Hi,
 
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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