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Introduction to 
Molecular Graphics on Desktop Computers

© 1997, 1998, 1999 Jean-Yves Sgro UW-Madison

Contents

Introduction
  1. Where to find coordinates: The Protein Data Bank (PDB) database
    1. The PDB database
    2. Reference
    3. Availability
    4. PDB file names
    5. Retrieving PDB files
    6. The PDB file format
      1. Example of 2 ATOM records
      2. List of records.
      3. Example of a PDB file
      4. Coordinates and reference axes
      5. Other formats
  2. Desktop computer graphics programs
    1. Introduction
    2. Graphical representations
  3. RASMOL
    1. Main features
      1. Graphics window
      2. Menu bar
      3. Command line
    2. Summary tables

Introduction

The visualization techniques of the structure of macromolecules are companion tools to the sequence analysis algorithms. New DNA sequences are being cloned and sequenced rapidely but the structure of the putative encoded proteins cannot be determined based only on their sequence. As the number of protein structures solved by x-ray crystallography is increasing it will become easier to find structural homologues to fit onto newly protein sequences. Molecular graphics play a key role in understanding current structures and creating (structural) models.

Molecular graphics have evolved over the last 30 years from a simple vector display on a high performance oscilloscope to sensor based virtual reality. Some desktop computers are now more powerful than mainframes of the last decade and there are free and commercial software programs to manipulate 3 dimensional structures for the creation of publication- quality images to illustrate research papers, proposals and to help visualize target molecules, their structural properties or their interaction with other molecules or ligands.

To be able to manipulate 3 dimensional structures on a desktop computer with a molecular graphics program is critical for today's molecular biologist and a necessary complement to sequence analysis projects.
Goal: During this session you will familarize yourself with the program RasMol. Your knowledge of RasMol will allow you to manipulate and explore in detail existing 3 dimensional structures. The outcome of this exploration will be a better understanding of structures and can help you with the creation of a figures or animations.

This material supplements the exercises and the program manuals.

But where do 3 dimensional structures come from ?

Biochemists and crystallographers have developped techniques to crystalize macromolecules. Indeed proteins, nucleic acids or their complex can form crystals in specific biochemical conditions. The crystals are very fragile and small (often less than a millimeter) but they still can be placed inside an x-ray beam. Because of the regular arrangement of the molecules within the crystals the x-ray will diffract in a very specific pattern which can be recorded on x-ray photographic film. With the help of powerful computer and programs, the mathematical analysis of the diffraction pattern allows the crystallographer to calculate where the electrons (of the atoms) of the protein should be located in 3D space inside the crystal. They then fit a wireframe representation of the amino acids inside the eclectron density. When the position of the atoms is refined, the structure is published and usually deposited at the Protein Data Bank at Brookhaven. These are the structures that you can fetch with Netscape and display inside on your desktop computer. A notable exception is for structures determined in the private sector, these coordinates are proprietary are the authors are not obligated to submit their data. There are a lot of months or years of work for each solved structure!

1dh crystals
L(+) lactate dehydrogenase crystals. Bar=100 µm. Ostendorp et al.(1996) Protein Science 5, 862
synthethase crystals
pentalenene synthase crystals. Lesburg et al. (1995) Protein Science 4, 2436
phosphoribulokinase crystals
phosphoribulokinase crystals. Roberts et al. (1995) Protein Science 4, 2442
Crystals are placed into an x-ray beam. The atoms of the proteins within the crystals diffract the incident x-ray and create diffraction patterns on a film. With complex mathematical calculations crystallographers obtain an electron density map into which the amino acid sequence is fitted with help of computer graphics. 
diffraction by electrons
Diffraction Amplitude waves of diffractied electrons can add or substract to each other. The result are the white dots on the diffraction image.
diffraction film
Diffraction image from a pentalenene synthase crystal. Lesburg et al. (1995) Protein Science 4, 2436
electron density map
Electron density map

Where to find coordinates: 
The Protein Data Bank (PDB) database

The PDB database

"The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data."

