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". 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 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) ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
