OK, it's morning, but I'm still confused. The atoms are, of course, displayed exactly as the bond table describes. Am I correct in my assumption that atomno is the atom order position in the coordinate table?
By way of example, minimize addHydrogens for ethane from JME and MarvinSketch both identify the three hydrogens attached to C1 (atomno=1) as H1, H2, H3 (atomno= 1,2,3 respectively) in the displayed model. The resulting molfiles are below. The connections are the same and correct. The atom number's in the table are correct, but table (3,4,5) are identified as atomno (1,2,3) in the rendered models. Otis JME string Jmol version 11.9.19 2010-01-12 17:49 EXTRACT: visible 8 7 0 0 0 1.2636106 -0.029628 0.0 C -0.051277 0.7295452 0.0 C 1.7662866 0.0891379 -0.983013 H 1.926285 0.3662737 0.798181 H 1.075 -1.108197 0.1847330 H -0.553937 0.6108022 0.9829441 H 0.1373665 1.8081129 -0.184782 H -0.713955 0.3336691 -0.798261 H 1 2 1 2 8 1 2 7 1 2 6 1 1 5 1 1 4 1 1 3 1 MavinSketch string Jmol version 11.9.19 2010-01-12 17:49 EXTRACT: visible 8 7 0 0 0 -2.891283 0.9768379 0.0 C -1.580023 1.7338637 0.0 C -2.755291 0.0078288 0.5025233 H -3.653254 1.5632088 0.5343901 H -3.218071 0.8094192 -1.036907 H -1.716015 2.7028728 -0.502519 H -1.253235 1.9012825 1.0369116 H -0.818052 1.1474929 -0.534386 H 1 2 1 2 8 1 2 7 1 2 6 1 1 5 1 1 4 1 1 3 1 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