As of March 4, 1998 there were 7197 released atomic coordinate entries, distributed as 6655 proteins, peptides, and viruses, 530 nucleic acids, 12 carbohydrates. One year later, on March 3, 1999, there are over 2200 more entries: 9419 Coordinate Entries, 8751 proteins, 656 nucleic acids and still 12 carbohydrates.

The PDB database home page is at http://www.rcsb.org/pdb where it is easy to perform a search in the database, retrieve structure files, verify the status of a structure which can be kept on-hold by authors up to one year after publication.

Reference

The reference for the database is usually given as:

Availability

All entries are available to the public via the world wide web.

However some authors choose to keep their entry on hold for as much as one year after the final acceptance. It is possible to know which entries are on hold from the server.

PDB file names

PDB files are designated by a PDB ENTRY number which is only 4 characters long. The PDB entries are now currently cited by authors in their research publications.

For example the PDB entry for rhinovirus 14 is 4rhv, poliovirus type3 Sabin is 1piv, L-Lactate dehydrogenase is 1llc and glucagon is 1gcn.

However many proteins are represented multiple times in the database as various mutants, models, bound with various compounds, or at various pH. For eaxmple, data for insulin in the cubic crystal form can be found for pHs 7,9,10 and 11 with PDB entries 1aph, 1bph, 1cph and 1dph respectively but there are still many more entries for this compound.

Retrieving PDB files

The PDB front page is the main source for PDB data retrieval. It is available from within the Netscape browser or other gopher browsers.

On the mainn page enter the PDB-ID code or use the SearchLite or SearchFileds options. For eaxmple to retrieve a PDB file for glucagon enter the word glucagon in the Compound: entry. You can also search by ID number or author, it may depend on the information you already have in hand. Once you have filled one or more of the text fields, press the Send Request button. The page will display a list of files matching the criteria you asked. For glucagon there is only one file 1gcn : GLUCAGON (PH 6 - PH 7 FORM).

The PDB file format

A complete guide to the PDB format can be found at http://www.rcsb.org/pdb/ under the "General Information" entry.

The current PDB format consists of lines of information in a file, 80 columns wide by default. Each line is called a record. There are several different types of records, such as JRNL for the records listing the bibliographic references, REMARK for authors' remarks, ATOM for the atomic coordinates etc. The records are arranged sequentially within the file to charaterize the molecule.

Example of 2 ATOM records

ATOM      1  N   HIS     1      49.668  24.248  10.436  1.00 25.00   1  1GCN  50
ATOM      2  CA  HIS     1      50.197  25.578  10.784  1.00 16.00   1  1GCN  51
Each line or record starts with the record type. The position of characters and numbers is of the utmost importance and cannot be changed without creating errors or crashing programs. If you edit the PDB file with a word processor make sure you do not disrupt the column position of characters or numbers. It is obvious that for REMARK records this has not the same importance.

For example the following 2 records are not equivallent: 

ATOM      1  N   HIS     1      49.668  24.248  10.436  1.00 25.00   1  1GCN  50
ATOM      1  N   HIS     1   49.668  24.248  10.436  1.00 25.00   1  1GCN  50
The latter record is in fact equal to: 
ATOM      1  N   HIS     1       9.668   4.248   0.436  0.00  0.00   1  1GCN  50
The first 3 real numbers on each line are in fact the x,y and z coordinates of the atom in three dimensional space. The position of this Nitrogen atom would be in a very different position with this erroneous modification.

It is therefore very important to keep the column arrangement unchanged. If you are editing the file with a word processor on your desktop computer use a monospace font like courrier to display the file.

List of records.

