fixed -- will upload shortly. Simple logic error. On Fri, May 21, 2010 at 8:37 AM, Robert Hanson <[email protected]> wrote:
> > > 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 > -- 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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