Jmol 10.9.89 (soon to be released) is primarily a bug fix for 10.9.88, where I made some mistakes adding features to "show draw" and "getProperty shapeInfo". But in addition, I cleaned up some of the atom specifications. Some of this reads as before, some points out features that have been available but not described, and some is new:
/*RasMol biomolecular residue specifications * The general specification of atoms in PDB "residues" follows the method used in RasMol. While the order of specifiers is somewhat flexible, the following order is generally applicable: [residueType]seqRange ^insertionCode :chainLetter .atomName %altLoc /modelNumber //*Wildcards * Unspecified components of the atom specification are indicated in some cases using a question mark and in others using an asterisk. The wildcard * can be used in place of [residueType]seqRange to indicate "any." For example: *select *.CA*. Wildcards can be used elsewhere in the specification, but it is preferred simply to not include a specifier altogether. Thus, *select [ALA].** is the same as *select [ALA]*. Note that * is not used in the form x* because there are some PDB atom names that include *. Asterisks also cannot be used in place of insertionCode or altLoc. Question marks are used to indicate "some character": *select *.C??*. Note that the number of question marks is significant. "*.?" only finds atoms with single-letter names such as "O" and "C"; "*.??" finds atoms with single-letter or double-letter names. The specification :?, ^?, and %? mean atoms with SOME chain, SOME insertion code or SOME alternate location indicated; use :, ^, and % alone to indicate the opposite -- "atoms specifically without any chain indication," "atoms specifically without any insertion code," and "atoms specifically not in an alternate location," respectively. *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* or even *select C??*. 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 <cid:[email protected]> using the format code %a. 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
