Using Chimera with the SFLD

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 noncommercial 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 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 as shown in the image.

To view such data with Chimera:

These steps 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.

The name of the downloaded file should end in “.chimerax” – if Chimera does not start automatically, you can start Chimera manually and then use it to open the file.