assignment 8

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.
picture that I foundpicture in RosMol

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.
(a)
command:
backbone
select glu173
sticks
color cpk
select arg177
sticks
color cpk

(b)
command:
set picking distance
ARG177A.NH(1011):GLU173A.OE(973)==== 6.454
ARG177A.NH(1012):GLU173A.OE(973)==== 5.567
ARG177A.NH(1011):GLU173A.OE(974)==== 4.829
ARG177A.NH(1012):GLU173A.OE(974)==== 3.644
measured in angstrom

3. Show a protein fragment with residues 622 to 699 only. Show them in cartoon form and color with temperature.
command:
reset
restrict 622-699

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.
command:
reset
wireframe 0.1
restrict within (6.0, phe721)
select phe721
color green
stereo
zoom 250