There are many records and subrecords types. They are listed below, grouped by function. A pdb file containing only the ATOM record lines without any other information can usually be opened without problems by visulization programs. After all this is where the three dimensional coordinates are! Some records are very rarely used. The records in bold in the following table are further defined as well. Other record definitions can be found at http://pdb.pdb.bnl.gov/Format.doc/Contents_Guide_2.html 
1. Title Section 
     HEADER OBSLTE TITLE CAVEAT COMPND SOURCE KEYWDS EXPDTA AUTHOR REVDAT SPRSDE 
     JRNL REMARK REMARK 1 REMARK 2 REMARK 3 REMARK 4 - 999 
2. Primary Structure Section
     MODRES DBREF SEQADV SEQRES
3. Heterogen Section 
     HET HETNAM HETSYN FORMUL 
4. Secondary Structure Section
     HELIX SHEET TURN 
5. Connectivity Annotation Section
     SSBOND LINK  HYDBND SLTBRG  CISPEP 
6. Miscellaneous Features Section
     SITE 
7. Crystallographic and Coordinate Transformation Section
     CRYST1 ORIGXn SCALEn MTRIXn TVECT 
8. Coordinate Section
     MODEL ATOM SIGATM ANISOU SIGUIJ TER HETATM ENDMDL 
9. Connectivity Section
     CONECT
10. Bookkeeping Section
     MASTER END 

------------------------------------------------------------------------------
RECORD TYPE       DESCRIPTION                                                 
------------------------------------------------------------------------------
JRNL             Literature citation that defines the coordinate set.
SEQRES           Primary sequence of backbone residues.
HELIX            Identification of helical substructures.
SHEET            Identification of sheet substructures.
TURN             Identification of turns.
SSBOND           Identification of disulfide bonds.
ATOM             Atomic coordinate records for standard groups.
TER              Chain terminator.
HETATM           Atomic coordinate records for heterogens (non amino-acids)
CONECT           Connectivity records.
------------------------------------------------------------------------------

Example of a PDB file

Here is a portion of the PDB file 1gcn.full describing the structure of glucagon, a 29 amino acid peptide in a single peptide chain in a mostly alpha helix conformation. Glucagon is a peptide hormone involved in the cellular usage of glucose.

The file has 311 lines or records. Most of the ATOM records are truncated here.

Note that each atom (ATOM records) for the amino acids has a record (assignment).

Note the function of a few records: SEQRES provides the sequence in three letter code. HELIX is a single line and tells which amino-acids are in an alpha-helix conformation. 

