Suggestion: Move .m8 file generation outside of template database to avoid read-only database conflict about colabfold HOT 3 CLOSED

If you just use the database name only "pdb100_230517" instead of the full path it should put the .m8 file in the desired output directory instead the database directory. This is a quoted example from issue 563. Hope this helps.

Currently, colabfold_search can generate a list of template PDB files together with MSA files. For example,

MMSEQS_PATH="/path/to/your/mmseqs2/for_colabfold"
DATABASE_PATH="/mnt/databases"
INPUTFILE="ras_raf.fasta"
OUTPUTDIR="ras_raf"

colabfold_search \
  --use-env 1 \
  --use-templates 1 \
  --db-load-mode 2 \
  --db2 pdb100_230517 \
  --mmseqs ${MMSEQS_PATH}/bin/mmseqs \
  --threads 4 \
  ${INPUTFILE} \
  ${DATABASE_PATH} \
  ${OUTPUTDIR}

from colabfold.

If you just use the database name only "pdb100_230517" instead of the full path it should put the .m8 file in the desired output directory instead the database directory. This is a quoted example from issue 563. Hope this helps.

Currently, colabfold_search can generate a list of template PDB files together with MSA files. For example,

MMSEQS_PATH="/path/to/your/mmseqs2/for_colabfold"
DATABASE_PATH="/mnt/databases"
INPUTFILE="ras_raf.fasta"
OUTPUTDIR="ras_raf"

colabfold_search \
  --use-env 1 \
  --use-templates 1 \
  --db-load-mode 2 \
  --db2 pdb100_230517 \
  --mmseqs ${MMSEQS_PATH}/bin/mmseqs \
  --threads 4 \
  ${INPUTFILE} \
  ${DATABASE_PATH} \
  ${OUTPUTDIR}

Just heads up this works only if you run a single sequence. If you run it in a fasta or csv file with multiple sequence, there's still some file naming issues that will throw you an error.

from colabfold.

If you just use the database name only "pdb100_230517" instead of the full path it should put the .m8 file in the desired output directory instead the database directory. This is a quoted example from issue 563. Hope this helps.

Currently, colabfold_search can generate a list of template PDB files together with MSA files. For example,

MMSEQS_PATH="/path/to/your/mmseqs2/for_colabfold"
DATABASE_PATH="/mnt/databases"
INPUTFILE="ras_raf.fasta"
OUTPUTDIR="ras_raf"

colabfold_search \
  --use-env 1 \
  --use-templates 1 \
  --db-load-mode 2 \
  --db2 pdb100_230517 \
  --mmseqs ${MMSEQS_PATH}/bin/mmseqs \
  --threads 4 \
  ${INPUTFILE} \
  ${DATABASE_PATH} \
  ${OUTPUTDIR}

This indeed solved the issue I was facing 👍
Thank you

from colabfold.