I would like you to think in a very physical way about biological problems. Is this "hole" approximately large enough for a DNA molecule? (Structure 1DH3 linked above shows DNA.) Give a brief answer. Give the distance between the atoms that you measured. Measure the approximate distance across the "hole". Give figures for the longest dimension (across the hole) and thickness (edge on so the hole is not visible). Measure the approximate size of this multi-protein complex. Color the molecule by secondary structure, make the water visible, rotate so the "hole" is obvious, and take a "picture" PASTE HERE. Notice that first you need to select a portion of the structure, then pick a command to change the display of the selected item. Explore the viewing options, color options, etc. Clicking on the view pane while holding down the 'Cntrl' key brings up command menus. View the structure of 1AXC from the PDB database JMol viewer. To change the color of secondary structure type "select helix " or "select sheet " and then use the menu option to set the color. To select a single protein chain, open the Console, then to select chain 'D' type (without the quotes), "select *:D ", and hit the execute button. Instructions on using JMol is on the list of links above. To start the lab I'll demonstrate the use of the JMol structure viewer. Learn how to view and manipulate protein structures using Cn3D and the Chime-based Protein Explorer. ![]() Understand PDB entry and structure analysis tools. Learn how to search and use the PDB and Entrez structure databases.
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