HEADER    HORMONE                                 17-OCT-77   1GCN      1GCN   3
COMPND    GLUCAGON (PH 6 - PH 7 FORM)                                   1GCN   4
SOURCE    PORCINE (SUS SCROFA) PANCREAS                                 1GCN   5
AUTHOR    T.L.BLUNDELL,K.SASAKI,S.DOCKERILL,I.J.TICKLE                  1GCN   6
REVDAT   5   30-SEP-83 1GCND   1       REVDAT                           1GCND  1
REVDAT   4   31-DEC-80 1GCNC   1       REMARK                           1GCND  2
REVDAT   3   22-OCT-79 1GCNB   3       ATOM                             1GCND  3
REVDAT   2   29-AUG-79 1GCNA   3       CRYST1                           1GCND  4
REVDAT   1   28-NOV-77 1GCN    0                                        1GCND  5
JRNL        AUTH   K.SASAKI,S.DOCKERILL,D.A.ADAMIAK,I.J.TICKLE,         1GCN   7
JRNL        AUTH 2 T.BLUNDELL                                           1GCN   8
JRNL        TITL   X-RAY ANALYSIS OF GLUCAGON AND ITS RELATIONSHIP TO   1GCN   9
JRNL        TITL 2 RECEPTOR BINDING                                     1GCN  10
JRNL        REF    NATURE                        V. 257   751 1975      1GCN  11
JRNL        REFN   ASTM NATUAS  UK ISSN 0028-0836                  006  1GCN  12
REMARK   1                                                              1GCN  13
REMARK   1 REFERENCE 1                                                  1GCN  14
REMARK   1  EDIT   M.O.DAYHOFF                                          1GCN  15
REMARK   1  REF    ATLAS OF PROTEIN SEQUENCE     V.   5   125 1976      1GCN  16
REMARK   1  REF  2 AND STRUCTURE,SUPPLEMENT 2                           1GCN  17
REMARK   1  PUBL   NATIONAL BIOMEDICAL RESEARCH FOUNDATION,             1GCN  18
REMARK   1  PUBL 2 SILVER SPRING,MD.                                    1GCN  19
REMARK   1  REFN                   ISBN 0-912466-05-7              435  1GCN  20
REMARK   2                                                              1GCN  21
REMARK   2 RESOLUTION. 3.0 ANGSTROMS.                                   1GCNC  1
REMARK   3                                                              1GCN  23
REMARK   3 REFINEMENT. REALSPACE REFINEMENT AND ENERGY REFINEMENT.      1GCN  24
REMARK   4                                                              1GCN  25
REMARK   4 THE GLUCAGON CRYSTALS ARE FORMED AT PH 9.2 AND THEN THE PH   1GCN  26
REMARK   4 IS CHANGED TO BETWEEN 6 AND 7.  CRYSTALS AT BOTH PH,S HAVE   1GCN  27
REMARK   4 HIGH TEMPERATURE FACTORS, AND DATA TERMINATE AT              1GCN  28
REMARK   4 APPROXIMATELY 3 ANGSTROMS RESOLUTION.  THE COORDINATES ARE   1GCN  29
REMARK   4 OBTAINED FROM THE 3 ANGSTROMS RESOLUTION ELECTRON DENSITY    1GCN  30
REMARK   4 MAP AND REFINED USING REAL SPACE REFINEMENT AGAINST          1GCN  31
REMARK   4 (2FOBS-FCALC),ALPHA CALC  ELECTRON DENSITY MAPS WITH         1GCN  32
REMARK   4 GEOMETRIC RESTRAINTS, FOLLOWED BY LEVITT ENERGY              1GCN  33
REMARK   4 MINIMIZATION.  NO SOLVENT CAN BE INCLUDED AT 3 ANGSTROMS.    1GCN  34
REMARK   4 WARNING - LOW RESOLUTION (3 ANGSTROMS) IMPLIES RATHER        1GCN  35
REMARK   4 INACCURATE COORDINATES AND MEANINGLESS TEMPERATURE FACTORS.  1GCN  36
REMARK   5                                                              1GCNA  1
REMARK   5 CORRECTION.  MOVE CRYST1 RECORD TO ITS PROPER POSITION.      1GCNA  2
REMARK   5  29-AUG-79.                                                  1GCNA  3
REMARK   6                                                              1GCNB  1
REMARK   6 CORRECTION. FIX NAMING AND HENCE ORDERING OF TWO ATOMS.      1GCNB  2
REMARK   6  22-OCT-79.                                                  1GCNB  3
