[phenixbb] Isolate Protofilament from helical reconstruction

[Tom Terwilliger]

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 <
christian.tueting at biochemtech.uni-halle.de> 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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-- 
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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