We are in the process of streamlining data transfer. Currently, the procedures are as follows.
For SCMI consortium members
Your local management group member or EM staff have access to SCMI storage servers. They will be able to copy your data to local machines for processing.
For users outside the SCMI
Currently, you will need to bring USB 3.0 external hard drives to your session and we will copy the data to those and ship them back after your session.
In order to complete motion correction and CTF estimation, you will need to know a few parameters about the microscope.
Spherical aberration, Cs
The Cs of our CRYO ARM 300 is 2.7mm. The Cs of our F2-Cryo is 2.0mm.
Modulation transfer function of the detector, MTF
These files come courtesy of the manufacturer, Direct Electron.
Other processing tips
There are some edge artefacts in bin 2 counting. To remove these, we suggest cropping 16px in all directions when motion correcting bin 2 images. In Relion, this means passing
-crop 4064,4064 16,16
to your motion correction job.
We request that SCMI is acknowledged in any publication (including posters and talks) that use data collected at the facility.
To acknowledge SCMI without a named scientist, or where the the scientist is a co-author:
"We acknowledge the Scottish Centre for Macromolecular Imaging (SCMI) for access to cryo-EM instrumentation, funded by the MRC (MC_PC_17135) and SFC (H17007)."
To acknowledge SCMI with a named scientist:
"We acknowledge the Scottish Centre for Macromolecular Imaging (SCMI) and <insert name> for assistance with cryo-EM experiments and access to instrumentation, funded by the MRC (MC_PC_17135) and SFC (H17007)."