Archive Magazine 1996/ARCHIVE_96.iso/discs/mag_discs/volume_9/issue_10/rasmol/!RasMol/!Help

Text File | 1996-04-03 | 22KB | 427 lines

RasMol 2.6 / 1.10 (02-Apr-96)

Purpose:      Molecular Graphics Visualiser
Author:       Roger Sayle ([e-mail])
RISC OS port: Martin Wⁿrthner ([e-mail])
Runs under:   RISC OS 3.1 or higher, supports RISC OS 3.5 true colour modes
              Requires at least 2MB RAM (see below "Saving memory")
Status:       FREEWARE, see "Copyright" below

Contents:
  * Introduction
  * Starting RasMol
  * First Steps
  * Loading files
  * Window size
  * The tool bar: Selection, Rotation, Translation, Zooming, Z-slabbing
  * Display quality and dithering
  * Saving and exporting
  * Configuration
  * Saving memory
  * Script files
  * PC script directories
  * Display types
  * The View sub-menu and the "Dot surface" option
  * Colours
  * The RasMol Command Line
  * Additional file types
  * Links to molecule databanks and WWW pages about RasMol
  * Copyright

  RasMol2 is a molecular graphics program intended for the visualisation of
proteins, nucleic acids and small molecules. The program is aimed at display,
teaching and generation of publication quality images. RasMol runs on
Microsoft Windows, Apple Macintosh, Acorn RISC OS, UNIX and VMS systems. The
UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display
(X11R4 or later). The program reads in a molecule co-ordinate file and
interactively displays the molecule on the screen in a variety of colour
schemes and molecule representations. Currently available representations
include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres,
ball and stick, solid and strand biomolecular ribbons, atom labels and dot
surfaces.

  The RasMol help facility can be accessed by typing "help <topic>" or "help
<topic> <subtopic>" from the RasMol command line. A complete list of RasMol
commands may be displayed by typing "help commands". A single question mark
may also be used to abbreviate the keyword "help".

  Copyright (c) 1992-1995 by Roger Sayle ([e-mail])


 Starting RasMol
 ---------------
  When started (by double-clicking on the application itself or on a file which
RasMol understands), RasMol installs itself onto the icon bar and opens two
windows. These are the Molecule window (black) and the RasMol Command Line
window. The Molecule window displays the currently loaded molecule and allows
you to rotate/translate/z-slab it using the mouse.

 First steps
 -----------
  To get an idea what the program is about, double-click on the file '1crn' (this
is a small protein file). If you have not already loaded RasMol, it should start up
now. The protein is displayed in wireframe mode in the Molecule window (behind the
Molecule window you can also see the Command Line window). Select the rotation tool
(the tool below the "pointer" tool), click SELECT somewhere in the Molecule window
and drag horizontally or vertically. This rotates the molecule about the x/y-axes.
Using ADJUST, you can rotate about the z-axis. Now click MENU and choose "Spacefill"
from the "Display" sub-menu. For a nice specular highlighting effect choose
"Specular" from the "Options" sub-menu (do not try "Shadows" as it is very slow).
If you are in a 16 or 256 colour mode, try the tool at the bottom of the toolbar
which dithers the image to the current palette. This improves the display quality
significantly but it takes a few seconds.
  To test other ways of displaying the molecule, try also "Ball&Stick" and "Back-
bone" from the "Display" sub-menu. While being in "Backbone" mode, select the
translation tool (the one below the rotation tool). Click ADJUST somewhere in the
window and drag slowly (!) vertically to zoom in/out.

Note that the program is fully multitasking, even while calculating complex images
like dot surfaces or shadows. While the program is calculating the pointer changes
to an hourglass while it is inside the RasMol window.

 Loading files
 -------------
  A Molecule files may be loaded by double-clicking on it or by dragging it
to the RasMol icon on the icon bar or to the Molecule window.
  Dragging a file to the Command Line window causes its full path name to be
inserted at the caret position. This makes loading files from the command line
easier.

 Currently recognised filetypes (allocated by Acorn) are:

 Industry standard name              DOS ext.   RISC OS name  type
 -----------------------------------------------------------------
 Brookhaven Protein Data Bank files  PDB        PDB           12A
 Alchemy files                       ALC        Alchemy       129
 Molecular Design Ltd. MOL files     MOL        MOL           128
 MOPAC files                         ???        MOPAC         127
 RasMol script files                 SCR        RasMolSc      12B

Note that files have to be filetyped correctly in order to be loaded by
RasMol. If you load a file and all you see is a black window then most
probably the file does not contain any connectivity information. Try
entering "connect" in the command line window.

