| version 1.13 | version 1.14 |
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| % | % |
| % $RCSfile: ug_tutorial.tex,v $ | % $RCSfile: ug_tutorial.tex,v $ |
| % $Author: mbach $ $Locker: $ $State: Exp $ | % $Author: mbach $ $Locker: $ $State: Exp $ |
| % $Revision: 1.13 $ $Date: 2002/10/28 21:35:14 $ | % $Revision: 1.14 $ $Date: 2002/10/28 23:32:30 $ |
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| % DESCRIPTION: | % DESCRIPTION: |
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| \section{Viewing a molecule: Titin} | \section{Viewing a molecule: Titin} |
| Once you have \JMV\ started, you can load a molecule by selecting ``Load a file'' from the ``File'' menu. This will bring up a dialog box asking for a file name. Type in ``1TIT'' and click ``Load file''. This will load the molecule Titin from the RCSB, a repository of molecular files. The screen should display ``Loading...'' indicating that it is currently loading the molecule, and then display it. You can move the molecule with the mouse buttons. For more detailed information on mouse movement, see the next chapter: ``User Interface Components''. | Once you have \JMV\ started, you can load a molecule by selecting ``Load a file'' from the ``File'' menu. This will bring up a dialog box asking for a file name. Type in ``1TIT'' and click ``Load file''. This will load the molecule Titin from the RCSB, a repository of molecular files. The screen should display ``Loading...'' indicating that it is currently loading the molecule, and then display it. You can move the molecule with the mouse buttons. For more detailed information on mouse movement, see the next chapter: ``User Interface Components''. |
| | You can also change the representation. When JMV starts, the default representation is ``Tube''. You can change this to a ball-and-stick model called ``CPK'' by opening the ``View'' menu, selecting the ``Representation'' option, and then selecting ``CPK'' from the choices presented. You can also change how the molecule is colored. By default, the color scheme is Index, which creates a smooth gradient from the first atom to the last. To change the color scheme to color the molecule by Residue name, under the ``View'' menu, select the ``Color by'' option, and select ``Residue name'' from the options there. The colors of the molecule will change, giving each residue type a distinct color. If you want to change the Titin molecule back to the original look, open the ``View'' menu, select ``Representation'', and select ``Tube'' to change the representation. To change the color back, select ``View'' from the menu, then select ``Color by'', and then ``Index'' from the menu that pops up from that. |