[phenixbb] SA_OMIT map at low resolution

邬金 wujin_ustc at hotmail.com
Tue Apr 21 04:09:57 PDT 2009



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   \

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? 



input_ncs_file= None



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


Many thanks,








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