Using
Molecular Viewer to see the features of Protein Structure
- To familiar with RasMol
- To understand protein structure features by RasMol commands
1. Make a GIF picture of the PDB file that you find in assignment 7 by RasMol. Display it in cartoon form and color it by structure. Please make the orientation of the molecule just like the molecule in the picture of assignment 7 - 2.
Ans :
2. Residues Glu173 and Arg177 are possible to form an ion pair (salt-bridge). (a) Draw a zoom-in picture of this pair. Show these two residues in sticks and color with cpk. The rest of protein in backbone form. (b) Measure the distance between Glu173A.OE and ARG177A.NH.
Ans : (
a ) 
( b ) 
3. Show a protein fragment with residues 622 to 699 only. Show them in cartoon form and color with temperature.
Ans : 
4. Make a stereo picture for only the atoms within 6.0 Angstrom of Phe721. Show this residue in green color, others in cpk and all the residues in wireframe 0.1 format.
Ans : 