This would be great! I like this feature in PE, and it would speed up work in Jmol. Frieda
On Jul 3, 2007, at 5:28 PM, Eric Martz wrote: > 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 ------------------------------------------------------------------------- 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
