[3dem] Relion T symmetry vs D2

[Bjoern Forsberg]

Hi Hudel,

Reconstructions of higher symmetries can get lost unless the initial 
reference is good and aligned, since the symmetrization will cause a 
strong "inertia" or reference bias. You therefore need to make sure your 
initial reference is both good and aligned.

To align a reference to T-sym, open it and any output from a relion-run 
where T-sym was used. Now, in chimera, rotate the reference you want to 
use so that it very closely aligns with the T-sym output. To be clear; 
the T-sym output does not need to be good or high-res, you just need to 
see which symmetry is enforced around which axis. Having aligned them, 
use Favourites->commandline and run

vop resample #x onGrid #y

where #x is the volume number of your reference and #y is that of your 
T-sym output. Save the new volume and use as a T-sym reference. Note 
also that with higher symmetries, it is recommended that you increase 
the orientation-sampling. This is because there's a smaller number of 
unique views to search, making it both computationally tractable and 
better for results to subdivide those views into smaller groups.

To comment on your other questions; there is no way to modify the 
symmetry definitions in RELION by flags, but you can alter the symmetry 
ops in the source code if you want. You can print the symmetry ops using 
the flags you show, but there are certain flags you must always specify 
to make relion get far enough to print them, like --i and --o. In this 
case it doesn't really make sense to demand those flags, but you can 
just put some dummy filenames there.

/Björn


On 2018-03-31 13:14, Luecke, Hartmut wrote:
>
> 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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