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What is Chimera?
UCSF Chimera
is a molecular graphics program that can be used to
view structures, sequences, and other data.
Chimera is available free of charge for
academic, government, non-profit, and personal use.
How does it work with the SFLD?
Some SFLD data can be opened and viewed directly with Chimera:
- structures: clicking the
Chimera icon
in individual structure pages or in lists of structures
(the rightmost column) will open the corresponding PDB file in Chimera
- sequence alignments:
Chimera is one of the viewing options provided for superfamily,
subgroup, and family alignments
- modeling sessions:
clicking the large Active Site image present in many
of the SFLD family pages will open the corresponding
interactive session in Chimera; the session will start up with
the same view, coloring, and labels as shown in the image
To view such data with Chimera, it is first necessary to:
- download
Chimera (versions released December 2004 or later)
- configure your system to open the data with Chimera
[For instructions, start Chimera and choose the User's Guide from
the Help menu. In the User's Guide, go to the Tools
section and from there, to the manual page for Browser Configuration.
Configure your browser for the Chimera web data (chimerax)
file type.]
These operations need only be performed once. The web browser may
ask for confirmation that files of the chimerax type should be
opened with Chimera, and then Chimera may ask for confirmation that
the file should be opened. These are safeguards to prevent
potentially harmful code from being executed when the source
of the file is not known or trusted.
However, the browser and Chimera can be instructed not to ask
these questions again.
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