steineggerlab/foldmason

No html output for easy-msa?

Closed this issue · 2 comments

DaRinker commented

Expected Behavior

Documentation says I can expect a "result.html" and a "result.fasta"

Current Behavior

Running foldmason version Version: 63949d9

Input pdb files were made by ESMfold (possibly relevant because ESMfold reports pLDDTs per-atom, unlike AF2)

Running the simple command:

foldmason easy-msa <my pdbs> result.fasta tmpfolder
The output files I get are:

  • result.fasta_3di.fa
  • result.fasta_aa.fa
  • result.fasta.nw

The resulting MSA looks good so not sure what's going on. Nor errors or exceptions reported.

gamcil commented

Looks like I need to update the docs - we turned off the LDDT calculation by default in easy-msa, to enable it again you can use --report-mode 1 for HTML or --report-mode 2 for JSON output (i.e. loadable in the server). If you have kept the structure database created in your last run (i.e. in tmpfolder/latest/structures), you could also directly use msa2lddt like:

# prints to console
msa2lddt tmpfolder/latest/structures result.fasta_aa.aa
# generate HTML report
msa2lddtreport tmpfolder/latest/structures result.fasta_aa.aa result.html
# generate JSON file
msa2lddtjson tmpfolder/latest/structures result.fasta_aa.aa result.json
  • 👍1
DaRinker commented

Perfect. Works as expected. Thank you.