Hi Rye,
only discrete objects have per state bonding information. Try this:
load multistate.pdb, discrete=1
Hope that helps.
Cheers,
Thomas
Rye Terrell wrote, On 12/05/12 18:20:
I'm loading a movie file now and it appears that the bonds determined in
the first frame are used throughout
Thanks Thomas.
That may or may not have worked, I can't tell. Usually after I load the
movie, I can hide all followed by show sticks, and this will show me
sticks for all frames of the movie. When I do this now, I get sticks for
the first frame, but nothing shows up on later frames. Even if I go
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
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
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
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
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
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.
