Yeast tRNAPhe: A RasMol Animation of the Structure

The RasMol animation version of the tutorial ("movie") uses RasMol 2.6 with a set of controlling scripts to display the secondary and tertiary structural features of tRNAPhe. A compressed file (uncompressed with StuffIt Expander) can be downloaded with a click on: tRNA_Tour.sit (160KB). The resulting folder, "tRNA Tour" contains all of the PDB and script files required to run the animation.
An MS Word file entitled "tRNA Tour ReadMe" (the same content as this page) is also included as well as this page, "tRNA_Tour.html".
The raw files (850KB) or the compressed file can also be downloaded by FTP at tRNA. Select the "tRNA" folder (or directory).

Instructions for use: Put RasMac 2.6 (or a copy) into the "tRNA Tour" folder. Start RasMac. At the command line prompt, enter "script tRNA.TOP". Place the command line window in the lower left corner of the screen. Adjust the display window size so that about 2/3 of the command line window is visible.

The sequential execution of the scripts is paused at a number of points. The pauses are indicated by the command line statement, "Press SPACE to continue". At these points, the viewer can use the mouse to rotate, to zoom, or to "pick" atoms in the image. RasMol menu items are not available during the animation. At the end of the scripted sequence, the "rasmol>   " prompt will appear on the command line.

Animation outline: The scripts called and the topics covered have been arranged in a hierarchy of five sections:

Section I: Overall Shape and Dimensions.
script "tRNAori.scr" Orient & center the wireframe model.
script "tRNAdim.scr" Add distance monitors & spacefill display.

Section II: Cloverleaf and "L" Schematic Diagrams.
script "tRNAclf.scr" The cloverleaf secondary structure diagram.
script "tRNALfm.scr" The "L-Form diagram & tertiary schematic.

Section III: Secondary Structure Features.
script "tRNAori.scr" Orient the wireframe model.
script "tRNAclr.scr" Color segments as in the schematic diagrams.
script "tRNAsec.scr" Various displays & color combinations. Zoom on Watson-Crick coaxial helices.

Section IV: Tertiary Structure Features.
script "tRNAori.scr" Orient the wireframe model.
script "tRNAclr.scr" Color segments.
script "tRNAter.scr" Highlight the tertiary interactions: spacefill-CPK.
  • Non-Watson-Crick base pairs.
  • Base triples.
  • Intercalated bases.
  • Anticodon bases.

Section V: Details of Molecular Interactions.
script "tRNAdet.scr" Close up views of the tertiary interactions highlighted in Section IV.
script "tRNAmet.scr" The four Mg2+-H2O clusters.
script "tRNAtem.scr" The crystallographic B-factors at the phosphates.
script "tRNAori.scr" Orient the wireframe model.
script "tRNAclr.scr" Color segments.

Details: The "tRNA.TOP" script displays all five sections, start-to-finish.
To view only one of these sections, without going through the entire sequence, use "script tRNA.TOP1", "script tRNA.TOP2", etc.
To see abbreviated instructions in the RasMol windows, begin the animation with "script tRNA.Intro".
The RasMol script icon on the six "top" scripts indicates that those scripts can also be used to start the animations directly (Mac: double click or drag-and-drop; Win: right button click) if a copy of RasMol 2.6 is in the "tRNA Tour" folder.

The organization of this animation follows the instructions and examples provided by Dr. Eric Martz on his RasMol Home Page. Several of the controlling scripts were copied from his examples.
Animations similar to this one are available there on the following topics:

  • "DNA structure" by E. Martz.
  • "Hemoglobin & protein structure" by E. Martz.
  • "Lac repressor/operator structure" by H. Brzeski.
  • "Antibody:antigen & protein structure" by E. Martz.
  • "Major histocompatibility complex:peptide" (antigen presentation) by E. Martz.
  • "Lipid bilayers and membrane channels" by E. Martz.
  • "Src 2 homology:phosphotyrosine" by E. Martz.

Back to tRNA Tour Introduction.