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| % $RCSfile: ug_intro.tex,v $ | % $RCSfile: ug_intro.tex,v $ |
| % $Author: mbach $ $Locker: $ $State: Exp $ | % $Author: mbach $ $Locker: $ $State: Exp $ |
| % $Revision: 1.9 $ $Date: 2002/10/30 23:35:19 $ | % $Revision: 1.10 $ $Date: 2002/11/01 20:49:52 $ |
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| % DESCRIPTION: | % DESCRIPTION: |
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| \chapter{Introduction} | \chapter{Introduction} |
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| %general intro text | %general intro text |
| \JMV\ is a Java Molecular Viewer written in Java and Java3D. It can be used to | \JMV\ is a Java Molecular Viewer written in Java and Java3D. You can use it to |
| load data files to display molecules in common molecular representations and | load data files to display molecules in common molecular representations and |
| color styles. Users can load files from a URL, from a local file, from the | color styles. You can load files from a URL, from a local file, from the |
| RCSB databank. or from the BioCoRE filesystem. JMV also provides display and lighting options, and support for | RCSB databank. or from the BioCoRE filesystem. JMV also provides display and lighting options, and support for |
| stereoscopic viewing. Java technology makes JMV platform independent, and | stereoscopic viewing. Java technology makes JMV platform independent, and |
| allows it to run within a web browser or as a standalone application. Thanks to the use of Java Beans, it is modular and customizable, so developers can build customized versions of the application. Since it can be used in web pages, it | allows it to run within a web browser or as a standalone application. Thanks to the use of Java Beans, it is modular and customizable, so you can build customized versions of the application. Since it can be used in web pages, it |
| is ideal for applications such as electronic textbooks, where static images can be replaced with an interactive tool. \\ | is ideal for applications such as electronic textbooks, where static images can be replaced with an interactive tool. \\ |
| Online information on JMV is available at: \htmladdnormallink{{\tt http://www.ks.uiuc.edu/Research/jmv/}}{http://www.ks.uiuc.edu/Research/jmv/}. | Online information on JMV is available at: \htmladdnormallink{{\tt http://www.ks.uiuc.edu/Research/jmv/}}{http://www.ks.uiuc.edu/Research/jmv/}. |
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| %% \BOLDLISTITEM{VRML File Display} JMV can also read in VRML version 2.0 files. This makes it possible to view molecular representations JMV cannot draw on its own, such as Cartoon, if the right VRML file can be found. It also allows JMV to draw non-molecular data. | %% \BOLDLISTITEM{VRML File Display} JMV can also read in VRML version 2.0 files. This makes it possible to view molecular representations JMV cannot draw on its own, such as Cartoon, if the right VRML file can be found. It also allows JMV to draw non-molecular data. |
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| \BOLDLISTITEM{Saving and Loading Views} Once you start JMV and load a molecule, and get it into a representation, color, and orientation that you like, you can then save that state so that you can see that same view later, or so others can see the same view. You also have the option of saving a JPEG of the JMV screen. | \BOLDLISTITEM{Saving and Loading Views} Once you start JMV and load a molecule, and get it into a representation, color, and orientation that you like, you can then save that state so that you can see that same view later, or so others can see the it. You also have the option of saving a JPEG of the JMV screen. |
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| \BOLDLISTITEM{Interaction with BioCoRE} \htmladdnormallink{{BioCoRE}}{\tt http://www.ks.uiuc.edu/Research/biocore/}, \footnote{http://www.ks.uiuc.edu/Research/biocore/} a collaborative environment for biomedical research, research management, and training, uses JMV. From within BioCoRE, you can view PDB files, and save states and pictures to BioCoRE's filesystem. | \BOLDLISTITEM{Interaction with BioCoRE} \htmladdnormallink{{BioCoRE}}{\tt http://www.ks.uiuc.edu/Research/biocore/}, \footnote{http://www.ks.uiuc.edu/Research/biocore/} a collaborative environment for biomedical research, research management, and training, uses JMV. From within BioCoRE, you can view PDB files, and save states and pictures to BioCoRE's filesystem. |
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