RasMol is a widely-used molecular graphics visualization tool for studying biological macromolecules like proteins, nucleic acids, and small molecules. It allows users to view and analyze 3D structures of molecules, typically from Protein Data Bank (PDB) files. RasMol is particularly popular in the fields of structural biology, bioinformatics, and chemistry for its simplicity and powerful visualization capabilities.

Key Features of RasMol:

1. 3D Molecular Visualization: Displays proteins, nucleic acids, and small molecules in various formats such as wireframe, ball-and-stick, space-filling, and ribbon.
2. Interactive Exploration: Users can zoom, rotate, and translate molecules to explore structures in detail.
3. Color Schemes: Allows coloring molecules based on atoms, residues, chains, or secondary structures (e.g., α-helices and β-sheets).
4. File Support: Reads molecular structure files in PDB, CIF, and other common formats.
5. Command-Line Interface: RasMol includes a command prompt where users can input commands to customize the visualization, such as highlighting specific atoms, residues, or chains.
6. Measurements: It allows users to measure distances, angles, and torsion angles between atoms

How to Use RasMol:

Download and Install: RasMol is available for Windows, macOS, and Linux. You can download it from the official website or other trusted sources.

http://www.openrasmol.org/

How to get protein/DNA 3D structure file from

1. Data retrieval

• Go to Protein Data Bank
• Go to SearchLite
  • Type in ” transcription regulation ” -> Search
• Your query found 185 structures
• Go to Pull down to select option:
  • Select ” Refine Your Query ” -> Go
  • Type in ” technique: x-ray ” -> Search
• Go to Pull down to select option:
  • Select ” Refine Your Query ” -> Go
  • Type in ” source: saccharomyces ” -> Search
• Your query found 9 structures
• Select 1D66. Go to {EXPLORE}

2. View Structure         

• Interactive 3D Display
  • Rasmol
  • FirstGlance (needs Chime)
• Still Images:
  •  Ribbons (250×250)  Cylinders (250×250)
  •  Ribbons (500×500)  Cylinders (500×500)
• Custom Size Images:
  • Size : Type ” 800 “
  • Format: Choose ” JPEG “
  • Creat Image

3. Download/Display File

• Display the Structure File:
  • complete with coordinates
  • “header only” (no coordinates)
• Download the Structure File:
  • noncompressed file
  • compressed file

4. Structural Neighbors

• CATH – Class, Architecture, Topology and Homologous superfamily
• CE – Combinatorial Extension of the optimal path
• FSSP – Fold classification based on Structure-Structure alignment of Proteins
• SCOP – Structural Classification Of Proteins
• VAST – Vector Alignment Search Tool

5. Geometry

• Dihedral Angles
• Common Bond Angles
• Bond Lengths

6. Other Sources

• Sequence Data – 14 links
• Structure Data – 55 links
• Motifs and Domains – 13 links
• Analysis – 50 links
• Visualization – 23 links
• Literature – 3 links
• Miscellaneous – 20 links

7. Sequence Details

8. Crystallization Info

9. NDB Atlas Entry

10. Quick Report

How many chains are there?

Now type the following commands in the Command Line window.

Command:

reset rotate z 90

zoom 150

rotate y 40 backbone (on) color chain

Click on each chain to report its ID letter code (last item of the report).

show sequence

This command reports complete amino acid sequence and information about chains.

Is there anything else in this PDB file besides the protein/DNA chains?

Command:

select hetero

Select things like water, metal ion or anything else except proteins, RNA and DNA.

spacefill color cpk

restrict not water

This hides water; click on what remains to find out what it is. The older PDB standard and files have some ambiguities; CD could mean either carbon delta or cadmium — here it is the latter.

The physiologic metal for gal4 is zinc; cadmium was substituted in the crystallized protein.

Where are the hydrophobic amino acids?

Command:

select hydrophobic color magenta wireframe 0.4

Note amphipathicity of alpha helices.

select not water spacefill (on) slab (on)

Slice thru the molecule to look at distribution of hydrophobic and hydrophilic residues. Move the slab plane with the mouse.

What holds the Cd ions in place?

Commands:

slab off select all backbone 0.3 color chain select cd spacefill (on) color cpk

select within(2.6, cd)

This selects all atoms within 2.6 Angstroms of the Cd++ ions.

spacefill on

color cpk

Click to discover the identity of the caging atoms.

How do we save this view?

commands:

save script gal4.spt zap

How do we restore the view later?

Commands:

script gal4.spt

Where are the alpha helices and beta strands?

Commands:

Select all Backbone (0.3) color structure

This colors alpha helices purple, and beta strands yellow (there aren’t any beta strands in 1d66.pdb).

structure

color structure.

This forces RasMol to make its own determination, i.e., using the DSSP definition of secondary structure.

Notice the appearance of blue “turns”.

How do I find the distance between two atoms?

Commands:

spacefill (on)

set picking distance

Now click on two atoms, and watch the report in the command line window. If you want label the two atoms with the distance, try this:

set picking monitor

Now click on two atoms near the edge of the molecule.

