[3dem] Relion T symmetry vs D2

[Luecke, Hartmut]

HeiHei!

I am refining a tetrahedral enzyme complex with Relion.  For some reason I cannot get symmetry “T” to work.  When I use D2 refinement gets to 3.2 Å resolution with nice side chain density, but with T symmetry (and the reference map rotated such that one of the 3-folds is along z) I get huge angular (in)accuracies of 20-30 degrees, aka refinement fails.

I checked this webpage:

https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Conventions_%26_File_formats

and noticed “3-fold axis on Z (deviating from Heymann et al!)”.  This does not state where the 2-fold are expected.  Furthermore, I cannot get the (misspelled) command mentioned below that table to work:

reline_refine --sym D7 --print_symmetry_ops

And neither this command:

relion_refine --sym T --print_symmetry_ops

which gives this error:


[hudel at aristotle]$ relion_refine --sym T --print_symmetry_ops

The following errors were encountered upon command-line parsing:

ERROR: Argument --i not found or invalid argument

ERROR: Argument --o not found or invalid argument

ERROR:

Errors encountered on the command line (see above), exiting...

File: /lsc/sources/relion/src/ml_optimiser.cpp line: 1286

[hudel at aristotle]$


Does anyone know how I should reorient my reference map (and mask) for full T (12x)  symmetry refinement instead of D2 (4x)?  For example the chimera or dynamo commands?  Or, better yet, is there a secret T setting in Relion that allows the 2-folds to remain on the principal axes (and a 3-fold on 1,1,1)?  Checking the source code I found Th and Td, but these have extra (achiral) symmetry elements.


Thanks, Hudel

--
Prof. Hartmut Luecke
Structural Biology and Drug Discovery
Nordic Centre for Molecular Medicine
Dept. of Medical Biochemistry
Gaustadalléen 21
0318 Oslo
Norway

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