MOlecular Structure Worksheet - Bio210 Molecular...

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Bio210: Molecular Structure (RasMol/Jmol) Name: ____________________________________ RasMol/Jmol Activity Sheets (to be completed and turned in next lab session) Circle your section: (Monday Tuesday Wednesday 2:45 Wednesday 6:15) RasMol is available as free download and can be found online at Windows: Download the “latest windows installer” and save to your desktop. Then activate the installer and you will generate the RasMol.exe file. You can run this file. You can even temporarily download this onto the computer lab computers, but be aware that it will be erased as soon as you logoff. The files you need can be found on Eclass in the lab folder folder labeled RasMol. Drag these into the ‘RasWin’ shortcut one by one to open them. Remember than you can alter the display, and you can select various atoms in the command window using ‘select ____’ and then ‘color _____’ Mac: Click download. The file should download to your “downloads” file as jmol-14.0.7 . “Unzip” and open the file jmol- 14.0.7. Open the file named Jmol.jar (you may need to 2-finger click and select open from the menu and then click ok to allow the file to open even though it is from an unknown source) Once jmol has opened, click jmol in the bottom right corner of the window. Select main menu . Select console and a new window should open ( Jmol script console 14.0.7… ). To open a molecule, download the file from eclass, then open it by selecting file in jmol, then select open from the menu and locate the file. For water (H2O), click File , select Get PDB , enter =HOH, click ok. Display controls: 2 finger click, select style , select scheme , from there you can switch between ball and stick , spacefill , etc; 2 finger click, select style , select structures , from there you can use ribbons and strands to help you visualize structure. You can use the Jmol script console to select certain structures and to change their color (-select: carbon –color red) You will not need RasMol/Jmol to answer all these questions, but it will be necessary for some of the questions and it will be helpful in thinking about 3-D structure of molecules along the way. Aquaporin instructions: OPEN the pdb file for aquaporin. Using the ball and stick and spacefill displays, see if you can determine where the water channel would be. (Note that this is in the closed conformation so you may have a difficult time seeing where the water moves through the channel.) In the command window: - Select ala, val, leu, met, phe - Color green 1. What class of amino acids do these (alanine, valine, leucine, methionine, and phenylalanine) fall into? These fall into the class of non-polar amino acids. Play around with the display by choosing “ribbons” and “strands”.
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