Issues

• α/β hydrolase catalytic triad (GXSXG / D / H) misaligned — 3Di vs AA scoring conflict?

  steineggerlab/foldmason#40 · Filter by author LSJ70 opened on Aug 27, 2026

• missing proteins in the results

  steineggerlab/foldmason#36 · Filter by author MargotL17 opened on Mar 3, 2026

• Request: FoldMason alignment of protein-protein interactions at scale

  steineggerlab/foldmason#34 · Filter by author Not-Chat opened on Jan 7, 2026

• foldmason CUDA aand//or MPI compliant ?

  steineggerlab/foldmason#31 · Filter by author EricDeveaud opened on Sep 23, 2025
  2

• 3Di+AA weights / bitfactors

  steineggerlab/foldmason#30 · Filter by author Proginski opened on Sep 22, 2025
  2

• extract clusters from --precluster

  steineggerlab/foldmason#29 · Filter by author shamphavis opened on Sep 10, 2025

• How many stuctures are sccepted by FoldMason webserver?

  steineggerlab/foldmason#28 · Filter by author ZXX95012 opened on Sep 7, 2025
  4

• Inconsistent FoldMason alignments with near-identical AF2 inputs

  steineggerlab/foldmason#27 · Filter by author RumoisteinKartenspiel opened on Jul 28, 2025

• segmentation fault with --refine-iters (bug?)

  steineggerlab/foldmason#26 · Filter by author vmkhot opened on Jul 7, 2025

• Obtaining tree branch lengths

  steineggerlab/foldmason#25 · Filter by author zoeyxyang opened on Jul 3, 2025

• request for foldmason server: accept input from foldseek server

  enhancement
  steineggerlab/foldmason#24 · Filter by author rubenalv opened on May 20, 2025
  2

• Using MSTA and HMMER like method to search common structure features in big database

  steineggerlab/foldmason#23 · Filter by author sevengo8378 opened on Apr 28, 2025
  4

• TM-align structure superposition doesn't reflect the underlying MSA

  steineggerlab/foldmason#21 · Filter by author apcamargo opened on Mar 17, 2025
  1

• "Found nan" during msa2lddtreport

  steineggerlab/foldmason#20 · Filter by author delalamo opened on Feb 19, 2025
  1

• I have a question regarding the results of FoldMason.

  steineggerlab/foldmason#19 · Filter by author tzjsdss opened on Feb 16, 2025
  2

• Getting foldmason aa.fa, ss.fa, and .nw files when running Foldseek locally

  steineggerlab/foldmason#18 · Filter by author khabj-snek opened on Feb 12, 2025
  2

• Running foldmason with 3Di sequence input, not PDB file

  steineggerlab/foldmason#17 · Filter by author iwilkie opened on Feb 12, 2025
  3

• A strange mistake：Error: msa2lddt died

  steineggerlab/foldmason#16 · Filter by author tzjsdss opened on Jan 20, 2025
  6

• Newick Tree file unable to open in Python or R (Malformed structure)

  steineggerlab/foldmason#13 · Filter by author parkjooyoung99 opened on Oct 14, 2024
  3

• Retrieving the aligned (superposed) PDBs

  steineggerlab/foldmason#12 · Filter by author jeversbioprodict opened on Sep 9, 2024
  6

• Foldmason not running on large set of proteins

  steineggerlab/foldmason#11 · Filter by author rrw1007 opened on Sep 4, 2024
  11

• FoldMason not running

  steineggerlab/foldmason#7 · Filter by author KristiPhammie opened on Aug 15, 2024
  6

• Request: output MSA from already aligned structures

  steineggerlab/foldmason#5 · Filter by author gezmi opened on Jun 20, 2024
  1

• Request: Access to column LDDT values

  steineggerlab/foldmason#4 · Filter by author hughhigin opened on May 30, 2024
  3

• Structuremsa consumes RAM until killed by OS

  steineggerlab/foldmason#3 · Filter by author hughhigin opened on Feb 15, 2024
  3