2010/5/21 Angel Herráez <[email protected]> > I am seeing this as a nice, recent addition in the "new.htm" > document: > > 122. select within(BASEPAIR) > # Jmol 12.0.RC5 adds the capability to select atoms based on RNA or > DNA base pairing. Thank you, Neena Grover! load 2qnh.pdb.gz;zoom > 300;wireframe -0.4;display rna;select *.P;label %n%r;select rna;set > rangeSelected; > # color property polymer;set picking center;slab on;depth 40;slab 60 > # display within(BASEPAIR,"GC") # just the GC pairs > # display within(BASEPAIR,"AU") # just the AU pairs > > There already were (RasMol-inherited) predefined sets "CG" and "AT". >
I don't think so. There may have been CG in RasMol, but there was never any capability that I know of in Jmol to detect hydrogen-bonded base pairs like that. > It would be important to emphasize comparison of these with the new > functionality (I will add that in the Wiki once I'm sure). > For example, does "within" select only paired bases while the sets > select individual bases, as I suspect? > > Also, this is very disturbing: > > select within(BASEPAIR,"GC") # 15176 atoms selected > select within(BASEPAIR,"CG") # 2066 atoms selected > > good test. I should have thought of that. Will check. > select within(BASEPAIR,"AU") # 2979 atoms selected > select within(BASEPAIR,"UA") # 291 atoms selected > > select within(BASEPAIR,"AT") # 0 atoms selected > select within(BASEPAIR,"TA") # 3 270 atoms selected > > (using 2qnh.pdb.gz at http://chemapps.stolaf.edu/jmol/docs/examples- > 11/new.htm <http://chemapps.stolaf.edu/jmol/docs/examples-%0A11/new.htm>) > > > > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Jmol-users mailing list > [email protected] > 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
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