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Hi, <BR>
<BR>
I would like to calculate sa_omit map for a low resolution structure (4.0 Ang) to validate the conformation in some regions. <BR>
<BR>
What's the proper way to do it? <BR>
<BR>
Followed the instruction, I tried:<BR>
<BR>
phenix.autobuild data=mydata.mtz model=mybestmodel.pdb omit_box_pdb=mybestmodel.pdb \<BR> omit_res_start_list=100 omit_res_end_list=200 omit_chain_list=L \<BR> composite_omit_type=sa_omit<BR>
<BR>I have several questions:<BR>
<BR>
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?<BR>
<BR>
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?<BR>
e.g omit region: 100-200 in chain L, M, N, O:<BR>
<BR>
omit_chain_list = L<BR>
omit_chain_list = M<BR>
omit_chain_list = N<BR>
omit_chain_list = O<BR>
omit_res_end_list = "200"<BR>
omit_res_start_list = "100"<BR>
<BR>
3. If I want to omit several loops in one copy, should I turn off NCS? <BR>
Like: <BR>
find_ncs=False<BR>
input<FONT color=#000000>_ncs_file= None</FONT><BR>
optimize_ncs=False<BR>
<BR>
4. How to define several omit regions in one chain?<BR>
<BR>
Many thanks,<BR>
<BR>
Jin<BR>
<BR>
<BR>
<BR>
<BR>
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