how to run flexible fitting for structure with helical symmetry

From: Zhang Yan (yanzhang_at_moon.ibp.ac.cn)
Date: Thu Jun 11 2020 - 03:24:31 CDT

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Dear all,
I have a cryo-EM map with around 4.0 angstrom resolution which has helical symmetry; I also have the corresponding x-ray atomic model. I want to perform molecular dynamic flexible fitting to fit the atomic coordinate to the cryo-EM map. The asymmetric unit for the structure is a tetramer. I noticed from the namd tutorial that when running a simulation with helical symmetry, a symmetry file set_symmetry.tcl is necessary. For my case, each asymmetric has 4 chains because it’s a tetramer. How can I prepare this symmetry file for my case?
Thanks in advance,
Best,
Yan

 
张艳
Yan Zhang，
Associate Professor，
Institute of Biophysics,
Chinese Academy of Sciences

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