MOLMOL Tutorial

Introduction

This document shows the use of MOLMOL in some examples. It is meant to be used together with the manual (users guide). Each example will first show a picture and give commented step by step instructions on how it can be created.

Notation

The commands are listed with all arguments in the way they appear in the log window and history. They can be entered on the command line in this form, but this is not what you would normally do. Every command can be activated from a pulldown menu, and the arguments can be entered in the dialog box that will appear. If this is the preferred way, it will be indicated with the notation Menu->Submenu->Entry below the command. Frequently used commands or combinations can also be activated from the buttons on the right side of the window. This is indicated by Button:name. Some actions are normally done with the mouse, this is indicated by Mouse. Other actions are most convenietly carried out by using one of the dialog boxes, this is indicated by Dialog:name. The dialogs can be opened by clicking the corresponding buttons (selection, style, color).

Whenever a command appears in the text, it can be used as link to the corresponding online manual page.

Preconditions

All examples are based on the NMR structure of BPTI determined by K. Berndt et al., this file is stored as data/1pit.pdb in your MOLMOL distribution. The tutorial assumes that you start the program from the directory that contains this file. Note that menus, buttons etc. can be configured by the system adminstrator or user. This tutorial assumes that the program is in its default configuration.

Examples

Example 1: Neon Figure of Bundle with Sidechains in Different Colors

Example 2: Ribbon Display

Example 3: "Sausage" Display

Example 4: Surface with Electrostatic Potential


Last modified: May 5, 1996

Reto Koradi, kor@mol.biol.ethz.ch