REMARK   7                                                              1GCNC  2
REMARK   7 CORRECTION. STANDARDIZE FORMAT OF REMARK 2.  31-DEC-80.      1GCNC  3
REMARK   8                                                              1GCND  6
REMARK   8 CORRECTION. INSERT REVDAT RECORDS. 30-SEP-83.                1GCND  7
SEQRES   1     29  HIS SER GLN GLY THR PHE THR SER ASP TYR SER LYS TYR  1GCN  37
SEQRES   2     29  LEU ASP SER ARG ARG ALA GLN ASP PHE VAL GLN TRP LEU  1GCN  38
SEQRES   3     29  MET ASN THR                                          1GCN  39
FTNOTE   1                                                              1GCN  40
FTNOTE   1 RESIDUES 1 THROUGH 5 ARE RATHER DISORDERED IN THE CRYSTALS.  1GCN  41
HELIX    1   A PHE      6  LEU     26  1                                1GCN  42
CRYST1   47.100   47.100   47.100  90.00  90.00  90.00 P 21 3       12  1GCNA  4
ORIGX1       .021231  0.000000  0.000000       0.000000                 1GCN  43
ORIGX2      0.000000   .021231  0.000000       0.000000                 1GCN  44
ORIGX3      0.000000  0.000000   .021231       0.000000                 1GCN  45
SCALE1       .021231  0.000000  0.000000       0.000000                 1GCN  46
SCALE2      0.000000   .021231  0.000000       0.000000                 1GCN  47
SCALE3      0.000000  0.000000   .021231       0.000000                 1GCN  48
ATOM      1  N   HIS     1      49.668  24.248  10.436  1.00 25.00   1  1GCN  50
ATOM      2  CA  HIS     1      50.197  25.578  10.784  1.00 16.00   1  1GCN  51
ATOM      3  C   HIS     1      49.169  26.701  10.917  1.00 16.00   1  1GCN  52
ATOM      4  O   HIS     1      48.241  26.524  11.749  1.00 16.00   1  1GCN  53
ATOM      5  CB  HIS     1      51.312  26.048   9.843  1.00 16.00   1  1GCN  54
ATOM      6  CG  HIS     1      50.958  26.068   8.340  1.00 16.00   1  1GCN  55
ATOM      7  ND1 HIS     1      49.636  26.144   7.860  1.00 16.00   1  1GCN  56
ATOM      8  CD2 HIS     1      51.797  26.043   7.286  1.00 16.00   1  1GCN  57
ATOM      9  CE1 HIS     1      49.691  26.152   6.454  1.00 17.00   1  1GCN  58
ATOM     10  NE2 HIS     1      51.046  26.090   6.098  1.00 17.00   1  1GCN  59
ATOM     11  N   SER     2      49.788  27.850  10.784  1.00 16.00   1  1GCN  60
ATOM     12  CA  SER     2      49.138  29.147  10.620  1.00 15.00   1  1GCN  61
ATOM     13  C   SER     2      47.713  29.006  10.110  1.00 15.00   1  1GCN  62
ATOM     14  O   SER     2      46.740  29.251  10.864  1.00 15.00   1  1GCN  63
ATOM     15  CB  SER     2      49.875  29.930   9.569  1.00 16.00   1  1GCN  64
ATOM     16  OG  SER     2      49.145  31.057   9.176  1.00 19.00   1  1GCN  65
/////////////////////////ATOM RECORDS TRUNCATED/////////////////////////////////
ATOM    239  N   THR    29       3.391  19.940  12.762  1.00 21.00      1GCN 288
ATOM    240  CA  THR    29       2.014  19.761  13.283  1.00 21.00      1GCN 289
ATOM    241  C   THR    29        .826  19.943  12.332  1.00 23.00      1GCN 290
ATOM    242  O   THR    29        .932  19.600  11.133  1.00 30.00      1GCN 291
ATOM    243  CB  THR    29       1.845  20.667  14.505  1.00 21.00      1GCN 292
ATOM    244  OG1 THR    29       1.214  21.893  14.153  1.00 21.00      1GCN 293
ATOM    245  CG2 THR    29       3.180  20.968  15.185  1.00 21.00      1GCN 294
ATOM    246  OXT THR    29       -.317  20.109  12.824  1.00 25.00      1GCN 295
TER     247      THR    29                                              1GCN 296
MASTER       34    2    0    1    0    0    0    6  246    1    0    3  1GCND  8
END                                                                     1GCN 298

