Dear Ruda,
We have a couple of scripts that can manually rotate particles given a vector or a triplet of Euler angles (Relion convention).
Please see 'Reorienting all particles' on https://github.com/OPIC-Oxford/localrec/wiki/Tips-and-tricks for instructions. To run the scripts you need to install Scipion (https://github.com/I2PC/scipion) and Localized Reconstruction (https://github.com/OPIC-Oxford/localrec).
Hope you will find this useful!
Best wishes,
Serban Ilca
---- Original message ----
>Date: Mon, 27 Mar 2017 08:44:36 -0400
>From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> (on behalf of Ruda Santos <[log in to unmask]>)
>Subject: Re: [ccpem] Manual rotation of euler angles in Relion
>To: [log in to unmask]
>
> Hi Bjoern,
> Thank you for your reply. As per your suggestion
> I’ve created a new issue on GitHub:
> https://github.com/3dem/relion/issues/220#issue-217228787
> Best regards,
> --
> Ruda Santos, MSc
> PhD Candidate, Department of Biochemistry and Cell
> Biology
> Stony Brook University
> +1 616 234 5257
> [log in to unmask] / [log in to unmask]
> On Sun, Mar 26, 2017 at 4:42 AM, Bjoern Forsberg
> <[log in to unmask]> wrote:
>
> Hi Ruda,
>
> The issue referred to is entirely unrelated, as it
> regards (by all indications) adequate default
> sampling under high symmetry. Your original
> question, lest I'm mistaken, concerns changes the
> source code in an effort to extend the
> capabilities of the program, to solve a highly
> specific problem. The fact that two situations
> display "similar" plots should of course not be
> used to infer similar origins or possible fault.
>
> My suggestion to you, is to create a new "issue"
> (which is really more of a discussion) on the
> github page, where you describe in clear terms
> what you want to achieve and what changes you made
> to achieve that. I cannot understand from the
> original question what symmetry your are trying to
> find, whether it is an additional symmetry on top
> of, or within the D7. Moreover, I don't understand
> what you changed in the code, nor what it's
> purpose was. If you are clear about all these
> things, it will be interesting and educational to
> discuss it. We cannot spend much time to instruct
> people on how to do such things, but the easier
> you make it for us, the more likely it is that
> we'll find it worth-while to help out.
>
> Since you can easily make a simple patch
> describing any code-changes, it is very easy to be
> very clear about it;
>
> git diff > changes.patch
>
> This will create a plain-text file detailing all
> the changes made to the code, which anybody can
> test out by simply enforcing the changes through
>
> git apply changes.patch
>
> Hope that helps!
>
> /Björn
>
> On 2017-03-24 17:36, Daniel Larsson wrote:
>
> This looks similar to a bug that I’ve reported
> here:
> https://github.com/3dem/relion/issues/214
> Particles that initially is mis-oriented seem to
> not be able to optimize across the asymmetric
> unit boundary and build up along the edge.
> Regards,
> Daniel
>
>
> On 23 Mar 2017, at 22:38, Ruda Santos
> <[log in to unmask]> wrote:
> Dear CCPEM,
>
> Does anyone have experience on using the code
> on euler.ccp to manually rotate euler angles?
> I did a reconstruction of a protein on D7
> symmetry and would like to do a local angular
> search on C2. I tried doing a 90 degrees
> rotation on the Z axis using
> Euler_angles2matrix() but the resulting
> particle distribution is distorted (images are
> attached).
>
> Any help would be greatly appreciated.
>
> Best regards,
> --
> Ruda Santos, MSc
> PhD Candidate, Department of Biochemistry and
> Cell Biology
> Stony Brook University
> +1 616 234 5257
> [log in to unmask]
> <Y axis view - 90 degrees on Z axis.png><X
> axis view - 90 degrees on Z axis.png><D7
> particle distribution.png>
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