Re: [scipion-users] Rotate_Particles function is no longer available?

[Grigory S. <sha...@gm...>]

Hi Leonardo,

I think you are looking at very outdated documentation.

PS. The script you are looking for is here:
https://github.com/OPIC-Oxford/localrec/blob/devel/scripts/relion_rotate_particles.py
but it no longer exists in the plugin

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Mon, Jan 23, 2023 at 2:54 PM Leonardo Talachia Rosa via scipion-users <
sci...@li...> wrote:

> Dear Scipion team,
> I hope you are well.
>
> I´m working with a Phage in which I need to change the symmetry axis of
> the particles and the 3D volume in order to do a symmetry_relaxation
> refinement. I saw similar approaches suggested in the links below.
>
> https://github.com/OPIC-Oxford/localrec/wiki/Tips-and-tricks#TnT-2 -
> Reorienting all particles
> https://www.nature.com/articles/s41467-021-24455-4 -
> Methods section - Decoupling *D* 3d symmetry for asymmetric (*C* 1)
> reconstruction
>
> However, the relion_rotate_particles.py is not recognized in the scipion
> command line, and I do not see a way to do a similar job using the scipion
> GUI. I installed the latest version of LocalRec plugin, but still the
> command is not recognised.
> Am I missing something obvious or this function has been disabled in the
> latest updates for some reason?
> Any other suggestions on how to do this rotation would also be welcome.
>
> Thank you for your time,
> Kind wishes,
> Leonardo
>
> --
> *************************
> Leonardo TALACHIA ROSA, PhD
> PostDoctoral Researcher
> Microbiology and Structural Biology
> Instituto de Química, Universidade de São Paulo - IQ-USP
> Av. Prof. Lineu Prestes, 748 - Butantã, São Paulo - SP
> **************************
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