Hi Jiying Jia,
Findclash tests for atom-atom close contacts.  Bonds are not considered, except that the default is to ignore interactions between atoms separated by 4 or fewer bonds and between atoms in the same residue.  You can change those settings with the “bondSeparation” and “intraRes” options of findclash.  Of course, it also depends on what you use as the “overlapCutoff" and “hbondAllowance" values.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 30, 2016, at 2:27 AM, Jiying Jia <jiajiyingxibei@gmail.com> wrote:
>
> Hi,
>
> Is there a way to detect whether there's bond cross in the conformation? Or check whether it's self-avoiding? The command "findclash" seems not to be able to do this.
>
> ------------------
> Best Wishes!
> Jiying Jia