Hi Jin, 1. I think that the general answer to your questions is that omit_box_pdb is good for 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...) 2. 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. 3. 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. 4. 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. Let me know if that doesn't do it! -Tom T

...

I would like to calculate sa_omit map for a low resolution structure (4.0 Ang) to validate the conformation in some regions.

What's the proper way to do it?

Followed the instruction, I tried:

phenix.autobuild data=mydata.mtz model=mybestmodel.pdb omit_box_pdb=mybestmodel.pdb \ omit_res_start_list=100 omit_res_end_list=200 omit_chain_list=L \ composite_omit_type=sa_omit

I have several questions:

1. "omit_box_pdb=mybestmodel.pdb": If I define the region that I want to omit, do I need to define the omit_box pdb as well? Should it be complete model or the omit region?

2. I have 4 fold NCS axis, if I want to omit a loop in four copies, how can I define 4 corresponding regions in different chains?

e.g omit region: 100-200 in chain L, M, N, O:

omit_chain_list = L

omit_chain_list = M

omit_chain_list = N

omit_chain_list = O

omit_res_end_list = "200"

omit_res_start_list = "100"

3. If I want to omit several loops in one copy, should I turn off NCS?

Like:

find_ncs=False

input_ncs_file= None

optimize_ncs=False

4. How to define several omit regions in one chain?

Many thanks,

Jin

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