Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded

[Jason V. <jas...@sc...>]

Hi Rye,

How about connect_cutoff in Å? There's also connect_mode
(http://www.pymolwiki.org/index.php/Connect_mode).

If you send me a copy of your file I can look at it.

Cheers,

-- Jason

On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell <rye...@ry...> wrote:
> I have a silicon bulk system. Pymol indicates that a handful of the atoms
> are bonded to each other. Many bonds are not indicated. Is there some value
> I can adjust that will make pymol indicate that more atoms are bonded? I
> usually do this by setting some cutoff radius, but googling around has
> yielded no results. I see that there is a way to bond atom pairs manually,
> but that would be incredibly tedious given the number of bonds there should
> be.
>
> Thanks for any help!
> Rye
>
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--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

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