Guidance on how to download the reported PDBs

[anar-rzayev]

Hello, thank you very much for your program. I wanted to ask about a specific step after we do easy-multisearch. Once we align the query structure and get the _report, I wanted to download all those ~1K PDB structures that I get from the FoldSeek. It seems in the current version, there is no automation of doing that?

Let's say, I have the following result

1tim.pdb_A	6c2g-assembly2.cif.gz_D	0.855	243	32	3	4	246	2	241	3.343E-36	1329	0
1tim.pdb_A	6c2g-assembly2.cif.gz_B	0.864	243	33	0	4	246	2	244	4.022E-37	1371	1
1tim.pdb_A	5zfx-assembly1.cif.gz_B	0.623	247	90	1	4	247	2	248	3.105E-32	1170	2
1tim.pdb_A	6nlh-assembly1.cif.gz_E	0.831	244	35	1	4	247	1	238	3.564E-37	1362	3

Is there any way I could download all these specific assembly chains that are structurally similar to my query?

[martin-steinegger]

--format-output 5 will return Calpha only PDB super-posed to query.