Part 1: Text-based measurement of atomic and molecular properties.

1. Download the zinc finger PDB file into your home directory.
2. Start InsightII and get the zinc finger PDB file. Edit this structure so that the two cysteines form a disulfide bridge. Fix, Fix, Fix your potentials, partial charges, and formal charges.
3. List properties of the molecule.
   • Click on Molecule/List, and list the extents of the molecule. The extents are the X, Y, and Z dimensions of the molecule (the orientation of the X, Y, and Z axes are defined in the WORLD coordinate frame) When is this information important???
   • List the chiralities of the molecule. Some chiralities of the CA (alpha carbon) atoms are "R", while most are "S". Investigate why this is so.
4. Using the Biopolymer module, Click on Residue/list. Type in ONLY the name of the molecule (with no ":" characters). This is ALMOST ALWAYS an excellent function to perform just after you read a PDB file into the program: it is much easier to select groups of residues once you know the names of the residues.
5. Click on Protein/List. List various properties of the protein. Which propertie(s) are listed "incorrectly"? Why is the program "incorrect"?
6. Click on Atom/List. Click on ExDetails and click execute. Two lines for each atom will be printed in the textport. Basic information, such as the name of the group to which the atom belongs, atom type, X,Y,Z coordinates, and which atoms are connected to the atom are listed for each atom (on the first line). Extra details, including the potential atom types, partial charges, and formal charges are listed on the second line for each atom. Notice the general range of partial charges.

   The N-terminal Nitrogen has a formal charge of +1, but the partial charge of this atom is -0.500! Why??? The answer: this atom is designated as the SWITCH atom for that group. The sum of the potential charges of the entire group is listed as the formal charge of the SWITCH atom for that group. Therefore, if you want to change the formal charge on an atom, you must also be sure that the sum of the partial charges of the group also equal the formal charge.

7. Click on Object/Blank and blank on the protein. This will turn off the display of the protein.
8. Using the Nucleotide/Append menu, create a 10-residue B-type DNA double helix named DNA.
9. OPTIONAL STEP (DON'T BOTHER DOING THIS TODAY. INSTEAD, JUST READ THROUGH THIS STEP AND GO ONTO THE NEXT STEP): The DNA duplex that you just restored consists of TWO molecules. Click on Object/List to list the names of these molecules, which will be "DNA_1" and "DNA_2". If you click on Connect Object and connect to one of the two strands, and you move the object, you will only move one of the two strands---you will lose the double helix conformation!. There are two methods that you can use to avoid this: A. While the double helix consists of two non-covalently-bound molecules, the two molecules are also defined as an assembly. Click on Assembly/list to list this DNA assembly. To move BOTH DNA strands together, Click on Transform/connect and connect to the DNA assembly (NOT one of the two molecules). B. To merge the two molecules together WITHOUT making a covalent bond between the molecules, click on Modify/Merge, and merge one molecule into the other. If you desire, you can rename the molecule using Object/rename. Then you can move the entire molecule with no problems.
10. Change the color of one strand to crimson (red) and the other strand to cream (white). Change the 5' end residue of the red strand to green and the 3' end residue to yellow.
11. Click on Nucleotide/measure. Define the 5' end (green residue) and the 3' end (yellow residue). Measure from the green residue to the yellow residue (what happens if you select a different region to measure?). Click Execute. Click on Texport On.
12. What is all of this junk in the window??? Scroll around the window and compare these values with the structure on the screen. What geometrical differences exist for A-DNA, B-DNA, Z-DNA, and a DNA/RNA hybrid? How do the parameters compare for nucleotides at the interfaces/ends of the A_DNA, B_DNA, Z_DNA, and DNA/RNA regions vs the nucleotides in the middle of these regions?
13. Repeat the measurement of the DNA parameters using the Nucleotide/measure menu, but save the measurement results to a file. Name this file DNA._meas in your home directory.
14. Click on Object/delete and delete the DNA. Blank "off" the zinc finger structure.

Part 2: Graphics-based measurement of atomic properties

1. Color the atoms of the protein by their partial charge values:
   1. Click on Molecule/color, and set up the menu to color all atoms of the protein.
   2. Set Color Method to property. property_level should be set to atom.
   3. Set Property to Partial_charge and Spectrum_Name to CHARGE_SPECTRUM. The CHARGE_SPECTRUM is a predefined scale that will color your atoms from red (-0.5) to blue (+0.5) depending upon their partial charge value. Note that there are other pre-defined spectra.
   4. Click on Execute, and the atoms will change to red and blue. The spectrum scale will also appear. This spectrum scale is automatically named MOL_SPECTRUM.
2. Editing Spectra:
   Click on Spectrum/edit. Select MOL_SPECTRUM and click OK. Edit the properties of this spectrum:
   1. Change the Over Range Color to green and Under Range Color to yellow. Recolor your molecule (Spectrum_name is MOL_SPECTRUM). Idtentify if any atoms have partial charges that are greater than the maximum (+0.5) or less than the minimum (-0.5) values of the spectrum.
   2. Edit MOL_SPECTRUM and change label options, scale options, the minimum and maximum colors. Recolor your molecule.
   3. Delete all spectra using the Object/delete menu.
3. Create your own spectrum
   Make a spectrum based on sequence number, then make a colorful ribbon.
   1. Click on Spectrum/edit, and click on New Spectrum. Enter a spectrum name. Set the minimum value to 1 and maximum value to 30 (the zinc finger has 30 residues). You MUST first type in the maximum value, then type in the minimum value. If you switch this order, the program will NOT set the minimum and maximum to the new values, since the minimum value must NEVER be equal to or greater than the maximum value. Click OK.
   2. Verify that your minimum and maximum values are OK.
   3. Split your spectrum (click on split). Define the maximum value of subrange #1 to be white, and the maximum value of subrange 1 to be 15. Define the minimum value of subrange #2 to be 15 and the minimum color to be white.
   4. Color your molecule:
      Select the Molecule/Color menu, and set color method to property.
      Set property_level to monomer.
      Set property to sequence_number.
      Set spectrum_name to your new spectrum.
   5. Make a solid rectangular ribbon.
4. Delete everything EXCEPT the zinc finger structure. Save your zinc finger structure as a folder named zinc_finger.psv. Quit InsightII.

Part 3: Verify that you have completed this portion of the assignment

See the Viewer Assignment page for details.