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Chimera Startup and Input At graphical startup, a Chimera splash screen appears, to be replaced in a few seconds by the or the interface. On Windows, Chimera can be started by clicking the chimera icon. To specify or at startup:.
drag the chimera icon with the right mouse button and select Copy Here from the menu that appears; this creates another shortcut icon called ' copy of chimera'. right-click the new copy of chimera icon, select Properties from the menu that appears. in the resulting panel, click the Shortcut tab and then append the desired and to the command in the Target field. The path to the Chimera executable, arguments of options, and input file pathnames should each be enclosed in double quotes if they contain any spaces, for example: 'C: Program Files Chimera bin chimera.exe' -stereo seq 'f: PDB Files protease.pdb'. click the new copy of chimera icon, Chimera can be started from the system command line: $ chimera.
Bracketed arguments are optional. The user's execution path should include the shortcut created by the installer, if any. Otherwise, the pathname to the executable should be included in the startup command. The executable is in the bin subdirectory of the Chimera installation directory (default /usr/local/chimera). On Mac OS X, Chimera can be started by clicking the chimera icon or by dragging and dropping certain file types on the chimera icon.
The drag-and-drop approach currently works for the (.chimerax) and PDB (.pdb). Chimera can also be started from the Terminal command line: $ chimerainstalldir/Contents/MacOS/chimera. Bracketed arguments are optional. The default chimerainstalldir is /Applications/Chimera.app.
This is one way to run multiple instances of the same Chimera installation on Mac; it can also be done. Chimera for Mac OS X (X Windows) requires an X server to be installed and running. Starting this version of Chimera will automatically start the X server if it is not already running. If a Chimera is, it is read at startup. If a midasrc file is found (see the ), it will be executed when the is shown.
Input files may contain structures to be displayed, commands or code to be executed, or other data. If Chimera is started in without command/script file input, a prompt will be supplied in the system shell for entering on standard input. Any of the can be opened from the system command line at the time of. File type can be specified by a that is part of the filename or by:filename, where is not part of the filename. If a prefix and a suffix are both given, the prefix overrides the suffix. Filenames, prefixes, and suffixes are case-sensitive. Unrecognizable prefixes are assumed to be part of the filename.
For many of the, files that are gzipped (as indicated by.gz following the regular filename) are recognized and opened. Similarly, compressed files (.Z) can be recognized and opened for many input types if gzip is on the user's execution path (can be run by entering gzip at the system command line). Input is generally specified as a pathname to a file or the name of a file in the current working directory. In some cases , the filename can be the database identifier of a file to be retrieved and opened.
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Internet connectivity is required to fetch files over the Web. Any of the can also be opened from within Chimera.
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The most general ways are:. with (local files), (files to be fetched from databases).
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from the Chimera, using the command (default type ) In addition, many bring up dialogs to open specific file types. On a Mac, dragging and dropping known on the Chimera icon will start Chimera (if not already started) and open the files. Models can be closed with the command, the, or File. Close Session. Exit from Chimera A Chimera session can be terminated by choosing File. Quit from the menu, or by entering the command in the.
Whether the user should be asked to confirm exiting from Chimera is set in the. UCSF Computer Graphics Laboratory / July 2018.