Hi Christian, You can use your helical twist and rise to create the operators representing your helical array with phenix.find_ncs and these parameters: - helix_extend_range = NoneRange in z to extend helical operators (A) - helix_trans_along_z = NoneAlong with helix_theta, defines helical parameters. Note: matrices are for mapping position k on to identity, this may be the opposite of what you would expect. - helix_theta = NoneAlong with helix_trans_along_z, defines helical parameters. Note: matrices are for mapping position k on to identity, this may be the opposite of what you would expect. Then you can say something like: phenix.find_ncs map_in=mymap.mrc ncs_in=my_ncs.ncs_spec resolution=3 and it will try to use those ncs operators and update them to make a new ncs_spec file. Once you have the operators, you can use map_box as you have in the past, adding symmetry_file=my_ncs.ncs_spec but it may not work as well as for non-helical symmetry. It will also give you the asymmetric unit of helical symmetry, not of your monomer. You can take the box you get, then find the symmetry in the box with find_ncs (using find_ncs_from_density) and then apply map_box again if you need to. Let me know if that doesn't work! All the best, Tom T On Wed, Nov 9, 2022 at 3:31 AM Christian Tüting < [email protected]> wrote:

Dear PHENIX mailing list,

I have a question regarding a helical reconstruction, done in cryoSPARC.

Usually, I work with "normal" symmetric particles, and there I can simply run phenix.map_box to isolate the asymmetric unit. This is somehow not possible with a helical map.

As we also don't have an atomic model yet, we cannot just crop it with map_box.

In our helical reconstruction, we have helical twist (in degree) and the helical rise (in Å) and a additional point group symmetry. We would like to isolate a single protofilament for further model building. Is this in principle possible in PHENIX?

Additionally, is there a way to rebuild the helical structure, analogous to apply_ncs?

Thanks

Christian

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