A ChimeraX similar structures file (filename suffix .sms) stores the results of searching protein structure databases using any of the following:
Running a search automatically creates a similar structures file with filename based on the query name, database searched, and search method, ending in the suffix .sms. The file is listed in the File History for easy access. The default save location is in ~/Downloads/ChimeraX under subdirectories Foldseek, MMseqs2, or BLAST, but a different location can be specified with the saveDirectory option of the above commands. In addition, results from using Blast Protein or the blastprotein command with a structure chain as the query can be saved to a similar structures file with similarstructures fromblast.
The ChimeraX-only .sms format is a JSON text file that contains the path to the query structure file, the database identifiers of the similar structures, their sequence alignments to the query, and in some cases, their α-carbon coordinates. The α-carbon coordinates allow showing backbone traces and clustering by backbone conformations with the Similar Structures tool. Only structure-based searches with the Foldseek method automatically include these coordinates, but they can be added to the .sms files from sequence-based searches (MMseqs2 and BLAST) with the command similarstructures fetchcoords.
Opening a similar structures (.sms) file from the File History or with the the File menu or open command shows the search results in the Similar Structures tool. If the corresponding query structure is already open, it will be associated with these results; if it is not open, ChimeraX will try to load the original query structure from the file path in the .sms file.