(...) As this example is based on a transcription factor that binds to
the DNA, resulting in "punctate", relatively narrow peaks, the default
option to re-center each peak around the point of greatest enrichment
is appropriate. This keeps the peaks at a consistent width (in this
case, the default summits=200 results in 401bp-wide intervals,
extending 200bp up- and downstream of the summit)
Buries in the docs (?DiffBind3) is a recommendation to use summits=100 for ATAC-seq, which results in 201bp windows.
It helps to look sat the distribution of fragment lengths in your data. If you've done paired-end sequencing and trimmed adaptors, you'll get a variety of sequence lengths. Generally in a good quality ATAC experiment most of the fragments will be around 50bp-100bp. If that is the case, the summits parameter can be set even lower, e.g. summits=50 or summits=75.