2 BUILD_EXTEND Keyword: editing topology, WORK_SEGM, delete, atom, residue File: build_extend.txt Last modified: 20-Oct-97 BUILD_EXTEND provides additional functions to BUILD block to enchance editing topology of the model. "BUILD_EXTEND" menu block is loaded with "MAIN_CMDS:load_build_extend.com". 3 DELE_ATOM Keyword: delete atom, atom delete Deletes the last picked atom ("MAIN_CMDS:dele_atom.cmds"). NO confirmation is required! 3 DELE_RESIDUE Keyword: delete residue, residue delete Deletes the last picked residue ("MAIN_CMDS:dele_res.cmds"). NO confirmation is required! 3 MERG_RES Keyword: merge two residues, residues merge Two consecutive residues (of the two last picked atoms) can be joined (MERG_RES) ("MAIN_CMDS:merge_res.cmds"). This should be applied when ATTACHING N and C terminals to a peptide chain. NTER and CTER are namely attached to a residue as a new residue that should be later on merged (joined) to the original one. 3 UPD_SEGM Keyword: update WORK_SEGM variable, WORK_SEGM, variable WORK_SEGM Updates variable WORK_SEGM with segment names of all currently present atoms ("MAIN_CMDS:update_segm.cmds") 3 SHW_SEGM Keyword: show WORK_SEGM variable, WORK_SEGM, variable WORK_SEGM Shows the value of variable WORK_SEGM. > show vari WORK_SEGM When the variable WORK_SEGM does not exist or it does not contain the segment names you want, your interaction with the program through the menu items will almost certainly result in NOTHING. 3 CLONE Keyword: clone atoms, duplicate atoms, atoms, active Clones the current "active" key atoms by making a copy and shifts them by a short distance. Useful during ab initio density interpretations when you simply want to apply the same topology a number of times (building beta strands or helical structures). The macro is "MAIN_CMDS:clone.cmds" Each time you have to provide (answer) with a new segment name and a sequence root. Works well in combination with hydrogen bond constraints, when you for example "constrain" beta sheets arrangements with twist.