OK, Pat, I have a solution. Use: select symop=nijk
what this says is "select for atoms that are the result of symmetry operation n AND involve a translation of ijk relative to the base atom of this symmetry class." select symop=1000 #the base atom set for x,y,z (always) -- the "asymmetric unit" select symop=2000 #the base atom set for the second-listed operation select symop=2100 #atoms from symmetry operation 2, but translated one unit cell along axis a. Note that because special positions may be generated by more than one symmetry operation, it is quite possible that select symop=2100 and select symop=3000 will be an overlapping set. This also means (I think) that select symop=2100 and symop=3000 will return those special positions, and select symop=2100 and symop!=3000 will return everything except those positions. About the comparisons: You can use any comparator: =, !=, <, >, <=, or >= select symop > 3 no problem and will return symop=4, symop=5, etc. But note, if you use select symop > 3000 then you are asking "within symmetry set 3, give me all atoms with translations > 000" Note that select symop!=3000 and select not symop=3000 are NOT the same thing. In the first case we are restricting ourselves to symop=3, but requesting not the base set; in the second case we are getting every atom of ANY symmetry set that is not the base set for symop=3. A bit complicated.....but then, this that's the nature of crystallography, I think. See anything in there I missed? Bob Patrick J. Carroll wrote: >Bob, > This problem of selecting molecules in the unit cell is a general >problem - I would like the user to be able to interactively build up the >packing diagram (of any compound) based on, e.g., hydrogen bonding like I >did using a big PDB file in : > > http://macxray.chem.upenn.edu/cells/99027cellFrame.html > >This can be done, as above, with a PDB file that includes all of the >molecules that you will eventually want to display. But, of course, this >requires that you figure out everything beforehand, write the PDB file and >then write a script to (kind of) re-trace the process. I would like it to >be more interactive. > > But you have given me some ideas to play with -- thanks. > > >Pat Carroll >Chem Dept >U of Penn > > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
