Using
Molecular Viewer to see the features of Protein Structure
- To familiar with RasMol
- To understand protein structure features by RasMol commands
- Deadline - 1/2/2002
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)Zoom in picture of the pair¡F(b)The distance between Glu173A.OE and ARG177A.NH is 3.644A¡C
3. Show a protein fragment with residues 622 to 699 only. Show them in cartoon
form and color with temperature.
Ans: Link¡C
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: Link¡C
