Missing Alignment Visualizations in html Output

[Jonasgrove]

I am seeing an issue with foldseek version "v9.427df8a" when using "--format-mode 3" to generate an html output. In some cases the interactive protein alignment visualization is missing from the output. When I run the same command on the same sequences using version "v7.04e0ec8" the protein alignment visualization is present. It seems something changed between these versions that causes this issue.

v9.427df8a Output

v7.04e0ec8 Output

Expected Behavior

Overlayed structures in interactive viewer present for all alignment hits generated by "easy-search".

Current Behavior

Some alignment interactive visualizations are missing in output.

Steps to Reproduce (for bugs)

foldseek easy-search pdbs pdbs result.html tmpFolder --format-mode 3 --alignment-type 1

Foldseek Output (for bugs)

Output html is missing interactive structure.

Context

When I run foldseek easy-search with --format-mode 3 specified I find inconsistent behavior between versions
"v9.427df8a" and "v7.04e0ec8". When using "v9.427df8a" some of the interactive overlayed structures are missing in the html output, but when using "v7.04e0ec8" they are all present.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Git commit used (The string after "MMseqs Version:" when you execute foldseek without any parameters): v9.427df8a
• Which foldseek version was used (Statically-compiled, self-compiled, Conda, etc.): Conda
• For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation: N/A
• Server specifications (especially CPU support for AVX2/SSE and amount of system memory): AMD EPYC 7R32 (Supports AVX2 and SSE4.2) and 30G memory.
• Operating system and version: Ubuntu 20.04.6 LTS

[martin-steinegger]

Thank you for reporting this. @gamcil could you have a look at it please?