Jmol 10.9.89 is now releases and available at http://www.jmol.org/files/
Nico Bob Hanson wrote: > 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 > > > > ------------------------------------------------------------------------- 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
