| version 1.8 | version 1.9 |
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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: 1.8 $ $Date: 2002/10/18 16:31:05 $ | % $Revision: 1.9 $ $Date: 2002/10/30 23:35:19 $ |
| % | % |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| % DESCRIPTION: | % DESCRIPTION: |
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| 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. Users 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 gives JMV platform independence, and | stereoscopic viewing. Java technology makes JMV platform independent, and |
| allows it to run within a web browser or as a standalone application. It also | 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 |
| uses Java Beans, making it modular and customizable, so developers 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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| Key \JMV\ features include: | Key \JMV\ features include: |
| \begin{itemize} | \begin{itemize} |
| \BOLDLISTITEM{General molecular visualization} JMV has the ability to read PDB files, and view the molecules in common representations and color schemes. | \BOLDLISTITEM{General Molecular Visualization} JMV reads PDB files, and displays the molecules in common representations and color schemes. |
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| \BOLDLISTITEM{Flexible Deployment} JMV can be run as an applet, as a standalone application, or within another application. | \BOLDLISTITEM{Flexible Deployment} JMV can be run as an applet, as a standalone application, or within another application. |
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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 same view. 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/} the Biological Collaborative Research Environment, 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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| \end{itemize} | \end{itemize} |
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