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.vertr...@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 <ryeterr...@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.vertr...@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 <ryeterr...@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
> >> > _______________________________________________
> >> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> > Archives:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >>
> >>
> >>
> >> --
> >> Jason Vertrees, PhD
> >> Director of Core Modeling Product Management
> >> Schrödinger, Inc.
> >>
> >> (e) jason.vertr...@schrodinger.com
> >> (o) +1 (603) 374-7120
> >
> >
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Product Management
> Schrödinger, Inc.
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
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