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PDB-REDO / alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
https://alphafill.eu
BSD 2-Clause "Simplified" License
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Not clear where ligand files should be located. #1

Closed tkella47 closed 2 years ago

tkella47 commented 2 years ago

Running Alphafill. Trying to create pdb-id-list.txt Downloaded the pdb fille from PDB-REDO for 4NXA. FastA file also where it should be. image If possible, would you be able to upload an example run?

mhekkel commented 2 years ago

The README does mention that the ligands file is supplied in the code. Now I don't know where you extracted your code, but in the directory containing the alphafill code there is a file called af-ligands.cif.

There is a help option in alphafill:

$ alphafill --help
alphafill [options] input-file [output-file]:
  --pdb-fasta arg                       The FastA file containing the PDB
                                        sequences
  --pdb-dir arg                         Directory containing the mmCIF files
                                        for the PDB
  --pdb-id-list arg                     Optional file containing the list of
                                        PDB ID's that have any of the
                                        transplantable ligands
  --ligands arg (=af-ligands.cif)       File in CIF format describing the
                                        ligands and their modifications
  --max-ligand-to-backbone-distance arg (=6)
                                        The max distance to use to find
                                        neighbouring backbone atoms for the
                                        ligand in the AF structure
  --min-hsp-identity arg (=0.349999994) The minimal identity for a high scoring
                                        pair (note, value between 0 and 1)
  --min-alignment-length arg (=85)      The minimal length of an alignment
  --min-separation-distance arg (=3.5)  The centroids of two identical ligands
                                        should be at least this far apart to
                                        count as separate occurrences
  --blast-report-limit arg (=250)       Number of blast hits to use
  --compounds arg                       Location of the components.cif file
                                        from CCD
  --components arg                      Location of the components.cif file
                                        from CCD, alias
  --extra-compounds arg                 File containing residue information for
                                        extra compounds in this specific
                                        target, should be either in CCD format
                                        or a CCP4 restraints file
  --mmcif-dictionary arg                Path to the mmcif_pdbx.dic file to use
                                        instead of default
  --config arg                          Config file
  -h [ --help ]                         Display help message
  --version                             Print version
  -v [ --verbose ]                      Verbose output
  --quiet                               Do not produce warnings

Here you can see there is a ligands options with default value _afligands.cif You can provide your own path to your ligands file here. You can also add that option to an alphafill.conf file.

Hopefully this will help you further.