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.
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.
3. Show a protein fragment with residues 622 to 699 only. Show them in cartoon form and color with 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.

1. 如習題7-2，至Structure Explorer-1BKN中的"View Strucure"，點選第三項的"Rasmol"則可下載此蛋白質結構的pdb檔案。用Rasmol開啟，以"cartoons"表示，並依結構上色，調整至適當方位，按"Import"儲存成GIF檔案。 Rasmol原始檔 圖檔顯示

2. 先將整個結構以"backbones"表示，依CPK上色，在指令視窗鍵入"select 173"及"select 177"，都以"sticks"表示。最後鍵入"set picking distance"後分別點選顯示出來的氧原子及氮原子，便能顯示出距離。 圖檔顯示

3. 鍵入"restrict 622-699"可只顯示出此段，再以"cartoons"顯示並依溫度上色。 圖檔顯示

4. 鍵入"restrict within(6.0,721)"，則只顯示出721號胺基酸周圍距離6.0 Angstrom的原子，再分別鍵入"wireframe 0.1"、依CPK上色。最後選擇721號胺基酸，著上綠色。 圖檔顯示