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Hi Sjors,

Hope you're doing well, and thanks for the new release of Relion3!

I just thought I'd ask a few questions about some of the new features mainly surrounding CTF refinement (and to a degree generally per-particle CTF estimation).

Per particle CTF estimation - when is it okay to do it?

Since we are going from 3 parameters per micrograph (U,V,Angle) to possibly 2x(# of particles) + 1 or 3x(# of particles) parameters where each CTF that needs to fit is presumably noisier than that of the whole micrograph, do we have anything to keep potential over-fitting in check? We seem to be introducing a tonne more fitting parameters with less data.

I seem to get the impression that per-particle CTF/CTF refinement always improves the reported resolution by about 0.2 A (for a 2.8-3.5 A map) and this worries me slightly. It is quite hard to tell whether the map has been genuinely improved or not at this level. However, I suppose if this is the trend, we must all start doing it to make sure our reconstructions keep up with the perceived average resolution of the community.

CTF refinement - any concerns for independent halfsets?

I noticed that the way CTF refinement works has been described to be comparisons against high resolution reference projections. Presumably this would normally be the output of a refinement run, where two halfmaps have been combined. Would this mean then that there is potential to introduce correlation at high resolution between the independent halfsets since the particles have "seen" the combined map? As I understand half-sets are also randomized every time you run a refinement and so even if CTF refinement was being done against half-maps the potential problem for the independent half-sets to be not quite independent still remains.

An empirical observation I made was that my FSC of a map after CTF [log in to unmask] was very close to the FSC of the refinement without CTF refinement @0.143 (equaling about an improvement in 0.2 A or so, as above). Perhaps just a coincidence, but was food for thought.

3D autopicking - picking particles with views that may not exist?

Are there any adverse effects from picking with views of a reconstruction that may be severely preferred (usually I find this manifests as a streaky mess). It just seems slightly concerning about biasing the picking with views that may or may not actually be present in the dataset. Are there any decision making within the algorithm to decide whether a projection is used as a reference or not, or are all projections used?

Best wishes

Shintaro

On Wed, Aug 1, 2018 at 6:17 PM, Sjors Scheres <[log in to unmask]> wrote:

Dear EM-ers,

After multiple months of in-house testing at MRC-LMB and the SciLifeLab, and several months of beta-testing by a few external expert groups, we think that RELION-3.0 is now ready for a more general round of beta-testing. To that purpose, you can download it from:

git clone https://bitbucket.org/scheres/relion-3.0_beta.git

The attached betaGuide.pdf contains a list of new features, and instructions on how to install and provide us with your feedback. Please read it carefully. As always, please use the ccp-em email list (and not a direct email) to ask questions on how to use RELION. We are grateful for your detailed bug reports through the issue tracker on bitbucket, which will help to make RELION better.

Have fun,

Jasenko, Takanori, Bjorn, Dari, Erik & Sjors

--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres

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Yours Sincerely,
Shintaro Aibara