Error when Creating DB from Existing DB File

diegozea commented 11 months ago

Expected Behavior

I expected to be able to create a database from an existing DB file as the command suggests:

foldseek createdb <i:PDB|mmCIF[.gz]|tar|DB> ... <i:PDB|mmCIF[.gz]|tar|DB> <o:sequenceDB> [options]

Current Behavior

When attempting to create a DB from a DB file, the following error message appears: "No structures found in given input."

Steps to Reproduce (for bugs)

Use an existing DB file. I have created a testing one from 3 pdb files using foldseek createdb . test_db.
Execute foldseek createdb test_db output_db
Observe the error message.

Foldseek Output (for bugs)

Error message: "No structures found in given input."

Context

I want to merge two databases, and one of them is the AlphaFold database. I thought creating a DB from a DB file would be the way to go. If this is not the intended functionality, how can we merge two databases? Alternatively, is there a method to merge two search results?

Your Environment

Git commit used: 946841ff3b15531349a9883358b3a3052b368da9
Which foldseek version was used: Foldseek_jll
For self-compiled and Homebrew: GCC v8
Server specifications: CPU supports AVX2 and SSE. System memory is 31Gb with 23Gb available.
Operating system and version: Debian GNU/Linux 11 (bullseye).

martin-steinegger commented 11 months ago

Why do you try to create a database from a database?

diegozea commented 8 months ago

Hi @martin-steinegger! I understand that we can only search one database at a time. I considered merging the databases to search multiple databases in a single search. Does that make sense to you? Best regards.

steineggerlab / foldseek