Thanks, Angel. Its good to remind me about the element names. I am not using them in FirstGlance, much of which was designed before Jmol version 1.0 :)
I recoded using [CA] and [CD] and that seems fine. The case at hand was how to hide an atom when it is clicked on. I am using if (atomname == groupname) e.g. CA == CA for calcium, whereas for alpha carbon, the atomname CA might have groupname GLY. Eric On 9/14/14 7:59 AM, Angel Herráez wrote: > Dear Eric > > I though the Calcium vs. Calpha issue was fixed years ago. > >> 'select *.cd' selects both carbons delta and cadmium (1d66). > I see, that's because the atom name is shifted by one space and Jmol > seems not to differentiate > " CD" for delta carbon > "CD " for cadmium > according to PDB spec > > Easiest is to use the element in the script: > select *.cd and _C > select *.cd and not _Cd > >> 'select *.ca' selects carbons alpha but NOT calcium (4aqr). > select alpha > select *.ca and _C > select *.ca and not _Ca > >> What I am using in FirstGlance that fails to select calcium is >> 'select *:A.ca&&hetero' >> (Well, this is not optimal anyway since it would also select alpha carbons >> in non-standard >> residues) > Indeed; best use: > select _Ca > >> I am now setting about to change my code to >> 'select [ca]:A' > select _Ca and *:A > > Hope that helps > > > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce > Perforce version control. Predictably reliable. > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
