Hello,

I want to search whether my models are close enough to be exactly apart from each other by the distance I specify.

findClash appear to be tailor-made for the exact task I was hoping to do, but unfortunately, it appear to only search nearby atoms, not the links, even if I select the entire model which has both markers and links incorporated as its component.

The only way that I can make my entire MarkerSet to be competent for findClash was to use Tom's dividelinks.py script (http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/dividelinks.py) to add n number of marker s along the link of two marker that I selected.

Q1. Can I ever specify MarkerSet Link by atom-spec commands, to use findClash on the inter-model links as well, not only for the markers?

Q2. Is there any other function than findClash that allow me to find any inter-model (never atoms within the same model) atom or link's distance that I specify exist?

Best,

Jun Ha Song.