Annemarie, I think this is just a bug in those older versions. (10.9 is just this past week available)
With 10.9 I get: load 1ale.pdb select *.?H 15 atoms selected select 1.2H 5 atoms selected select *.2H 5 atoms selected So that seems to be working correctly. See http://www.stolaf.edu/academics/jmol for the latest files. Bob Hanson Annemarie Honegger wrote: > I am using Jmol 10.3 .1 or 10.2 > > In a PDB file, If hydrogens are present, the hydrogens on the same > atom are distinguished > by a number preceeding the atom label, e.g. > > ATOM 1 N ALA 1 0.039 -0.028 0.000 1.00 0.00 > > ATOM 2 CA ALA 1 1.499 -0.043 0.000 1.00 0.00 > > ATOM 3 C ALA 1 2.055 1.361 0.000 1.00 0.00 > > ATOM 4 O ALA 1 1.301 2.383 0.012 1.00 0.00 > > ATOM 5 CB ALA 1 1.956 -0.866 -1.217 1.00 0.00 > > ATOM 6 OXT ALA 1 3.314 1.524 -0.012 1.00 0.00 > > ATOM 7 1H ALA 1 -0.315 -0.995 0.000 1.00 0.00 > > ATOM 8 2H ALA 1 -0.300 0.461 0.841 1.00 0.00 > > ATOM 9 3H ALA 1 -0.300 0.461 -0.841 1.00 0.00 > > ATOM 10 HA ALA 1 1.847 -0.534 0.928 1.00 0.00 > > ATOM 11 1HB ALA 1 3.058 -0.939 -1.274 1.00 0.00 > > ATOM 12 2HB ALA 1 1.571 -1.903 -1.181 1.00 0.00 > > ATOM 13 3HB ALA 1 1.610 -0.425 -2.172 1.00 0.00 > > TER > > > When I click on one of these hydrogens, the identifier is returned > correctly, e.g > [ALA]1.1H #7 > > The "atom expressions" documentation does not specify a valid way to > address > these hydrogens. If I try to specify this hydrogen in a "select" > command, e.g. > > select 1.1H > or > select *.1H > > I get an error message, > "unrecognized expression token: 1.1 : select 1.1H" > in the first case, > " end of expression expected : select *.1H" > in the second case > > Funnily, > > select *.?H > does find the three hydrogens on the nitrogen atom > > How can I select a particular one of these hydrogens? I cannot use > the atom number, since > I need my script to work on different structures. > > Thank you for your help > > > Annemarie Honegger > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
