Hmm, it read OK on my computer. Lesson learned! See http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#atomexpressions
for the full text. The key point, really is for people who are using Jmol for projects NOT involving proteins and nucleic acids. It's still evolving a bit, but basically it Atom names for other file types Atom names can also be used for some non-PDB/mmCIF file types. For example, in organic and inorganic CIF files, the atom_site_label field is used for the atom name. If an atom has the label "C34" you can select it using select *.C34 or, more simply, just select C34 Note that for file formats OTHER than PDB and mmCIF, there is no need for "*.", because in these cases there is no "group name" and thus no ambiguity between atom names and group names. Similarly, Jaguar, NWChem, Tripos MOL2, Wavefunction Odyssey, SHELX, and Wavefunction Spartan files list atoms as "H3" and "O2". Atoms for these file types can be selected using these names, and the names can be displayed in labels using the format code %a. The default label for file types having atom name assigned looks like this: %a/%M #%i For example: H34/3 #51 What's old is that you always could refer to this atom as select *.H34/3 (even though it wasn't advertised). What's new is that now you can dispense with the "*." and use the more natural: select H34/3 or, to select all H34 in multi-model sets: select H34 In general, this method won't be recommended for PDB models. The ambiguity between "C" as "peptide carbonyl carbon" and "C" as "cytosine" in PDB files is a problem there. It is resolved by adhering to precedent: If an atom has a group name (PDB and mmCIF files only), then C or [C] only matches the group name, and you can always still use *.C to mean peptide carbonyl carbons. In addition, I plan to make sure that no readers assign just element symbols to atom names, so that "select C" never means "select carbon". (In 10.9.89 the GAMESS reader does this, but I'm fixing that. It really is a bug, for other reasons as well.) There's a bit more work to do to fully implement this. What I wanted to emphasize here is that 1) This is fully backward compatible. 2) There is no effect on sites that use PDB/mmCIF models. 3) It should be more natural and useful for non-biomolecular models. Bob ------------------------------------------------------------------------- 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