Coordinates and reference axes

By far the most important data are the ATOM (amino-acid atoms), and HETATM (heterogeneous atoms of ligands) records. The three dimensional XYZ coordinates are the first three real numbers on each line. For example 49.668 24.248 10.436 for the first ATOM record (Nitrogen atom of Histidine amino-acid number 1).

These coordinates are in a Cartesian coordinate system. This means that the x,y and z axes are perpendicular to one another and their length is 1. The unit length is 1 Å (equal to 0.1 nm [nanometer] in the international notation).

This is a prefered system of reference for most biological users, however it is worth knowing that in some cases the frame of reference is the length of the crystallographic "unit cell". In this case the axes are labelled a,b and c. They are not necessarily perpendicular to one another and do not necessarily have the same length. If the coordinates are expressed as a function of these axes they are usually refered to as fractional coordinates. Most chemical databases give the coordinates in this fashion. In the PDB formated file, he CRYST1 and SCALEn records are related to these axes but for our purpose can be ignored.

Other formats

There are many other formats which are used in molecular graphics!

Even the PDB format itself has some specific "expansions" by some particular programs for their own use. However the PDB files that you will retrieve from the PDB database will not contain any of these additions and therefore you need not worry about this.

Other molecular graphics programs require their own specific format for display. The program BABEL, available on all major computer platforms (Mac, DOS and most popular Unix) reads the followinginput formats:
Mopac Cartesian, Mopac Internal, Mopac Output, CSD GSTAT, CSD CSSR, Free Form Fractional, Macromodel, MM2 Output, PDB Alchemy, XYZ, Mac Molecule, Chem3D, MicroWorld, Ball and Stick, MOLIN
and writes the following output formats:
Mopac Cartesian, Mopac Internal, Gaussian Input, IDATM, Macromodel, Mac Molecule, MM2 Input, MM2 Ouput, PDB file, Alchemy, XYZ, Ball and Stick, Chem3D, MicroWorld, Report of interatomic distances,angles,and torsions.

This can give you an idea of the number of formats "out there"! The program BABEL is available at: ftp://ccl.osc.edu/pub/chemistry/software/MAC/babel/ and has a home page at http://mercury.aichem.arizona.edu/babel.html. 

Desktop computer graphics programs

Introduction

Computer graphics programs (whether they run on a desktop computer or on an expensive workstation) read, interpret and display the PDB file (or other formats) into graphical images which you can manipulate in three dimensions and modify interactively on your computer screeen.

The programs can be:

Free or Expensive
Simple or Difficult
Useful or Not so useful
Visualization or Modeling
There are many free visualization-only programs. 3D modeling is available on a limited basis in WebLabviewerLite but more expanded in the Pro version. Most free programs are for display only.

Here are some FREE programs:
 
 

  1. Long list of FREE Software
    2. http://klaatu.oit.umass.edu:80/microbio/rasmol/othersof.htm#viewrend
  2. RasMol (Mac, Windows, Unix). Powerful line command.
    3. http://www.umass.edu/microbio/rasmol/
  3. CHIME Web browser plug-in. Complex menus.
    4. http://www.mdli.com/support/chime/chimefree.htm
  4. WebLab Viewer Lite (FREE) or Pro. (Mac, Windows 95,98,NT). Beautifully renderedOpenGL graphics.
    5. http://www.msi.com/download/index.html
  5. MOLVIEW (Mac)- makes quicktime movies, beautiful renderings
    6. http://www.expasy.ch/spdbv/mainpage.htmlhttp://bilbo.bio.purdue.edu/~tom/
  6. SwissPDBViewer (Mac)
    7. http://www.expasy.ch/spdbv/mainpage.html
  7. Cn3D (See in Three-Dee) (Mac, Windows, Unix). Additional equence alignment window.
    8. http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
  8. kineMAGE(Mac, Windows, Unix)
    9. http://www.faseb.org/protein/kinemages/MageSoftware.html
Depending on your working environment it may be worth using a program that runs on various platforms. Rasmol is a very powerful program to explore molecules, WebLabViewer provides superior graphics at the expense of speed compared to rasmol. Depending on the task I use this or that program. For example I often open the PDB files with rasmol for a quick exploration, and then revert to a program with better graphics for creating final images.

Rasmol reads in the PDB file directly without any modifications which is an adavntage. It provides a line-based and menu-driven interface which allow scripting and the easy manipulation of structures. This is the main program we will use.
A new way of showing 3D structures on the world wide web is to use 'java applets' which will display the structure right inside your Netscape page. However there are no user controls to color or change the display, only interactive rotation and zoom. Since we've already seen the file for glucagon here is a small window where you can see the CA (carbone alpha) tracing of the peptide and verify that it is in an alpha helix conformation!

 

 You need to run a JAVA-compatible browser like Netscape 2.02 or later and have java activated within the optional parameters (Network Preferences). With java, his image would be interactive.
image of interacive window
(ALT and horizontal mouse movement will zoom (right->left) or scale down (left->right)

Graphical representations

The 3D coordinates of the ATOM records represent the position of a single point in 3D space. The molecular graphics programs can draw a line between the various atom positions to create a wireframe representation. If only the alpha carbones are used then it is a C-alpha tracing. Alternatively the program may draw a sphere at the location of each point to represent the volume of each atom and create a space-filling model representation. More complex molecular graphics programs can calculate and display the continuous molecular surface as a continuous "skin" envelopping the molecule. Other more cartoonish representations are the Jane Richardson's style ribbon diagram showing the various secondary structure elements particularly well.

