hmm, yes, atom numbers. that would be the case any time you do a merge with
set appendNew false
which is what we are doing here.
That should be fixed now for the next release of Jmol.
On Sun, Jan 17, 2010 at 1:16 AM, Otis Rothenberger <o...@chemagic.com>wrote:
> Bob-
>
> Very very nice. I know you were not targeting JME, but on my home
> server, JME and Marvin (via beans application copy/paste) behave
> identically on the few structures that I tried. Our site is for high
> school teachers/students, so the light weight JME is a good approach
> for us.
>
> Once the hydrogens are added, I see duplicate atom numbers when I try
> to select by atomno. The bond tables must be off, but it's late. I'll
> take a closer look at the bond tables tomorrow.
>
> Otis
>
> On Sun, Jan 17, 2010 at 12:42 AM, Robert Hanson <hans...@stolaf.edu>
> wrote:
> > OK, so Nico has released 11.9.19, and it should have your
> >
> > calculate hydogens
> >
> > or
> >
> > minimize addHydrogens
> >
> >
> >
> > On Sat, Jan 16, 2010 at 12:35 AM, Otis Rothenberger <o...@chemagic.com>
> > wrote:
> >>
> >> I should mention that the page also has a "ChemSketch" link. This link
> >> simply does an inline molfile load of a molfile pasted in the page's
> >> text field.
> >>
> >> A Marvin Beans "View Source" as molfile can be copy pasted into the
> >> field. It's not as slick as an auto transfer, but clicking the
> >> "ChemSketch" link followed by Clicking the UFF link gets the job done
> >> for the Marvin Beans structure in the text field.
> >>
> >> Otis
> >>
> >> On Fri, Jan 15, 2010 at 8:01 PM, Otis Rothenberger <o...@chemagic.com>
> >> wrote:
> >> > Bob,
> >> >
> >> > I have a page that does this with the JME drawing applet. I'm not sure
> >> > if this will help:
> >> >
> >> > http://chemagic.com/web_molecules/script_page_large.aspx
> >> >
> >> > The Draw Structure link opens the JME editor. The Load Structure sends
> >> > the molfile to Jmol. While I have a UFF link on the page, the Load
> >> > Structure link automatically runs the UFF on the loaded structure.
> >> >
> >> > Hope this helps.
> >> >
> >> > Otis
> >> >
> >> >
> >> >
> >> >
> >> > On Fri, Jan 15, 2010 at 2:01 PM, Robert Hanson <hans...@stolaf.edu>
> >> > wrote:
> >> >> Does anyone have a page that we can play with that would allow Marvin
> >> >> input
> >> >> of 2D structures and Jmol rendering of them in 3D?
> >> >>
> >> >> --
> >> >> Robert M. Hanson
> >> >> Professor of Chemistry
> >> >> St. Olaf College
> >> >> 1520 St. Olaf Ave.
> >> >> Northfield, MN 55057
> >> >> http://www.stolaf.edu/people/hansonr
> >> >> phone: 507-786-3107
> >> >>
> >> >>
> >> >> If nature does not answer first what we want,
> >> >> it is better to take what answer we get.
> >> >>
> >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> >> >>
> >> >>
> >> >>
> ------------------------------------------------------------------------------
> >> >> Throughout its 18-year history, RSA Conference consistently attracts
> >> >> the
> >> >> world's best and brightest in the field, creating opportunities for
> >> >> Conference
> >> >> attendees to learn about information security's most important issues
> >> >> through
> >> >> interactions with peers, luminaries and emerging and established
> >> >> companies.
> >> >> http://p.sf.net/sfu/rsaconf-dev2dev
> >> >>
> >> >> _______________________________________________
> >> >> Jmol-users mailing list
> >> >> Jmol-users@lists.sourceforge.net
> >> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >> >>
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Otis Rothenberger
> >> > http://chemagic.org
> >> >
> >>
> >>
> >>
> >> --
> >> Otis Rothenberger
> >> http://chemagic.org
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Throughout its 18-year history, RSA Conference consistently attracts the
> >> world's best and brightest in the field, creating opportunities for
> >> Conference
> >> attendees to learn about information security's most important issues
> >> through
> >> interactions with peers, luminaries and emerging and established
> >> companies.
> >> http://p.sf.net/sfu/rsaconf-dev2dev
> >> _______________________________________________
> >> Jmol-users mailing list
> >> Jmol-users@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
> >
> > --
> > Robert M. Hanson
> > Professor of Chemistry
> > St. Olaf College
> > 1520 St. Olaf Ave.
> > Northfield, MN 55057
> > http://www.stolaf.edu/people/hansonr
> > phone: 507-786-3107
> >
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> >
> >
> ------------------------------------------------------------------------------
> > Throughout its 18-year history, RSA Conference consistently attracts the
> > world's best and brightest in the field, creating opportunities for
> > Conference
> > attendees to learn about information security's most important issues
> > through
> > interactions with peers, luminaries and emerging and established
> companies.
> > http://p.sf.net/sfu/rsaconf-dev2dev
> >
> > _______________________________________________
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
>
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
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