What are my options for OMIT maps if I have 4 fold NCS axis?
• Using the keyword omit_box_pdb is a good way of omitting a single small region, or a series of small regions, one at a time. If you want to get a complete sa_omit map or many regions, then skip the omit_box_pdb command and let autobuild make a composite omit map covering the whole a.u.. Use the omit_box_pdb to define a single region that you want omitted (such as a few residues or a loop…) • If you have ncs, you cannot conveniently delete all the copies at once with omit_box_pdb. You can delete the 4 copies one at a time by specifying a list of omit regions however. • To omit a list of regions, do it like this: omit_res_start_list=”100 500″ omit_res_end_list=”200 600″ omit_chain_list=”L M” to omit chain L residues 100-200 and then separately chain M residues 500-600. • It shouldn’t matter much if you turn off ncs while doing an omit map because the ncs copy won’t be used in density modification during the process. However NCS will be used to restrain any coordinates.