 Window size
 -----------
  The size of the Molecule window determines the speed of the application and
also how much memory is used. The default size of the display is 480 by 480
pixels. By choosing "Scale" from the main menu you can change the scaling of
the window. 100% corresponds to 480 pixel. The width of the window is a
percentage of its height, so a window at a scaling of 50% and a width of 150%
would be 240 pixels high and 360 pixels wide.
  To set the default size, change the configuration of the program (see below
"Configuration").
  Note that the memory you save by decreasing the window size is not given
back to the system, so to save memory, change the window size used at start-
up by changing the configuration.

 The tool bar: Selection, Rotation, Translation, Zooming, Z-slabbing
 -------------------------------------------------------------------
  The tool bar contains five tools. From top to bottom these are:
The selection tool, the rotation tool, the translation/zooming tool, the
z-slabbing tool and the dithering tool. The latter is described in detail
in the section "Display quality and dithering".
  The first four determine which interactive mode the program is in, i.e.
how mouse clicks/drags are interpreted:

Select mode: If you click on an atom, information about it is displayed in
             the Command Line window. Note that even though this is called
             "selection mode", this has nothing to do with selecting groups
             of atoms or single atoms using the command "select" on the command
             line (for more information on this powerful feature, type "help
             select" on the command line).
Rotation mode: Dragging horizontally using SELECT rotates the molecule about
               the y-axis. Dragging vertically using SELECT rotates the molecule
               about the x-axis. Dragging vertically or horizontally using ADJUST
               rotates the molecule about the z-axis.
               Note that rotation works differently from the way it works in
               ArtWorks or Draw where you drag along an arc. In RasMol you
               should simply drag either horizontally or vertically.
Translation/zoom mode: Dragging using SELECT translates ("moves") the molecule
                       accordingly in the xy-plane. Dragging using ADJUST zooms
                       in/out (i.e. it translates the molecule along the z-axis).
Z-slab mode: This only has a visible effect if the "z-slabbing" option is ticked
             in the "Options" menu. Z-slabbing allows you to see "inside" the
             molecule by slabbing it against a vertical plane. The slab plane can
             be moved along the z-axis by dragging with either mouse key.
Dither tool: See next passage

 Display quality and dithering
 -----------------------------
  RasMol produces bitmaps with 256 colour palettes, so they do not display very
well in RISC OS 256 colour modes with the standard fixed palette. In particular
space filling representations look very poor in 256 colour modes.

  Therefore the RISC OS version of RasMol is able to produce dithered output
using more or less the same algorithm ChangeFSI uses to dither images. This
takes a few seconds, but the results are worth while the delay. Dithering works
in both 256 and 16 colour modes. As dithering is quite time-consuming, it is only
performed on request, that is if you click on the "Dither" tool (the bottom tool
on the tool bar). Of course, as soon as the display changes (e.g. because you
change a display option or you rotate the molecule), the picture is recalculated,
so it has to be dithered again. Normally, you would first set all the options you
want, e.g. "Spacefill" and "Specular" etc. and then only when everything is
OK dither the image for final output.

  Note that if you subsequently save the image as a sprite, the dithered version
is saved! This is a good option if the main purpose of the picture is to be
viewed, in particular on machines without true colour modes. If however, you
are planning to print the image, you are advised to save the undithered
version (you can revert to the undithered version by choosing "Recalculate"
from the main menu). Even though this looks worse on screen it prints much better
in particular if it is scaled before printing!

  To compare RasMol's internal dithering with ChangeFSI, try exporting the
undithered sprite (which contains a full 256 colour palette) and feed it through
ChangeFSI.

 There are several other ways of improving output quality:
 1) for RiscPC owners with VRAM:
    * Change to a 32768 colour mode
 2) for owners of a CC ColourCard:
    * Change the 256 colour palette e.g. using the "PalMaker" utility. This
      gives the same display quality as a 16 millon colour mode!
 3) * save the sprite and feed it through ChangeFSI as suggested above

 Saving and exporting
 ---------
  The current display can be saved as a sprite using the menu item "File.Save
sprite" from the main menu. This saves the image as a 256 colour sprite with
a full 256 colour palette (not suitable for RISC OS 2 unless you load the
sprite into !Paint and remove the palette). If the currently displayed image
is dithered, the dithered version is saved. Note that it is not possible to
save a 16 colour sprite, even if the current image has been dithered to 16
colours. Feed the undithered image through ChangeFSI to achieve this effect.

  "File.Export.GIF" allows you to save the current image (only if it is not
dithered) as a 256 colour GIF file with a 256 colour palette.

  "File.Export.EPS (bitmap)" saves an EPS file containing the bitmap.

