Thanks for the help everyone. Angel, the vrml output does "freeze"
cylinders, so for simple situations with only one double bond I can
position the molecule appropriately and get the structure I want. But
when double bonds exist in different planes, I get a 3D snapshot as a
vrml file with inconsist
feature request.
On Tue, Sep 22, 2009 at 3:38 PM, wrote:
> On Tue, September 22, 2009 3:30 pm, Robert Hanson wrote:
> > multiple bonds -- I guess this depends upon your definition of "ideally."
> > Others feel that "ideally" the bonds should rotate so that there is never
> > a
> > question as to
On Tue, September 22, 2009 3:30 pm, Robert Hanson wrote:
> multiple bonds -- I guess this depends upon your definition of "ideally."
> Others feel that "ideally" the bonds should rotate so that there is never
> a
> question as to their order. In addition, this introduces the ambiguity in
> cases su
don't do that. You are producing a 55,000+ line script that IS processed.
Only when the entire script is parsed is the check done that displays the
error or does the exit. Just don't do that!
On Tue, Sep 22, 2009 at 3:15 PM, Eric Martz wrote:
> Dear Bob,
>
> You replied to this message with your
Right. It has limited applications. I'm not sure I'm really very keen on
that animation you have there, though...
On Tue, Sep 22, 2009 at 3:10 PM, Eric Martz wrote:
> Dear Bob,
>
> Thanks for reminding me that I should be using "load trajectory" for
> multiple-model PDB files where only the coord
Dear Bob,
You replied to this message with your "load trajectory" suggestion,
which seems to me to be related to a separateh thread.
I am still interested in whether something simple can be done to keep
Jmol from freezing with the two-command sequence below.
-Eric
>On Sun, Sep 20, 2009 at 11
Dear Bob,
Thanks for reminding me that I should be using "load trajectory" for
multiple-model PDB files where only the coordinates change, not the
atoms. I note that only one frame can be displayed at a time in
trajectory mode. Often I want to show a ligand from the docked frame
in other frame
Hi Daniel
Adding to what Bob has already replied,
> from the Jmol application or signed applet:
> write "XXX.vrml"
> or
> write VRML "XXX.xxx"
In addition, Daniel, you have "export to VRML" in the pop-up menu (depending on
the
version of Jmol, in "Save" or in "File"). It will eventually be in
from the Jmol application or signed applet:
write "XXX.vrml"
or
write VRML "XXX.xxx"
multiple bonds -- I guess this depends upon your definition of "ideally."
Others feel that "ideally" the bonds should rotate so that there is never a
question as to their order. In addition, this introduces the
Dear Bob,
At 9/20/09, Robert Hanson wrote:
>That's fixed. They are no longer incompatible. I'll get a version out
>on chemapps.stolaf.edu later today.
Thanks for fixing the incompatibility!
>Anything else on your mind, Eric?
>
>Bob
Well, Bob, I'll be sure and let you know if anything else comes
Hi everyone.
Question about bond order and exporting:
I'm working with an animation program which understands VRML. There are many
molecular visualization tools out there and several can export to vrml...the
problem is, I haven't found one that can display bond order AND export the
resulting s
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