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Re: [Jmol-users] Handling Isotopes
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From: Bob H. <ha...@st...> - 2007-11-30 00:18:18
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Barney, Jmol wasn't reading that column; it is now (11.3.50), so look for an update. I've registered C-11 as slightly ligher in color than C-12. The way you select these is with an underscore ahead of the isotope number: select _11C select _13C For deuterium and tritium you can also use: select deuterium select _2H select D select trititum select _3H select T And you can color the elements this way to your liking, as well: color _11C green Bob Hanson Barny Shergold wrote: >Hi, > >I'm new to the mailing list and I would really appreciate some help. My >client uses a chemical that has many carbon atoms in it and one of them >is actually Carbon-11. When I use and SDF file (show below) it models >all the carbon atoms the same. Is there any way that Jmol can show an >isotope? I just need that one Carbon atom to look a little different. > >If you notice the 6th Carbon atom down it has a -1 next in the 5th >column, this is the carbon atom in question and I assume the -1 is to >indicate it is Carbon-11 (ie 12 - 1 = 11) > >Is there anything I can do to get that Carbon at atom to announce its >difference? > >Any help would be much appreciated as this is part of my degree >dissertation. > >Kind Regards > >Barny Shergold > > > > >450825 > -OEChem-11290711172D > > 46 48 0 1 0 0 0 0 0999 V2000 > 3.4030 -2.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 > 2.5369 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 3.4030 2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 4.2690 -0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 4.2690 2.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 > 4.2690 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1350 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.4030 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.2690 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.5369 2.5000 0.0000 C -1 0 0 0 0 0 0 0 0 0 0 0 > 5.1350 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.0010 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.0010 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1350 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1350 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1350 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.8950 -1.0347 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.8950 1.0347 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.8010 -0.5208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.8010 0.5208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.2690 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.0010 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.2690 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.0010 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1350 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.2690 1.8800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 3.6584 3.3923 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 4.0569 4.0826 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 4.8250 1.4631 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 5.6719 1.6900 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 5.4450 2.5369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 2.0000 2.8100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 2.8469 3.0369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 2.2269 1.9631 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 5.4450 3.4631 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 4.8250 4.5369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 5.6719 4.3100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1350 1.6200 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 6.8878 -1.6546 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 6.8878 1.6546 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 8.3368 -0.8329 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 8.3368 0.8329 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 6.5380 -2.1900 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 3.7321 -3.8100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 6.5380 -3.8100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1350 -4.6200 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 1 21 1 0 0 0 0 > 2 8 2 0 0 0 0 > 3 5 1 0 0 0 0 > 3 8 1 0 0 0 0 > 3 10 1 0 0 0 0 > 4 9 1 0 0 0 0 > 4 14 2 0 0 0 0 > 5 6 1 0 0 0 0 > 5 7 1 0 0 0 0 > 5 26 1 0 0 0 0 > 6 11 1 0 0 0 0 > 6 27 1 0 0 0 0 > 6 28 1 0 0 0 0 > 7 29 1 0 0 0 0 > 7 30 1 0 0 0 0 > 7 31 1 0 0 0 0 > 8 9 1 0 0 0 0 > 9 15 2 0 0 0 0 > 10 32 1 0 0 0 0 > 10 33 1 0 0 0 0 > 10 34 1 0 0 0 0 > 11 35 1 0 0 0 0 > 11 36 1 0 0 0 0 > 11 37 1 0 0 0 0 > 12 13 1 0 0 0 0 > 12 14 1 0 0 0 0 > 12 17 2 0 0 0 0 > 13 15 1 0 0 0 0 > 13 18 2 0 0 0 0 > 14 16 1 0 0 0 0 > 15 38 1 0 0 0 0 > 16 21 1 0 0 0 0 > 16 22 2 0 0 0 0 > 17 19 1 0 0 0 0 > 17 39 1 0 0 0 0 > 18 20 1 0 0 0 0 > 18 40 1 0 0 0 0 > 19 20 2 0 0 0 0 > 19 41 1 0 0 0 0 > 20 42 1 0 0 0 0 > 21 23 2 0 0 0 0 > 22 24 1 0 0 0 0 > 22 43 1 0 0 0 0 > 23 25 1 0 0 0 0 > 23 44 1 0 0 0 0 > 24 25 2 0 0 0 0 > 24 45 1 0 0 0 0 > 25 46 1 0 0 0 0 >M ISO 1 10 11 >M END > >------------------------------------------------------------------------- >SF.Net email is sponsored by: The Future of Linux Business White Paper >from Novell. From the desktop to the data center, Linux is going >mainstream. Let it simplify your IT future. >http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |