Click on a link below to see what it does. You can also type a command in the box below the model to see its effect. The script run in this case was "5hvp.cif". The default load script used here is ";color altloc;restrict none;configuration 0;cartoon on;select not *%;wireframe 0.15;spacefill 0.15".
This prototype page illustrates the reading of alternate locations in mmCIF and PDB files. Note also the use of set defaultLoadScript
color altloc
The header for this page has set the default load script to be color altloc;restrict none;configuration 0;cartoon on;select not *%;wireframe 0.15;spacefill 0.15, which says, "Color the atoms based on their alternative location. Display all configurations (full molecular alternatives) as cartoons, then for all atoms that are not invariant (not *%) and display them as wireframe."
The configuration command does two operations in one. First it selects for a single alternative location option, (*%,*%A), for example, then it runs a recalculation of the secondary structure in order to adjust the shapes of the helixes, turns, and sheets to this particular set of alternative locations. The "n" refers the sequential number of the alternative location in the file. Some files use alternative location characters "1,2,3...", some use "A,B,C...", some use idiocyncratic listing. The configuration command works regardless of the labeling system used by the author. The purpose of restrict none is to clear the display prior to this selection/display process so that only the selected configuration is displayed.
You certainly do not have to use configuration. *%A selects for only the "A"-labeled alternative locations; *% selects for all locations that HAVE NO alternative location marking. The combination of these -- select *% or *%A -- then constitutes one full molecular alternative. To select specifically for all atoms involved in any alternative location, select not *%.
