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Tool: Blast Protein

Blast Protein searches for similar protein sequences using a BLAST web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI). Any protein structure chain in ChimeraX can be used as the query. The blastprotein command implementation additionally allows using a sequence open in ChimeraX as the query.

For hits corresponding to structures in the Protein Data Bank (PDB), the structures can be retrieved and automatically superimposed onto the query chain.

Like other tools, this interface can be opened from the Tools menu (more...). See also: matchmaker

Search Parameters

Clicking the Blast button initiates the search.

BLAST Results

When results are returned, the hits are listed in a table below the search parameters in the Blast Protein window.

A text-search box allows finding hits that contain terms of interest. Pull-down menus to the right of the search box allow adjusting the number of hits shown at a time and which columns of information are included in the table. Clicking a column header sorts by the values in that column.

Some columns are available for NR sequences regardless of whether they are in the PDB subset:

Additional columns of information are available for PDB sequences:

The Blast Protein tool, including search results (but not window size or location) is saved in ChimeraX sessions.


Basic Local Alignment Search Tool (BLAST). The BLAST software is provided by the NCBI and described in:

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.

Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. J Mol Biol. 1990 Oct 5;215(3):403-10.

UCSF Resource for Biocomputing, Visualization, and Informatics / May 2019