR.

Version 3: 'ras_introscripts_np4.txt'. This version contains fully annotated views (i.e. with detailed figure descriptions). Its purpose is to illustrate how a script should be highly descriptive and thus can act as a stand-alone lesson. The annotations (i.e. figure descriptions) are detailed and the script flows as if telling a story to the viewer. Please use this script as a "role model" for how your final project script should look.

OK lets start:

• Obtain the PDB file '1KOI.pdb'. It can be found locally at U:\instructor_deposit\Rasmol or on the course website under Computer Section/Shared PDB's and RASMOL Scripts. Save the pdb as '1KOI.pdb' (without quotes).

• Open a text editor (TextPad).

• Follow along. We will go as far as we can and then you can finish at your own will by referring to the pre-prepared scripts above. If at any time you become lost, either stop me of refer to Version 1: ras_introscripts_np4raw.txt ' which I handed out.

END OF TUTORIAL EXCERSIZE :)