(This will work best if there is black background between the two atoms.) Watch what these do:

color monitor white set monitor off

The number disappears!

monitor off

The dotted line disapperas!

set picking ident

The above restores the normal clicking function of identifying the atom. RasMol can also report angles and torsion angles. See www.umass.edu/microbio/rasmol/distrib/rasman.htm#setpicking

How do I find the bonds between protein and DNA?

Commands:

reset Backbone color green backbone 0

rotate z 91

translate y -17

zoom 200 select dna color white spacefill center selected

select dna and backbone color yellow

Now you can see the DNA, with backbone and base pairs in different colors, and you can see the backbone of the protein as a thin green line.

select within(3.1, dna) and not dna

If you left out “and not dna”, you’d select the DNA also! The above command should select 35

atoms. color cpk dots

Now press the “up arrow” key until you see the “within” command, and add to the end of it and not water. Press Enter, and 19 atoms should be selected.

spacefill 0.6;

Now the putatively bonded protein atoms are small solid spheres within dot-spheres, while the hydrogen-bonded water oxygens are hollow red dot-spheres.

select within(3.1, protein) and dna color cpk

Now you can zoom in and click on prospective donor and acceptor atoms to identify the residue to which they belong and evaluate the liklihood that a given pair is in fact hydrogen-bonded (or otherwise bonded).

How do I see the inside of a molecule?

Commands:

Don’t rotate the molecule with the mouse at any time during this sequence.

reset select All spacefill

color Chain. rotate x 83

zoom 200 set hetero off

Toggle off waters

select dna color cpk slab

Toggle on slab mode

The front half of the molecule has been cut away. You see the cut face, and everything behind it.

set slabmode section;

Now only the cut face is show. Everything in front of and behind the cut plane is hidden. Only the atoms hit by the “knife” are shown.

slab 76

Now you see a GC base pair, cut through the plane where the three Watson-Crick hydrogen bonds are. (This won’t work if you moved the molecule with the mouse anytime since the reset.) slab 68

What is this? Use the mouse to move the slab plane (Hold down Ctrl, then click and drag up and down). Can you find a base pair which is completely out of Watson-Crick position? (Answer is at the end of this document.)

How do I keep the DNA from rotating off screen?

Commands:

reset

restrict none Clear the screen restrict dna spacefill

rotate z 90

zoom 200

Try rotating around the axis of the DNA helix (move the mouse up and down).

Notice how the DNA rises and falls as it rotates around the center of mass, which includes the

invisible protein.

center selected

Now try again and notice the difference.

How do I get multiple representations of the same atoms?

Commands:

restrict :d color cpk

:d means all atoms in chain D.

backbone 1.

Be sure to include the decimal point after the one, which makes RasMol interpret it as Angstroms.

When you type display commands, existing representations are not turned off (unlike with the display menu).

“Sticks” are wireframe with a nonzero radius. Balls are spacefill with a uniform radius. Watch these:

spacefill off wireframe 0.5

wireframe 0.1

spacefill 0.3

backbone 0.1

zoom 500

How do I label an atom?

Commands:

set picking label

Now click on a few atoms.

color labels white label off

set picking ident

Click on an atom and notice its atom ID number (3rd word in the report). We’ll refer to the number as ### in the command below.

select atomno = ###

label “My Favorite Atom” label %n%r

Label residue name and number

label

Label all information of the selected atoms

label off Notes:

The options for “set picking” command are:

The available label specifiers are

How do I see the molecule in stereo?

Commands:

stereo (on)

Now you need to translate to the left to center the image.

By default, you get cross-eyed stereo. To get wall-eyed stereo:

stereo -5

Viewing stereo takes practice, can be hard on the eyes, and is not necessary for most purposes. Rotation without stereo gives you an excellent perception of major 3D relationships. However, if you view molecular graphics frequently, learning how to view images in stereo will enable you to see complex spatial relationships more clearly. Gale Rhodes has provided an excellent introduction to stereo viewing at macweb.acs.usm.maine.edu/chemistry/GR/GraphicsGallery/StereoView.html

How to specify chains, residues and atoms of your molecule?

The most general syntax of specifying an atom in Rasmol is, for example,

lys45:a.nz

This specifies N zeta of lysine 45 of chain A. Some other examples of the atom expressions are:

Useful tips

To erase the display of molecules in the Main Window, type

restrict none

Exploring the Molecule of Your Choice Getting Started

Now fetch a PDB file for the molecule of your choice from PDB

A. How many chains are there?

Commands:

Backbone color chain

At any time, you can restrict your view to one or a subset of the chains present. Click to find out the chain letter. Suppose you want to hide all chains except B and D:

restrict :b or :d .

To restore the view to all chains,

select all.

If you want to look at only part of a large PDB file (greater than 500,000 bytes), it will greatly improve RasMol’s performance if you make a copy of the PDB file from which you delete all atoms except the series you wish to view. To do this, select the desired atoms/chains/residues/ligands in RasMol, then

save pdb filename.pdb

Open the new PDB file in RasMol for further work. Be sure you didn’t omit important ligands!

Are any ligands present?

