I'm loading a movie file now and it appears that the bonds determined in the first frame are used throughout the entire movie, even if atoms move further apart than the cutoff. Is my perception correct here? If so, can I make the bonds be calculated for each frame?


On Tue, Dec 4, 2012 at 11:43 AM, Rye Terrell <ryeterrell@ryeterrell.net> wrote:
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:
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>> > projects.
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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