• RE: Difficulties using docker

    Hello everyone,
     
    I contacted the assistance regarding these my doubts and below I leave the answer in case it is of interest to anyone else.
     
    Some answers for your questions:
    1) See the settings.save_binding_site_atoms option.
     
    2) The settings.reference_ligand_file setting refers to the reference ligand for which you want an RMSD calculated and wants a file name / path string, not a MoleculeReader. This is different to the 'reference ligand' that can be used to define the binding site (see here); the naming is confusing, so apologies for that.
     
    3) At the moment, this must be done by the low-level API and isn't documented:
    settings._settings.set_save_lone_pairs(False)
     
    4) It can be done if a reference ligand is used (see above) but is not likely to be meaningful other than for the reference ligand itself (i.e. if it is redocked). GOLD will attempt to calculate an RMSD for other structures but I wouldn't trust the numbers myself.
     
    I hope that helps, but please get back to us if you have more questions.
    Francis
  • Difficulties using docker

    Hi,

    I'm a user without much experience and I'm trying to use Docker in the same way that I use GOLD (Wizard) and I have some doubts. Could someone help me?

    1 - In the Wizard I use the box: "Generate a cavity atoms file from the selection". How to use in API?

    2 - I am using it to add the "Reference ligand" in the "Select Ligands" step:

    native_ligand = 'native.mol2'
    settings.reference_ligand_file = native_ligand

    But I have seen the use of MoleculeReader is it necessary to use it?

    By the way in the CSD Python API documentation - Setting up a docking run - Essential steps

    There is a step:
    >>> MLL1_ligand_file = 'SAH.mol2'
    >>> MLL1_ligand = MoleculeReader(MLL1_ligand_file)[0]
    >>> settings.add_ligand_file(MLL1_ligand_file, 10)

    Why is MoleculeReader being used if MLL1_ligand is not called?

    3 - In my studies I leave unchecked the "Save lone pairs" box in the output options. How would I do it through the API?

    4 - Is it possible to calculate the RMSD between the results obtained for each input molecule, between m1 to m10?

     

    Best regards,

    Leonardo