Viewing conserved domains of AARSs

In this section, you will study structural alignments between several different Class II tRNA synthetase catalytic domains, from various organisms.

The required files have been already prepared by P. O'Donoghue[4] and superposed with the structural alignment program STAMP [9]. You will investigate a subset of the Class II tRNA synthetase structures with the program VMD.

• Move to the prepared directory of AARS structures with cd ~/tbss.work/Bioinformatics/AARS

• Start VMD by typing at the Unix command prompt: vmd

• Open the TkCon console by selecting the VMD menu command Extentions:TkCon

• Now run a TCL script that will, in one step, load all the structures into VMD. Type at the VMD TkCon console:
  • source loader.tcl
  • load_pdb_files .

• With the TCL script applyAll.tcl you can apply different coloring and rendering modes for all loaded structures at once. Try different combinations of rendering and coloring to examine similarities and differences of the structures. Type at the VMD console:
  • source applyAll.tcl
  • applyAll lines backbone
  • applyAll cartoon molecule
  • applyAll newRibbons structure

• Try a script that assigns renderings to different parts of the structures. Type at the VMD console:
  • source applyStructs.tcl