RASMOL/RASWIN

 

RASMOL/RASWIN

Show information and Background

Aim

To display information about the protein selected and to change the background color.

Description

RasMOL is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structure, such as those found in the protein data bank . It was originally developed by Ronger Dayle in the early 1990s.RasMOL includes a scripting language, to perform many functions such as selecting certain protein chains, changing colours etc. Jmol Sirus software have incorporated this language into their commands.

 

Procedure

STEP 1: Open RasMol

STEP 2: Open a new PDB file of protein

Command

RasMol.>Show information

RasMol.>background white

Output(take print)

Result

Information about the selected protein was displayed and background color was changed to white.         

 

 Show Sequence

Aim

To list the residues that compose each chain of the protein and displays the symmetry.

Command

RasMol.>Show Sequence

Output(take print)

Result

The sequence information and symmetry of the protein was displayed using the corresponding RasMol command.    

  

Protein Secondary Structure

Aim

To display information about various secondary structural elements.

Command

RasMol.>structure

Output(take print)

Result

The number of  secondary structures in the protein was displayed

 

 Aliphatic Aromatic Amino Acids

Aim

To find the aliphatic and aromatic amino acids present in the protein

Command

RasMol.>select aliphatic

RasMol.>colour red

RasMol.>label

RasMol.>select aromatic

RasMol.>colour violet

RasMol.>label

Output(take print)

Result

Aliphatic and aromatic amino acids present in the protein were found and they were given different colors and labeled.

Colored aliphatic in red

Labelled aliphatic

Colored aromatic in violet

Labeled aromatic

 

 

Hydrogen Bridges

Aim

To represent the hydrogen bond between side chains and backbone.

Command

RasMol.>hbond on

Output(take print)

Result

The number of hydrogen bonds was…..and hydrogen bonds were displayed.

 

 

 Calculation of Bond angle

Aim

To calculate the bond angle between three adjacent atoms in protein molecule.

Procedure

Type the command

Select three atoms for which the bond angle has to be calculated.

After picking the atoms, the bond angle is displayed as a label as well as the command line

Command

RasMol.>set picking angle

Output(take print)

Result

The angle between the three selected atoms xxxxxx(--), yyyyy(--) and zzzzz(--)was calculated as ------o using RasMol

 

   

Calculation of Bond length

Aim

To calculate the bond length  between two  atoms in the  protein molecule.

Procedure

Type the command

Select two atoms for which the bond length  has to be calculated.

After picking the atoms, the bond length is displayed as a label as well as the command line

Command

RasMol.>set picking distance

Output(take print)

Result

The angle between the two selected atoms xxxxxx(--), yyyyy(--) and zzzzz(--)was calculated as ------o using RasMol

 

   

Calculation of Torsion angle

Aim

To calculate the torsion angle  between four adjacent atoms in the  protein molecule.

Command

RasMol.>set picking torsion

Output(take print)

Result

The angle between the four selected atoms wwww(--) xxxxxx(--), yyyyy(--) and zzzzz(--)was calculated as ------o using RasMol

 

 

 

 

 

 

 

 

 

 

 

 

 

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