probset_2_2009 - BMB 100A Problem Set #2 Fall, 2009 Name_...

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BMB 100A Problem Set #2 Fall, 2009 Name_________________ (RasMol excercises, DNA structure, free energy and equilibrium) 1. Load one the freeware molecular graphics programs RasMol or PyMol into your computer using the links provided on the class web site. Bring up the structure of GpA, using the PDB file gpa.pdb which you can load from the web site. Practice rotating the molecule on the screen, using the mouse (hold the mouse button down, and move the mouse around). Practice zooming in on details, by holding down the shift key and mouse button simultaneously, and moving the mouse. Try out the different ways to render the molecule, under the "display" menu. Use the functions of RasMol or PyMol to determine the following: a. Give the xyz coordinates for the N9 atom of the guanine in the GpA structure (it will appear on the command line after you first click on the "pick coord" selection under the "settings" menu, and then click on the atom in the graphics window.) b. Measure the interatomic distance between the N3 position of the guanine and the N9 position of
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probset_2_2009 - BMB 100A Problem Set #2 Fall, 2009 Name_...

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