  "File.Export.Vector PS" is a very powerful option which is not fully
implemented yet. However, for some representations it should work already.
This output can be fed through a PostScript interpreter, e.g. RiScript to
produce a Drawfile. However, do not expect too much, both vector PS export
and RiScript are rather unstable still.

 Configuration
 -------------
  RasMol provides some basic configuration options that can be set by choosing
"Choices" from the icon bar menu.
The "Time slice" option determines how much CPU time the program takes.
Decreasing the value means that the desktop is slowed down less, but it may
take longer to calculate an image. Increasing the value means that more
CPU time is taken. If you enter 0, then multitasking is disabled completely
while images are calculated.

  The "Default scale" and "Default width" entries correspond to the menu entries
of the same name. They can be used to set the values to be used at start-up
time of the program. Note that a smaller window uses less memory.

  Note that if you disable the toolbox by deselecting the "Display toolbox"
option, RasMol reverts to the standard interpretation of mouse operations as
used by the X11 or MS Windows version:

 with Ctrl held down:  z-slab mode
 with Shift held down: SELECT: rotate about z-axis
                       ADJUST: zoom mode
 else: SELECT: translate in the xy plane
       ADJUST: rotate about x- and y-axes

 Saving memory
 -------------
  RasMol just about starts up on a 2MB machine. For the first time, you might
have to do a clean boot and switch to a 16 colour mode before RasMol would
start. To save memory permanently, reduce the window size (not using the main
menu, but using the iconbar "Choices" item) and click on the Save button. Then
reload the application. Most options do not need any extra memory and most
molecules are rather small. You should however avoid the "Dot surface" option
as this takes lots of extra memory.

 Script files
 ------------
  Script files may contain an arbitrary number of RasMol commands. For details
refer to the RasMol manual. Script files must have the file type "RasMolSc"
in order to be recognised by RasMol. Double-clicking on a script file or
dragging it to one of the RasMol windows starts the script. Scripts do not
multitask, but you can abort them by pressing and holding down the Escape key
until the hourglass disappears.
  A script file which reproduces the current setup can be saved using the
"File.Save script" menu item. It does not include all options, e.g. the "Dot
surface" option is ignored. However, it is a good point to start from if you
want to be able to restore a certain set of options later.
  Note that using scripts you can produce running demonstrations: Use the
refresh command to force the screen to be updated while the script is running.
The pause command can be used to ask the user to press a key to go on. When
doing so it is advisable to use the echo command to print some text in the
command window like "Press any key to go on".

 PC script directories
 ---------------------
  Some people have built script directories which contain molecule files and
scripts. Usually, there is one main entry script to be started called
something.TOP. On the PC platform you would change the current directory to
the script directory and then run the script. This way, the script can
reference the molecule files without any pathname but simply by specifying
their name.
In order to make porting of these directories easier, RasMol provides the
following feautures:
- automatic conversion of PC filenames to Acorn filenames, e.g. a command
  "load DNA.PDB" is automatically converted to "load DNA/PDB".
- if a file is not found, RasMol looks inside the directory specified by
  the system variable RasMol$FilePath
So all you have to do is to give the main script file (the one ending in
/TOP) the correct type "RasMolSc" and add a !Run file to the directory which
reads as follows:

 Set RasMol$FileDir <Obey$Dir>
 Filer_Run */TOP

Double-clicking on the !Run file sets up the variable and starts the script.

 Display types
 -------------
  When loaded, a molecule is displayed in Wireframe mode. To change the
display mode, bring up the main Menu by pressing the middle mouse button over
the Molecule window. From the "Display" submenu you can choose your preferred
display style from the following:
 - Wireframe         - Ball&Stick
 - Backbone          - Ribbons
 - Sticks            - Strands
 - Spacefill         - Cartoons
 The default is Wireframe. This is also the fastest way of displaying the molecule.
Use this style if you want to translate/rotate the molecule a lot, as these operations
work in real time in Wireframe mode.
 The sub-menu of "Wireframe" lets you to choose solid or dashed lines (the "dashed"
item is a shortcut for the "wireframe dash" command).
 The sub-menu of "Sticks" allows you to enter the thickness of the sticks. Pressing
"Default" fills in the default value (which is 40, or 80 if the molecule has more than
256 atoms).

 For more details on these styles, type "help <display style>" on the RasMol
command line.

 The View sub-menu and the "Dot surface" option
 ----------------------------------------------
  These are minor options like whether or not axes are to be displayed. The only
really important item is "Dot surface" which displays a Van der Waal's dot surface
around each atom. The density may be specified in the sub-menu, 100 is the default
value, but you can enter values up to 1000. Note that the dot surface is actually
calculated and stored in memory, so this option takes some computation time and
also quite a bit of memory if the molecule is large. Using the "colour dots" command
you can create some interesting effects, e.g. "colour dots potential" which colours
the dots according to their electrostatic potential.