Here are a some examples of such representations for the glucagon peptide:
 
 
bonds bonds ribbon helix ribbon
atoms all atoms molecular surface surface
The representation of the molecule by the program will depend on what the user chooses amongst the program options.

The color chosen for each atom or the global colorization of various structures or domains of the molecule will have a very important impact on the final image for clarity and artistic value in addition to the style chosen for the rendering.

Fortunately some programs allow mixed rendering, that is the representation of various parts of the molecule in different styles.

In addition to the rendering of the atoms themselves, programs also provide tools to add hydrogen bond lines or written labels at specific location.

See examples of pre-rendered images with Rasmol at

http://heme.gsu.edu/glactone/PDB/pdb.html

RASMOL

Many of the features described above are available in RASMOL. This program is available for all computer types and have slightly different names on a Macintosh (RasMac), a PC (RasWin) or a unix workstation (RasMol) but behaves essentially in the same way on all platforms. Thus, what you learn on a Macintosh here can be used as-is on the other computers. This is why RASMOL has become widely used on the Internet World Wide Web and has been chosen as the main program for this course. An offspring of Rasmol is CHIME, a web browser plug-in with additional features. The lack of line command makes it more complex and cumbersome to use, but can help create beautiful "virtual museums" when all the parameters are placed together in a web page by an instructor. For example see "The Virtual Museum of Minerals and Molecules" (http://www.soils.wisc.edu/virtual_museum/index.html).

RasMol has been developed by Roger Sayle (ras32425@ggr.co.uk or rasmol@dcs.ed.ac.uk) at the University of Edinburgh's Biocomputing Research Unit and the BioMolecular Structure Department, Glaxo Research and Development, Greenford, U.K. The RasMol home page is located at:

http://www.umass.edu/microbio/rasmol/

 

 
 
 
 
 
 
 
 
 

The program comes with an extensive manual and has an on-line help command available. The following notes are only a short guide to the program possibilities.

Main features

On a Macintosh, RasMol opens by double-cliking on the RasMol program icon (rasmol icon) or a PDB file with a RasMol icon document (rasmol document icon).

 This program runs on many other types of computer, therefore, in addition to the menu options, the program functions with a wide array of line commands.

 Upon launching, the program opens 2 windows, a graphics or canvas window which will display the molecule and a text window for typing the additional commands and options not found in the menu bar.
 
 

Graphics window

The canvas window opens by default with a black background and has two scroll bars, on the right and at the bottom. These are one of many options to rotate the molecule interactively. The window can be resized like any other Macintosh window.

 

 graphics window
The mouse cursor is a cross-hair while in the canvas window, to allow picking of atoms (for example to echo in the text window what is the atom number).

 The displayed structure can be rotated interactively with the mouse. The manual does not give keystrokes specific for the Macintosh. Here are summarized the movement mouse functions:
 
 
ROTATION By pressing the mouse while within the canvas window the structure can be moved in all arbirary direction ("virtual track-ball").
TRANSLATION Pressing the OPTION key will translate (drag) the display in the same direction as the mouse movement. It is not necessary to depress the mouse button itself.
SCALING Pressing the SHIFT key while moving the mouse vertically from TOP to BOTTOM zooms on the center of the display. The BOTTOM to TOP direction would reduce the size.
Z-ROTATION Pressing BOTHSHIFT and OPTION while moving the mouse will rotate the molecule around the "Z axis", that is the axis which is perpendicular to the flat screen of the computer. You are watching at the screen roughly along this axis!
CLIPPING Pressing CONTROL and moving the mouse will move the clipping plane if this option is enabled.

Menu bar

The menus are located in the top menu bar on the Macintosh, on the canvas window on other platforms. On the Macintosh the menu bar contains the following menu and submenu items:
File Edit Display Colour Options Export Windows
Open...
Save As...
Page Setup...
Print...
Quit		 Undo Cut
Copy
Paste
Clear
Select All...		 Wireframe Backbone
Sticks
Spacefill
Ball & Stick
Ribbons
Strands
Cartoons		 Monochrome CPK
Shapely
Group
Chain
Temperature
Structure
User		 Slab Mode Hydrogens
Specular
Shadows
Stereo
Label		 Gif... Postcript...
PPM...
Sun Raster...
BMP...
PICT...		 Main Window Command line
 
 
 

 
Note: On other computers the Edit and Windows menu items may not be present.