Commands:

select hetero spacefill color cpk

Click on a ligand to see its 3-letter “residue” code, assigned in the PDB file. You can select ligands with their 3-letter codes. Often the PDB file contains remarks about the ligands (open it in a text viewer, such as Wordpad or Word).

Often the view is cluttered with water oxygens. (Remember, hydrogens cannot be resolved by X- ray crystallography.) Protein crystals are quite “wet” and gelatinous; the structures obtained from crystals agree well with structures obtained from proteins in solution by NMR. Most of the water molecules in crystals diffuse randomly, making them “blurry” and invisible. The rare visible water molecules were tightly bound and immobilized. To hide the water,

restrict not water .

What is the secondary structure?

Commands:

cartoon

colour structure

Alpha helices are red, beta strands yellow, turns blue, and everything else is white. Often the PDB file specifies secondary structure with HELIX and SHEET records. If it does, RasMol obeys it. If it does not, RasMol makes its own determination. You can force RasMol to make its own determination with the command

structure.

Where are the N and C termini?

Commands:

color group (Backbone display is best for this.)

Each chain should begin blue, changing color through a rainbow series (green, yellow, orange) and end in red. If the chain(s) is mostly blue,

set hetero off (leaving Hetero Atoms unchecked), then again type color group

Here are mnemonics. Synthesis begins with the old end; new residues are added to the new end.

Blue = cold = old (N terminus of proteins, 5′ end of nucleic acids) Red = hot = new (C terminus of proteins, 3′ end of nucleic acids)

The amino terminus has the blue CPK color of N; the carboxy terminus, the red CPK color of O. The 3′ hydroxy terminus of nucleic acids has the red CPK color of O.

Where are the hydrophobic side chains?

Commands:

select all spacefill select protein

color [180,180,180]

select protein and backbone color [100,0,100]

select protein and not (backbone or hydrophobic) color magenta

Optionally

select not protein color greenblue

The hydrogen bonding requirements of backbone atoms are generally satisfied within the backbone. Hence backbone atoms are not usually extensively hydrogen bonded to nonbackbone atoms. Backbone atoms are assigned a dark (magenta) color, indicating they are weakly hydrophilic. Hydrophobic side chains are gray to indicate their high carbon content. Polar or charged sidechains are bright magenta to indicate their strongly hydrophilic nature. Magenta is used to represent a mixture of equal parts of red and blue (red for O=positive and blue for N=negative charges or partial charges).

Large patches of hydrophobic sidechains on the surface of the protein suggest that these regions contact something hydrophobic, rather than water. Examples could be proteins that form multimers with each other, or proteins that surround themselves with or bind to lipids.

Where are the disulfide bonds?

Commands:

wireframe; ssbonds 0.8

The disulfide bonds should now be visible as rods 0.8 Angstroms in radius. It may help to

color ssbond(s) yellow.

The first ssbonds command reports the count as “Number of bridges”; if the count is zero, your molecule doesn’t have any! If you got a nonzero count, but don’t see any ssbonds, you probably didn’t have the cystine-containing protein selected. Solution:

Select All

and repeat the above commands.

Backbone color chain

Now only the alpha carbon positions are shown. None of the other atoms in the cystines are shown. Since the ssbonds connect sulfur atoms on the sidechains of cystines (not shown), the ssbonds appear to “float in space”. You can render the ssbonds as connecting the alpha carbons of the cystines with

set ssbond(s) backbone.

Where are the hydrogen bonds?

Commands

select All backbone colour structure restrict helix; backbone 0;

hbonds 0.5;

color hbonds white

RasMol shows only the backbone hbonds. It is not capable of displaying hbonds between sidechains, beween chains, between ligands and their binding sites, etc.

As with the ssbonds, the hbonds appear to be “floating in space” since the atoms which they bond are not shown in a backbone display. The hbonds can be schematized as linking backbone alpha carbons with:

set hbonds backbone

Now

hbonds off

and repeat the above sequence but instead of restrict helix, substitute

restrict sheet.

And again, substituting

restrict not (helix or sheet).

Where are the interchain bonds? The ligand:protein bonds?

As explained under hydrogen bonds, the hbonds command in RasMol is not capable of displaying interchain hbonds. To find bonds of all sorts between moieties, you must use the within command, customizing the example in the section above on 1d66.pdb to your molecule. A standard hydrogen bond has a length of 3.0 Angstroms between the donor and acceptor atoms (for example, N and O). This is made up of a 1.0 Angstrom covalent bond between the hydrogen and its covalently bonded atom, plus a

2.0 Angstrom hydrogen bond between the hydrogen and the hbonded atom. Therefore, a distance of 3.0 or generously, 3.2 Angstroms is appropriate for the within command. Hydrophobic bonds tend to be longer (carbon to carbon), up to 4.0 Angstroms.

There is no ideal way to “paint in” an arbitrary hydrogen bond. The best way to indicate such a bond is with the set picking monitor command (see section above entitled “How do I find the distance between two atoms?”). This draws a dotted line between the atoms, optionally labeled with the distance in Angstroms. The limitation is that you cannot make the monitor line thick (as in a stick representation of a bond).