Hi,

> rlnOrientationalPriorMode or rlnAngleTiltPrior

I don't know how they work in tomography. I hope others in the list can
answer.

> Or would it even be possible to pass this information
> as a tilt angle in the header of a particle .mrc file or .mrcs stack?

This is not implemented.

Best regards,

Takanori Nakane

> Thanks for your reply.
>
> Do you believe there is any other way of passing this information to
> Relion via a metadata label without attempting to combine the tomographic
> tilt angle and the refined particle Euler angles? Looking through a few
> more of the flags, rlnOrientationalPriorMode or rlnAngleTiltPrior seem
> like possibilities? Or would it even be possible to pass this information
> as a tilt angle in the header of a particle .mrc file or .mrcs stack?
>
> Best regards,
> Tom
>
>
>
>
> On 16 Jul 2019, at 17:12, Takanori Nakane
> <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> Hi,
>
> I have never worked on tomography features of RELION,
> but "grep" suggests that these labels are defined but never used.
>
> $ grep -r EMDL_MICROGRAPH_TILT src/
> src/metadata_label.h:    EMDL_MICROGRAPH_TILT_ANGLE,
> src/metadata_label.h:    EMDL_MICROGRAPH_TILT_AXIS_DIRECTION,
> src/metadata_label.h:    EMDL_MICROGRAPH_TILT_AXIS_OUTOFPLANE,
> src/metadata_label.h:        EMDL::addLabel(EMDL_MICROGRAPH_TILT_ANGLE,
> EMDL_DOUBLE, "rlnMicrographTiltAngle", "Tilt angle (in degrees) used to
> collect a micrograph");
> src/metadata_label.h:
> EMDL::addLabel(EMDL_MICROGRAPH_TILT_AXIS_DIRECTION, EMDL_DOUBLE,
> "rlnMicrographTiltAxisDirection", "Direction of the tilt-axis (in
> degrees)
> used to collect a micrograph");
> src/metadata_label.h:
> EMDL::addLabel(EMDL_MICROGRAPH_TILT_AXIS_OUTOFPLANE, EMDL_DOUBLE,
> "rlnMicrographTiltAxisOutOfPlane", "Out-of-plane angle (in degrees) of
> the
> tilt-axis used to collect a micrograph (90=in-plane)");
>
> Best regards,
>
> Takanori Nakane
>
> Dear CCPEM,
>
> I am currently trying to write a script to implement constrained single
> part
> icle tomography in Relion, complementary to the subtomogram averaging
> capabi
> lity (as described in "Protein secondary structure determination by
> constrai
> ned single-particle cryo-electron tomography” (Bartesaghi et al, 2012) and
> implemented in EMAN2.3 “Alignment algorithms and per-particle CTF correctio
> n for single particle cryo-electron tomography” (Weaver et al 2016)).
>
> Thus far, many of the required operations seem to be relatively simple
> (deriving per-tilt image particle coordinates and defoci from position in
> the tomogram, splitting aligned tilt series into single images and then
> extracting particles from the individual tilted images for refinement in
> Relion as with single particle images)
>
> In particular, I am trying to combine the tilt-series geometry with the
> refined Euler angles in a STAR file from a 3D refinement of subtomogram
> particles, and then apply this to the 2D sub-tilt series images as a
> constraint. Having looked through all the Relion metadata labels I have
> found the flags rlnMicrographTiltAngle, rlnMicrographTiltAxisDirection
> and
> rlnMicrographTiltAxisOutofPlane. Are these parameters only used for tilt
> pair analysis or could I use them to provide angles for the sub-tilt
> series refinement?
>
> I was wondering if anyone else has tried this or has any insight to
> offer?
> Any thoughts would be much appreciated.
>
> All the best,
> Tom
> The Francis Crick Institute Limited is a registered charity in England
> and
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