 The Display menu provides an easy way to change the aspect of the molecule, or portions of the molecule, currently displayed in the canvas window. We saw examples of such representation of the glucagon molecule earlier. The last three items (Ribbons, Strands and Cartoons) are a variation on the ribbon diagram.

 The Colour (note the British spelling, although the program will accept the american color spelling) menu Structure will color alpha helices, beta sheets and turns in pink, yellow and blue respectively. It is an easy way to inspect the structure of a new, unfamiliar molecule.

 The menu has a limited number of options. There are no submenus to choose from. Rather, most of the power of RasMol is contained within the line commands.

Command line

The command line (text) window opens with a statement similar to the following: 
RasMol Molecular Renderer
Roger Sayle, August 1995
Version 2.6
[8bit version]

RasMol>
Interactive commands are typed at the RasMol> prompt, but are still typed there even if the cursor is over the graphics window.

 Commands are given one at a time on separate lines and are case INsensitive. The number of white spaces is not important.

 Rasmol recognizes a number of commands, internal parameters and atom expressions.
 
 

Summary tables

Summary of commands/keywords currently recognised by RasMol
backbone background cartoons centre clipboard colour connect cpk
dots define echo exit hbonds help label load
print quit renumber reset restrict ribbons rotate save
script select set show slab source spacefill ssbonds
strands structure trace translate wireframe write zap zoom
List of internal parameters altered by the set command
ambient axes background bondmode boundbox display fontsize hbonds
hetero hourglass hydrogen kinemage menus mouse radius shadow
slabmode solvent specular specpower ssbonds strands unitcell vectps
Predefined color schemes assigned by the colour command (spelling color is accepted).
(Numbers in brakets are for Red Green Blue Values ranging from 0 to 255).
blue [0,0,256]  black [0,0,0]
cyan [0,255,255]  green [0,255,0]
greenblue [46,139,87]  magenta [255,0,255]
orange [255,165,0]  purple [160,32,240]
red [255,0,0]  redorange [255,69,0]
violet [238,130,238]  white [255,255,255]
yellow [255,255,0]
List of predefined sets
AT acidic acyclic aliphatic alpha amino aromatic Backbone
Basic Bonded Buried CG charged cyclic cystine helix
hetero hydrogen hydrophobic ions large ligand medium neutral
nucleic polar protein purine pyrimidine selected sheet sidechain
small solvent surface turn water
Summary classification of common amino-acids by RasMol
Predefined
set		 ALA  ARG  ASN  ASP  CYS  GLU  GLN  GLY  HIS  ILE  LEU  LYS  MET  PHE  PRO  SER  THR  TRP  TYR  VAL 
A  R  N  D  C  E  Q  G  H  I  L  K  M  F  P  S  T  W  Y  V 
acidic  *  * 
acyclic  *  *  *  *  *  *  *  *  *  *  *  *  *  *  * 
aliphatic  *  *  *  *  * 
aromatic  *  *  *  * 
basic  * *  * 
buried  *  *  *  *  *  *  *  * 
charged  *  *  *  *  * 
cyclic  *  *  *  *  * 
hydrophobic  *  *  *  *  *  *  *  *  *  * 
large  *  *  *  *  *  *  *  *  *  *  * 
medium  *  *  *  *  *  * 
negative  *  * 
neutral  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  * 
polar  *  *  *  *  *  *  *  *  *  * 
positive  *  *  * 
small  *  *  * 
surface  *  *  *  *  *  *  *  *  *  *  *  * 

CONCLUSION

Molecular graphics on the desktop computers have become very powerful and it can only get better. The recent developments combining sequence analysis and computer graphics simulations and modeling on workstations are now ready to migrate to the desktop, or benchtop, and will become routine companions for the analysis of protein as homology modeling becomes more popular and more feasible with the accumulation of new or refined molecular structures. 
© 1997, 1998, 1999 Jean-Yves Sgro
last modified November 20, 1999