I was wondering if it is possible to download all biological assemblies from the PDB at once (so not the standard asymmetrical files). For example, I want a file containing the coordinates of all atoms in a trimer, instead of only the coordinates of a monomer.

I saw that you can batch download with a shell script, but I'm not sure if you can also do that for biological assemblies.

  • $\begingroup$ Alternatively, you could download a "standard" file from the PDB (either in the PDB format or in mmCIF) and generate assemblies locally with one of many programs/toolkits have such capability. $\endgroup$
    – marcin
    Feb 11 at 15:04
  • $\begingroup$ I'm not aware of a program/toolkit with which you can do that automatically for a large set of PDB files. If you know of a way to do that then that would be perfect. $\endgroup$
    – Jacob
    Feb 12 at 9:15
  • $\begingroup$ To process multiple files you will probably need a simple script. Note that PDB entries often define several alternative biological assemblies. As for toolkits, I'm most familiar with gemmi (because I maintain it): you could generate assemblies from the command-line with gemmi convert --assembly=1 ... or from Python. I suppose that BioJava, cctbx, PyMOL, etc also have such a capability. $\endgroup$
    – marcin
    Feb 12 at 18:46
  • $\begingroup$ Thanks a lot, I'll give that a try. $\endgroup$
    – Jacob
    Feb 15 at 19:18

If you go to the wwPDB ftp site https://ftp.wwpdb.org/ in your browser you can find the biological unit structures (and anything else available in the PDB). The caveat of course is that a biounit structure has to have been generated for your structure.

By way of some examples, to get all biological units you could do (note the ftp instead of https in front of the URL):

wget ftp://ftp.wwpdb.org/pub/pdb/data/biounit/PDB/all/*

or to get a version organized in directories:

wget ftp://ftp.wwpdb.org/pub/pdb/data/biounit/PDB/divided/*

Note that this would take a few days to download everything, though. After the first download, you can add a -N to the wget command to just download new files.

For getting just one file:

wget ftp://ftp.wwpdb.org/pub/pdb/data/biounit/PDB/divided/00/100d.pdb1.gz

Hope this helps.


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