Instructions for RASMOL 2.6

There are two versions Rasmol and rasmol5. They are very similar Rasmol5 is a later version but not necessarily better.

When you open Rasmol the command line is also automatically opened - but hidden on the bottom toolbar.

Raswin.exe is programme

Rasmenu is command line. To get this when in Rasmol programme click Alt/tab until the command line appears.

RasmolHELP is for an earlier version but most of it applies to version 2.6.

Some instructions are given using the command line (CL), some are given using the menus on the main screen

The HELP programme (from main screen) has everything in it if you know what to look for.

Select user manual.

For commands look in Command references (in the Table of contents); type the commands in the command line box.

For Predefined sets (eg all aromatics or all basic etc) find what they are called in the Predefined sets listed in the Table of Contents.

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File / Open (main screen) To get your file. It will usually have a pdb extension.

Set background white (CL) if you prefer white or want to print out the product (can print black background but product is poor and expensive).

Select (CL) This selects amino acids.

Eg Select trp Colour (CL) blue Display spacefill

Can select particular sequences (eg 34-76)

Can select just acidic amino acids (Select acidic)

To get all of model Select all

NB you may have to select parts of protein that are not amino acids separately eg cal (calcium) ret (retinal) etc.

Restrict (CL) (followed by amino acid number) allows you to look at small bits of molecule

eg restrict pqq,cal,103,104

Centre (CL) Use this command so that you can rotate the molecule about an axis of your choosing; eg Centre 103 will now rotate about amino acid 103

Zoom shf/lt mouse

Rotate (x axis or y axis); use left mouse

Rotate (z axis) shf/rt mouse lllllllppoo

Move whole thing rt mouse

NB: to get a feel for the programme I suggest you select a protein then play with all the commands in the Display, Colour and Options screen menus.