Hi all,
I’m very new using Rosetta to make structure refinement. I’v read lots of related articles and also read the Tutorial: Rosetta tools for structure determination in
cryoEM density. But I still not sure how to start my first Rosetta try.
I have a helical map with about 3.9 angstrom resolution. The asymmetric unit for this helical structure is a tetramer. And the structure also has D5 symmetry except helical symmetry. I have generated the symmetry file using the tool “make_symmdef_file.pl”. The rosetta script the .xml suffix was same as the one in the protocol. I have the following questions:
1. When I tried to run the refinement script, I can get just one refinement pdb file named “3tetramers_INPUT_symm_0001.pdb”. I thought I need to get lots of pdb files like *_symm_????.pdb. Then I select the best one as my result. But now I only get one. I don’t know where I’m wrong. How can I get lots of optimized pdb files with different scores?
2. I know there many score functions and mover in the xml script. How can I know which score function and which mover should I select to use?
3. On the other hand, I’m also not sure how shall I prepare the start pdb file? The asymmetric unit is tetramer with 4 chains, I renamed them uniformly as one chain. Is this ok? If not so, I found it is difficult for me to generate the symmetry files which is necessary for symmetry refinement.
Sorry for so many naive question. Any suggestion or help are appreciated.
Related file was attached.
Thanks in advance.
Regards,
Yan
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