[Chimera-users] How to detect bond cross

[Jiying Jia]

Hi, Elaine,

Thanks. I will look at the options of findclash for more details.

------------------
Best Wishes!
Jiying Jia

On Thu, Jun 30, 2016 at 6:18 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> ----------
> 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 at 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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160701/36b0ce9e/attachment.html>