I am trying to practice data processing using a dataset I downloaded from EMPIAR. The dataset consists of Unaligned multiframe movies in .mrcs format.
My questions:
Is <.mrcs> format amenable to data processing by CryoSPARC? I have heard that this format is usually used for RELION.
What is the difference between <.mrcs> and <.mrc>?
To , I need information like gain reference, accelerating voltage, spherical aberration , total exposure etc. Where can I find this data? I thought it would be saved at EMPIAR (since all this information needs to come from the microscope facility) - but I cannot find it, so I also checked the XML file for it.
Thank you in advance!
I am new to CryoEM and to CryoSPARC , therefore, apologies for lame questions!
Re 1 and 2 - mrc and mrcs are the same, they differ only in filename extension. RELION requires the mrcs extension rather than mrc for multiframe mrc files, to distinguish them from maps or micrographs, while CryoSPARC does not (so if needed, you can change the filename from mrcs to mrc or vice-versa to make the relevant software package happy).
Re 3, EMPIAR entries are unfortunately somewhat variable in the amount of information provided in the actual entry - you may need to check the source papers for details regarding data collection and processing.
I don’t think RELION cares about whether MRC or MRCS for micrograph movies, but it does care for particle stacks (will error if particle stacks are not .mrcs)… I’m sure I’ve got an old Falcon 3 dataset which is .mrc… will check when I get a chance later.
And you’re right about EMPIAR being variable in terms of information provided.
I recognise the EMDB/EMPIAR folks are too busy to go through and curate every dataset in microscopic (ooh… bad pun, sorry… ) detail, but a simple INFO.txt for datasets with, e.g.: HT, Cs, angpix, total dose and whether gain flip/rotate needed shouldn’t be too hard to add. The fun comes when the EMPIAR entry, EMDB entry and article give different info… or don’t mention things like “collected in super res but physical pixel dimension reported”, which admittedly isn’t a disaster but might trip people up…
I tried changing .mrcs to .mrc and it still did not work. I have gotten all other information, however, I am unable to find gain reference. The data I am trying to process is https://www.ebi.ac.uk/empiar/EMPIAR-11757/.
Been racking my brain over this for a week now but to no avail. This should not be that hard to figure out , I thought!
Looks like these were collected with EPU, so they may already be gain corrected - have you tried importing without a gain reference?
If you do need a gain and don’t have one, you can always generate one by averaging a set of movies (preferably clean ones without carbon or gold in the frame), using relion_estimate_gain.
) detail, but a simple INFO.txt for datasets with, e.g.: