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.
Display--Cartoons > Colours--Structure
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.
select all >Display-- Backbone > select glu173 > Sticks > select arg177> Sticks > Settings--Pick Label
(b)Glu173A.OE1---ARG177A.NH1 :6.454 Angstrom Glu173A.OE2---ARG177A.NH1 :4.829 Angstrom Glu173A.OE1---ARG177A.NH2 :5.567 Angstrom Glu173A.OE2---ARG177A.NH2 :3.644 Angstrom
Settings > Pick Distance
3. Show a protein fragment with residues 622 to 699 only. Show them in cartoon form and color with temperature.
restrict 622-699 > Display--Cartoons > Colours--Temperature
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.
restrict within (6.0,phe721) > wireframe 0.1 > color cpk > select phe721 > color green > stereo