Understood Bob. I think having a parameter for it would be good and I
think the default should be:
multipleBondSpacing = 0.35
multipleBondCylinderThickness = 0.75 (or however you want to code it)
Rich
On [2010-Sep-10] Robert Hanson wrote:
> This isn't thickness, it's distance apart. We could a
I, too, have always thought that it was a bit weird to see the double bond
lines move around, and I think perhaps it really was just because nobody had
devised a simple way of defining the bond plane, finding the normal, and
working with that. One thing to realize is that prior to my implementing t
My strong preference would be to move the default to fixed (eg, "set
multipleBondSpacing = 0.35"). My opinion is that the double bonds always
rotating to face the viewer is a little creepy -- sort of like Mona Lisa's
eyes following you around the room!:)I very much feel that the
double bo
Don't ask me to make sure the dotted line is on the inside. Just TOO
complicated.
On Fri, Sep 10, 2010 at 9:45 AM, Shore, Jay wrote:
>
>
> Thank you Bob.
> I really really like it.
> I think that it looks great.
> I was happily surprised that when I “set smartARomatic false; reset
> aromatic” on
This isn't thickness, it's distance apart. We could add a parameter for
that, though.
On Fri, Sep 10, 2010 at 8:42 AM, wrote:
> On Fri, September 10, 2010 9:19 am, Robert Hanson wrote:
> > that can be experimented with at
> > http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?topic=11
> >
Thank you Bob.
I really really like it.
I think that it looks great.
I was happily surprised that when I "set smartARomatic false; reset aromatic"
on your benzene it kept the bonds in the plane when I rotated the molecule. It
did end up putting the dashed bond on the outside after rotating onc
On Fri, September 10, 2010 9:19 am, Robert Hanson wrote:
> that can be experimented with at
> http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?topic=11
>
> I think this could be a new default. Let's talk about it.
>
> On Fri, Sep 10, 2010 at 7:31 AM, Robert Hanson wrote:
>
>> Uploading now
that can be experimented with at
http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?topic=11
I think this could be a new default. Let's talk about it.
On Fri, Sep 10, 2010 at 7:31 AM, Robert Hanson wrote:
> Uploading now a slight modification of this idea:
>
> # new feature: multipleBondS
Uploading now a slight modification of this idea:
# new feature: multipleBondSpacing
# set multipleBondSpacing = -1 (default, varies with viewing angle)
# set multipleBondSpacing = -0.5 (half that distance; varies with viewing
angle)
# set multipleBondSpacing = 0.35 (positive ==> fixed multi
On Thu, Sep 9, 2010 at 4:36 PM, Shore, Jay wrote:
>
>
>
> I wonder if it would be easier to put it in the Sticks class – would that
> make it easier for use with external renderers (e.g. povray)?
>
>
doesn't matter. The exporters use exactly the same rendering code. They just
interpret the graphi
I wonder if it would be easier to put it in the Sticks class - would that make
it easier for use with external renderers (e.g. povray)?
For triple bonds, one could try to define a plane for each molecule so all
triple bonds were oriented the same way. A vector, orthogonal to the triple
bond
On Thu, Sep 9, 2010 at 11:59 AM, Shore, Jay wrote:
>
> I think that the issues involved with the rendering are more complicated
> than I had initially realized.
>
> I had thought that I could just stop the distance between the double bonds
> from changing if I constrained myself to rotation about
I think that the issues involved with the rendering are more complicated than I
had initially realized.
I had thought that I could just stop the distance between the double bonds from
changing if I constrained myself to rotation about one axis - right now I am
not sure if that is true of desir
Bob,
My choice of words is leading to some confusion.
In the current implememtation as the model is rotated the double bond
rotates so the user sees two sticks in almost all orientations. This
requires rotating the bond cylinders as the molecule rotates. Sometimes
the aliasing of edges of the cyl
I'm not sure I'm understanding, Rich.
You're saying hand-rotating the model, you are willing to see some jumping
around (not the current situation), but for movies you would like to see it
smoother (current situation). But also for movies you would like to always
have the double bond in the plane
Something else to consider is the intent of the display. Sitting at the
screen rotating a molecule by hand to get to a particular view of the
molecule is one thing. Creating a movie which is is presumably intended to
illustrate something about the molecule is another.
In the former having things j
[should move this to Jmol-Developers list...]
Jay, before you go after this, I'd like to hear what you expect to observe
under various conditions --
A --- bond is vertical and is rotated along its axis.
B --- bond is vertical and is rotated perpendicular to its axis until it is
pointing into the
Thank you Bob for your thorough explanation. I think that I finally understand.
While jmol's biggest advantage may be with its ability to let users interact
with structures, it is also an excellent tool for making movie, especially with
the povray export. If I wanted to make a movie of a mol
On Mon, Aug 23, 2010 at 11:01 AM, Shore, Jay wrote:
>
> I really like jmol’s multiple bond representation – it is the only
> visualization tool that I know of that actually
> that actually does multiple bonds.
>
> The distance between the cylinders (that represent a double bond) changes
> when th
I really like jmol's multiple bond representation - it is the only
visualization tool that I know of that actually
that actually does multiple bonds.
The distance between the cylinders (that represent a double bond) changes when
the molecule is rotated depending on the relative orientation of t
On Tue, Jul 13, 2010 at 1:34 PM, Shore, Jay wrote:
>
>
> Any suggestions as to where I should look in the code to try
> to remove this effect?
>
>
no idea. It's important it does it this way, actually. What were you
thinking would be better?
> Thanks,
> Jay
>
>
>
>
> On 7/12/10 11:33 PM, "Rober
Images were exported from jmol using the povray export.
I modified the povray export procedure to include two lights.
ffmpeg was then used to make a quicktime movie and convert
the quicktime movie to swf to be posted. I use the quicktime
for my ppts, the swf was used just to post so that you coul
Nice movie -- how do you do that?
Enjoy the effect. Actually, the two lines are passing THROUGH each other,
hidden by the spacefill. More dramatic with
wireframe only
:)
Bob
On Mon, Jul 12, 2010 at 9:31 PM, Shore, Jay wrote:
>
> Hello All,
>
> I think that there might be a possible problem w
Hello All,
I think that there might be a possible problem with the representation of a
double bond.
It seems that when a molecule with a double bond is rotated about an axis
orthogonal to
the double bond and in the plane of the screen, the distance between the two
cylinders
that represent the
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