Jaim, I think ths may be what you need, picking up the older definition of "ligand":
http://wiki.jmol.org/index.php/AtomSets ligand: The new definition (Jmol 12.2) includes atoms that do not belong to protein, nucleic or solvent. That includes water, other solvent, ions and carbohydrate, but excludes nonstandard amino acid or nucleotide residues. Clasically defined as hetero and not solvent (and so not always what you would expect from the word ligand). e.g. load =1A5U; select atp; // 186 atoms selected select atp and hetero; // 186 atoms selected select atp and ligand; // 0 atoms selected select atp and nucleic; // 186 atoms // that's the problem, atp is seen as nucleic and hence not ligand select ligand; // 70 atoms select hetero; // 2066 atoms select hetero and not solvent; // 256 atoms select hetero and not solvent and not ligand; // 186 atoms select hetero and not solvent and not ligand and atp; // 186 atoms So maybe getProperty atomInfo {hetero and not solvent and not ligand } ?? quite a complex output though I think the best way may be to define based on hetero and not connected to other groups, but that needs some ellaboration. And in the end the only exit seems to be getProperty atomInfo which is very complex and so needs careful parsing, certainly not so straightforward as ligandInfo Another idea: Do you need just the list of names? Maybe parsing the file header for HETNAM ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
