diff --git a/docker/README.md b/docker/README.md index e9269146889620a5933e8dab30c98b2db5b71ae7..a3fa9d1cbaa8aff82db2a5cccc73be8ccf8fe908 100644 --- a/docker/README.md +++ b/docker/README.md @@ -25,23 +25,27 @@ Input Requirements ------------------ The container can read protein structures in PDB (.pdb) or mmCIF (.cif/.mmcif) -format. Compressed files are accepted, too (.gz suffix, i.e. 1crn.pdb.gz). +format. Compressed files are accepted, too (.gz suffix, e.g. 1crn.pdb.gz). -Providing SEQRES sequences is recommended, this is the actual protein sequence -which is not necessarily fully covered by the structural data. If not provided, -sequences are extracted from the structural data. SEQRES must be provided as one -or several sequences in a single FASTA file. +Providing SEQRES sequences (via the option `--seqres`) is recommended. SEQRES +describes the actual protein sequence of consecutively connected amino acids. +It is not necessarily completely covered by the structural data, think of +missing terminii in a model or gaps. If not provided, sequences are extracted +from the structural data. SEQRES must be provided as one or multiple sequences +in a single FASTA file. * One sequence: All chains of the input structure(s) must align to it, the structures are either monomers or homo-oligmers. -* Several sequences: Required for hetero-oligomers, uses name based +* Multiple sequences: Required for hetero-oligomers, uses name based chain/SEQRES matching The container calculates sequence profiles using -[HHblits](https://github.com/soedinglab/hh-suite) for each unique SEQRES -sequence. If you already have the respective profiles available in a3m format, -you can speed things up. This only works if you also provide SEQRES as an input -and the master sequence for each profile must match one of the SEQRES sequences. +HHblits ([DOI](https://doi.org/10.1186/s12859-019-3019-7), +[Git](https://github.com/soedinglab/hh-suite)) for each unique SEQRES sequence. +If you already have the respective profiles available in a3m format, you can +speed things up (via the option `--profiles`). This only works if you also +provide SEQRES as an input and the master sequence for each profile must match +one of the SEQRES sequences. <a name="qmeanpull"></a>Obtain the image (Docker `pull`) --------------------------------------------------------