Not sure what I was doing wrong before, but that worked like a charm! Thanks.

Also, pyMol is really sweet. I've been bugging my group to use it for a few days now. :D

Cheers,
Rye


On Tue, Dec 4, 2012 at 11:40 AM, Jason Vertrees <jason.vertrees@schrodinger.com> wrote:
Hi Rye,

set connect_cutoff, 0.5

load 1.xyz

produces different bonding than if you left the connect_cutoff value
to its default, 0.35. Set it to 0.85 and then load the file and you'll
see the Unknown atoms in the middle bonded as well.

Cheers,

-- Jason

On Tue, Dec 4, 2012 at 11:33 AM, Rye Terrell <ryeterrell@ryeterrell.net> wrote:
>
> Hi Jason,
>
> Thanks for the tip. I still couldn't get it to work. I'll google around some
> more, but here's the file. Thanks for any help.
>
> Cheers,
> Rye
>
>
> On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees
> <jason.vertrees@schrodinger.com> wrote:
>>
>> 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 <ryeterrell@ryeterrell.net>
>> 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
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Keep yourself connected to Go Parallel:
>> > BUILD Helping you discover the best ways to construct your parallel
>> > projects.
>> > http://goparallel.sourceforge.net
>> > _______________________________________________
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>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> Director of Core Modeling Product Management
>> Schrödinger, Inc.
>>
>> (e) Jason.Vertrees@schrodinger.com
>> (o) +1 (603) 374-7120
>
>



--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120