Hi Matthias, The species name in the Alphafold database sometimes includes the strain name. Would you want the search to find all species matching the initial part of the species text? I added to ChimeraX 1.9 a tool called Similar Structures under menu Tools / Structure Analysis that can search for structures using Foldseek or MMseqs2. You might be interested this when searching the AlphaFold database since the BLAST search is very slow for the 200 million structures in that database where foldseek and mmseqs2 are quite fast (tens of seconds). The Similar Structures tools is different from the BLAST tool in that it is intended to compare the database structures to a query, so you have to have a query structure, not just a query sequence to use it. https://www.rbvi.ucsf.edu/chimerax/data/foldseek-jul2024/foldseek.html I considered adding a species-specific search option for the similar structures command but didn't add that and instead I have used Elaine's suggestion when using it to sort by the Species column. But I agree an option to show only the results for one species would be useful. I was looking at influenza proteins where the species usually had a strain appended (when searching PDB) so I would definitely need the matching to just match a specified prefix "influenza". The search web services being used don't support specifying a species, so it won't speed up the search. ChimeraX will just get the results for all species but only show you the ones for the species you specified. Because of that the limits on the maximum number of results won't be just for the species you specify but for all results. Tom Example output search Alphafold database with MMseqs2 (uses RCSB web service, took about 10 seconds), sorted by Species column. 
On Jan 28, 2025, at 10:56 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thanks a lot for the reply. I was aware of the filtering, but constraining the search would be more efficient. If this could be implemented in a future release of ChimeraX, I believe it would be useful for many :)
Thanks a lot and best wishes, Matthias
Sent from Outlook for Android <https://aka.ms/AAb9ysg> From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, January 28, 2025 5:47:48 PM To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> Cc: ChimeraX-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Limit blast search to species
Hi Matthias, There is no option to restrict the search itself. However, when you get the results back, you can show the "Species" column and (optionally) sort the results by that. See screenshot attached. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
<Screenshot 2025-01-28 at 8.42.57 AM.png>
On Jan 27, 2025, at 11:12 PM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team, I wondered if it is possible to limit a BLAST search to only a single species when querying a selected database. This would facilitate identifying homologs in your favorite model organism, rather than picking up the most closely related homolog overall (i.e when using the alphafold database). Many thanks, Matthias
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