For flexibility analysis, it would be helpful to have star files for all reasonable particles not just the ones that end up in the final model.
Best wishes
James
> On 29 Mar 2022, at 01:24, Takanori Nakane <[log in to unmask]> wrote:
>
> Hi,
>
> This is a very interesting question.
>
> There are many use cases of EMPIAR datasets and the most
> convenient format depends on what one wants to do on the data.
> If one wants to develop an autopicking algorithm, motion
> corrected micrographs are most useful. If one is working on
> flexibility analysis, stacks of polished particles would be
> most convenient.
>
> Another question is reproduction vs improvement.
> Do you want the ability to reproduce the published analysis as closely
> possible or the ability to improve it by using latest algorithms
> invented after the original publication?
>
> These are open questions and below are my two cents.
>
> Raw movies (1) are the best from the data archiving perspective.
> This also gives the best chance of improving the resolution and/or deriving
> more information from the dataset in future.
>
> Final STAR files for each class (4a) are a very useful addition
> and should allow "close" reproduction of the published structure.
> This implicitly includes information of good and bad movies (2) because
> bad movies don't give final particles.
> One cannot get "exact" reproduction, because some parameters are
> not stored in the STAR file.
> For example, if you run motion correction with different parameters,
> movies are aligned differently and particle coordinates won't
> much those in the deposited STAR files. Even if one stores all processing
> parameters, most parallel algorithms are inherently stochastic.
>
> Particle stacks (4b) allow closest reproduction and are the most convenient
> format for those working on flexibility analysis. But stacks are
> very large and can be larger than motion corrected images,
> because particle boxes often overlap significantly, especially when
> the box is large to compensate for large defoci. This is why I deposited
> particle stacks in addition to raw movies for the GABA receptor (EMPIAR-10500)
> but not for the atomic resolution apoferritin (EMPIAR-10424). The final particles
> were larger than the original movies!
>
> Aligned movies (3) are usually smaller than the original movies but one cannot
> run RELION's polishing or M so the final resolution would suffer.
>
> In summary, I would deposit raw movies at least and final STAR files as well.
>
> > In terms of what metadata to include, I am thinking scope & Cs, detector, total dose, and number of frames. Any other additional metadata that would be helpful to include? Maybe expected defocus range?
>
> Cs, pixel size, dose per frame and the orientation of the gain reference are essential for
> reprocessing. I often had to discover the orientation by trials and errors when I reprocessed
> many EMPIAR datasets before.
>
> Best regards,
>
> Takanori Nakane
>
>> On 2022/03/29 5:02, Oliver Clarke wrote:
>> Hi all,
>> We are planning to soon deposit a new EMPIAR dataset, and I was hoping to get some recommendations from the community as to the best practices in terms of making EMPIAR depositions useful for developers (as there are a number of options).
>> Options:
>> 1. Full set of raw movies in TIF format (including "bad" movies with ice, gold etc) plus gain reference, with metadata in "Details" section of image set. In terms of what metadata to include, I am thinking scope & Cs, detector, total dose, and number of frames. Any other additional metadata that would be helpful to include? Maybe expected defocus range?
>> 2. "Clean" set of movies, including only those that contained particles contributing to the final reconstruction?
>> 3. Motion corrected micrographs?
>> 4. Particle coordinates - perhaps one star file for each class? Is it worth also uploading particle stacks? Any preferences on format, or any essential additional metadata that should be included?
>> I am thinking we will upload 1, 3 & maybe 4 - but would be curious as to what the most useful data would be for the community.
>> Cheers
>> Oli
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