[Chimera-users] Does anyone know how to specify a "MarkerSet Link" to be used for findClash

[Jun Ha Song]

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.
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