I would like to poll this group to find out how many Jmol users are in favor of adding support for command aliases. I have considerable experience with command aliases in Protein Explorer, and I would find them very helpful in Jmol. For example, in Protein Explorer, typing the command
s p expands to "select protein". r n w expands to "restrict not water". bb expands to "backbone" bbf expands to "backbone false". cox 223355 expands to "color [x223344]". an expands to "atomno=". Aliases not only save about 90% of the keystrokes when typing commands, but they avoid the problem of misspellings - e.g. typing "seelect protien" and then having to correct it (perhaps more than once). Protein Explorer's aliases are on by default, and come with it. They are specified in a plain text file that users can edit to remove, add, or change aliases. Each command entered by the user is first processed for alias expansion. If you inadvertantly type an alias when you didn't mean it, it is obvious because the command is displayed in its alias-expanded form. Jmol's command syntax is more complicated than that in Protein Explorer/Chime. Jmol would probably need an "escape" character that, as a prefix to a word in a command, would suppress alias expansion. For example, if you defined an atom set as having the name "p", and if the escape character were "\" (I'm sure it should be something else but I don't know what), s \p would expand to "select p" instead of "select protein". And of course a setting would be needed to turn alias expansion off (Protein Explorer has a checkbox in its Preferences). Protein Explorer's default list of aliases is here: http://www.umass.edu/microbio/chime/pe_beta/pe/shared/help_ali.htm If you are in favor of having command alias support in Jmol, please let me know (on list or off list as you prefer). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