 Colours
 -------
  This submenu implements the RasMol "colour" command. For Wireframe, Sticks,
Spacefill and Ball&Stick mode, you would normally use the CPK colouring which
is chosen by default when a molecule is loaded. Choosing a menu item always
sets the colour scheme for the whole of the molecule.
  If you want to colour
part of a molecule use the "select" and "colour" commands from the command
line.
  For details on the colour schemes listed on the menu, type "help <colour
scheme>". Note that choosing "User" only makes sense if the currently loaded
file is a PDB file which contains user-defined colour information.

 The RasMol Command Line
 -----------------------
  The Command Line window allows you to enter RasMol commands. These are described
in the main RasMol manual. Typically, the menu entries only give a quicker way of
accessing the most frequently needed command line features. Therefore most of the
menu options are only described briefly in this RISC OS-specific file. For further
information, use RasMol's command line help system. Entering "help" displays
information about the help system.
  It is worth noting that you need to use the command line to use the program
to its full extent. For example, most menu options apply to the whole molecule,
e.g. the display type or colour settings. Using the command line, however, it is
possible to select parts of the molecule (e.g. all Hydrogen atoms or only specific
amino acids) and apply display style or colouring commands to them. In fact, most
RasMol commands only affect the current selection (type "help select" to find out
how to select groups of atoms). Many commands take parameters which make them more
versatile than their menu conterparts.
  Other features include calculation and display of hydrogen bonds, SS-bonds,
calculating connectivity information for molecule files without bonding etc.

 Additional file types
 ---------------------
  Files of the following types can only be loaded using the command line:
Tripos' Sybyl Mol2 file format, the CHARMm file format and  MSC's XMol XYZ
file format. To load these, type "load <format> <filename>" (where <format>
is "mol2", "charmm" or "xyz" respectively) and press Return. Alternatively,
type "load <format> " and drag the file to the Command Line window. Then
press the Return key.

  Note that you can only have one file loaded at a time. If you try to load
a file from the command line while there is a file in memory, you get an
error message. If this happens, clear the database by entering "zap", then
try again. If you load a file by dragging it to the program or by double-
clicking on it, the database is cleared automatically before the file is
loaded.

 Links to molecule databanks and WWW pages about RasMol
 ------------------------------------------------------
An enormous collection of proteins is available from the Brookhaven Protein
Databank at www.pdb.bnl.gov. Other useful addresses:

The RasMol home page:        http://klaatu.oit.umass.edu:80/microbio/rasmol/
This page contains lots of links to places to get molecule files from.

Okanagan University molecule files: http://www.okanagan.bc.ca/chem/molecule/

 How to contact the authors
 --------------------------
  Please direct any comments about the RISC OS version to me:
   Martin Wuerthner
   Jahnstrasse 18
   71116 Gaerrtingen
   Germany
   [e-mail]

  Please direct any non-RISC OS-specific comments about the program to
Roger Sayle, because he really wrote the whole thing and all the credits
are due to him:
   Roger Sayle
   [e-mail]

 Copyright
 ---------
  This program, the RISC OS port of RasMol 2.6, may be distributed freely
provided that all its files are supplied unaltered and no profit is made
on its distribution. The implementation of the RISC OS specific features is
Copyright ⌐ 1996 by Martin Wⁿrthner ([e-mail]).
The main part of the program is Copyright ⌐ 1992-94 by Roger Sayle.

For further copyright information refer to the following passage quoted from
the RasMol manual:

QUOTE BEGINS

  This document and the software, RasMol Version 2.6 which it describes,
are Copyright ⌐ 1992,1993,1994 by Roger Sayle ([e-mail]).

  The information supplied in this document is believed to be true but no
liability is assumed for its use or for the infringements of the rights of
the others resulting from its use.

  Information in this document is subject to change without notice and does
not represent a commitment on the part of the supplier. This package is
sold/distributed subject to the condition that it shall not, by way of trade
or otherwise, be lent, re-sold, hired out or otherwise circulated without
the supplier's prior consent, in any form of packaging or cover other than
that in which it was produced. No part of this manual or accompanying
software may be reproduced, stored in a retrieval system on optical or
magnetic disk, tape or any other medium, or transmitted in any form or by
any means, electronic, mechanical, photocopying, recording or otherwise for
any purpose other than the purchaser's personal use.

  This product is not to be used in the planning, construction, maintenance,
operation or use of any nuclear facility nor the flight, navigation or
communication of aircraft or ground support equipment. The author shall not
be liable, in whole or in part, for any claims or damages arising from such
use, including death, bancruptcy or outbreak of war.

QUOTE ENDS