Download Cryo-EM data via EMPIAR through FTP

If you need some Cryo-EM data to play with or for testing some new software etc. then an easy way to obtain either micrographs and/or particles is from EMPIAR. However if you wanna do it much less hassle-free than using going through the web interface, you can use FTP to download large amount of data from their server.

Below I have made a small example scenario from an Ubuntu terminal, that shows how I would normally do this, using EMPIAR entry 10028 as an example .

In this example I am after some picked particles only.  Everything I type (or do) is in bold.  I login as anonymous, which everyone can do, and there is no password, so just hit return/enter when prompted.

I also use the “prompt” command which enables me to download all of the .mrc files without having to type “y” (for yes) every time, when prompted if I want to download this file.

the “10028” part of the path I change to, is the entry identifier,  exchange that with the entry your are looking for. Also the directory hierarchy are not identical for each entry, so use “ls” to see where to go.


>ftp  ftp.ebi.ac.uk

Connected to ftp.gslb.ebi.ac.uk.
220- ftp1.ebi.ac.uk FTP server
220- WARNING: please note that the private part of this ftp service
220- has been migrated to ftp-private.ebi.ac.uk on 3rd June 2010.
220Name (ftp.ebi.ac.uk:rXX): anonymous
331 Please specify the password.
Password: “hit return/enter”

230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.

>cd pub/databases/empiar/archive/10028/data/Particles

250 Directory successfully changed.


drwxr-xr-x 2 ftp ftp 110592 Jun 10 2015 MRC_0601
drwxr-xr-x 2 ftp ftp 86016 Jun 10 2015 MRC_1901
-rw-r–r– 1 ftp ftp 28627547 May 29 2015 shiny_2sets.star

>cd  MRC_0601

250 Directory successfully changed.


Interactive mode on.

>mget *.mrcslocal: 001_particles_shiny_nb50_new.mrcs

remote: 001_particles_shiny_nb50_new.mrcs
200 PORT command successful. Consider using PASV.
150 Opening BINARY mode data connection for 001_particles_shiny_nb50_new.mrcs (50285824 bytes).
226 Transfer complete.


221 Goodbye

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