Angel Herraez wrote: >> Can you think of anything inside jmol that helps me to visualize this >> "abstract" superposition mapping? > > On a first thought, there may be many wasy to indicate that: csame > color, lines between matching atoms, etc. > > The key point is > how and where is your "assignment (superposition)" indicated? > > Please, provide details and an example file
okay I attached three sources. [1] source file ind sdf format [2] target file in sdf format and a mapping. the mapping looks like: [ MAP ] 1:16 2:15 3:10 4:14 5:9 6:11 7:13 8:12 where 1:16 means atom one from file [1] corresponds to atom 16 in file [2] and so on. okay to be clear - I do not expect JMol to do more than it is intended for - but maybe there is a functionality built-in Jmol that can help us here to visualize that. maybe a jmol script... many thanks in advance... raphael [1] 1 SItclserve07250621173D 0 0.00000 0.000001 15 15 0 0 0 0 0 0 0 0999 V2000 1.8890 1.7851 -0.0009 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7730 0.7724 -0.0022 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0858 -0.6712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5031 1.1816 0.0003 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2422 -1.0420 0.0024 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0081 -1.6639 -0.0002 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5969 0.1889 -0.0004 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2842 -1.2547 -0.0029 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7534 0.5597 0.0023 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4675 2.7903 -0.0028 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5015 1.6497 0.8905 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5052 1.6479 -0.8894 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7317 2.2371 0.0033 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2206 -2.7194 0.0013 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0840 -1.9805 -0.0034 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 2 0 0 0 0 3 5 2 0 0 0 0 3 6 1 0 0 0 0 4 7 1 0 0 0 0 6 8 2 0 0 0 0 7 9 2 0 0 0 0 7 8 1 0 0 0 0 1 10 1 0 0 0 0 1 11 1 0 0 0 0 1 12 1 0 0 0 0 4 13 1 0 0 0 0 6 14 1 0 0 0 0 8 15 1 0 0 0 0 M END [2] 2 SItclserve07250621173D 0 0.00000 0.000001 28 31 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0800 0.3600 -1.3600 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2000 -0.0800 -2.0800 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4000 0.3000 -3.7000 S 0 0 0 0 0 0 0 0 0 0 0 0 -2.8800 -0.5600 -3.6600 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1400 -0.9600 -4.7000 S 0 0 0 0 0 0 0 0 0 0 0 0 -5.4400 -2.0400 -3.5200 S 0 0 0 0 0 0 0 0 0 0 0 0 -6.7000 -2.4400 -4.5600 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6400 -3.1800 -3.8400 N 0 0 0 0 0 0 0 0 0 0 0 0 -8.7200 -3.5600 -4.6000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.8400 -4.3000 -4.2200 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.8000 -4.5600 -5.2200 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.6400 -4.0800 -6.5400 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4800 -3.3400 -6.8800 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5200 -3.0800 -5.8800 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1400 -2.2200 -6.2200 S 0 0 0 0 0 0 0 0 0 0 0 0 -3.1600 -1.0800 -2.4000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.2000 -0.8000 -1.4600 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1400 -1.1800 -0.1000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0200 -0.7600 0.6200 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 0.3073 0.5750 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6844 0.9465 -1.8254 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.9647 -4.6534 -3.2178 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.6691 -5.1336 -4.9740 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.3901 -4.2742 -7.2780 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3350 -2.9845 -7.8787 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9147 -1.7609 0.3553 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9317 -1.0164 1.6551 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 10 15 1 0 0 0 0 15 16 1 0 0 0 0 8 16 1 0 0 0 0 5 17 2 0 0 0 0 17 18 1 0 0 0 0 3 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 1 20 1 0 0 0 0 1 21 1 0 0 0 0 2 22 1 0 0 0 0 11 23 1 0 0 0 0 12 24 1 0 0 0 0 13 25 1 0 0 0 0 14 26 1 0 0 0 0 19 27 1 0 0 0 0 20 28 1 0 0 0 0 M END ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users