ChimeraX docs icon

Tool: Blast Protein

Blast Protein runs a protein sequence similarity search using a BLAST web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI). See also: AlphaFold, matchmaker

The Blast Protein tool can be opened from the Sequence section of the Tools menu and manipulated like other panels (more...). It is also implemented as the blastprotein command.

Search Parameters

The first menu allows choosing a protein chain from the currently open atomic structures to use as the query. Note: the blastprotein command additionally allows using a sequence (for which no structure may be available) as the query, such as to find templates for comparative modeling. See also: alphafold search

Clicking Apply (or OK, which also dismisses the dialog) runs the search, whereas Close dismisses the dialog without starting a search. Help opens this page in the Help Viewer, and Reset restores the parameters to factory default settings.

BLAST Protein Results

When results are returned, the table of hits is shown in a separate window. These results are saved in ChimeraX sessions. If you wish to prevent the results from docking into the main window (which may resize it), see Tool windows start undocked in the Window preferences.

Checkboxes in the bottom section of the panel control which columns of information are shown in the table of hits, with buttons:

Clicking a column header sorts by the values in that column.

Double-clicking a row with a corresponding structure fetches it, and if a structure chain was used as the query, automatically superimposes the hit onto the query using matchmaker. AlphaFold-predicted structures are colored by confidence value.

One or more hits can be chosen (highlighted) in the list by clicking and dragging with the left mouse button; Ctrl-click (or command-click if using a Mac) toggles whether a row is chosen. The result panel's context menu can be used to fetch and superimpose all of the corresponding structures, or to show their multiple sequence alignment with the query in the Sequence Viewer.

Some columns are available no matter which database is searched:

Additional columns for AlphaFold entries:

Additional columns for PDB entries (from searching PDB or NR):


Pseudo-multiple alignment. The pseudo-multiple alignment from BLAST is not a true multiple alignment, but a consolidation of the pairwise alignments of individual hits to the query. This output corresponds to the BLAST formatting option (alignment view) “flat query-anchored with letters for identities.”

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 / November 2021