Baton_build [mol] [start residue] [direction] [manipulate Baton]
This command is used to build a CA trace. It uses a measuring stick in the form of a di-peptide which can be moved around and can be pivoted about one end. The baton is actually a di-peptide from which the user must make an object of a single bond between the CA atoms before using this command. When the command is activated, the di-peptide object appears at the current screen centre and consists of a single split coloured bond. The dial set can be used to translate the di-peptide object, and to pivot the object around the green atom. When Yes is activated, the coordinates of the red residue are taken and written into the molecule that is being contructed. The baton jumps to this new position and the process can be repeated until the command is cleared with No. If an object called CA exists, it will be updated after each Yes command.
One of the problems associated with the Bone_Ca_Id command, where long or short inter-CA separations can be produced, is overcome by using Baton_build. After approxmately 5 pivots of the baton, it may be necessary to use the translation dials again to get the di-peptide and the density back in register. The command can be used to build the whole structure, but is particularly useful for building difficult loopy bits that the other Trace commands have had problems with. Since the di-peptide is in fact a poly-alanine, the Slider_lego command can be used to check out side chain sizes.
The position and orientation of the di-peptide can be changed by the Baton_mode command when Baton_build is active. When the No or Clear_flag commands are activated, this option activates Lego_auto_mc and Lego_auto_sc to construct both main and side chains from the CA trace that has been generated.
Examples: Before using the command, information for the di-peptide must be in the users database. A database file di.o is supplied and can be added by
O> read di.o
The user must then create the di-peptide object by
O> mol di ca ; end
The Baton_build command can then be used.
The position and orientation of the di-peptide can be changed by the Baton_mode command when Baton_build is active. When the No or Clear_flag commands are activated, this option activates Lego_auto_mc and Lego_auto_sc to construct both main and side chains from the CA trace that has been generated.