Answers.Body: <p>If you go to the wwPDB ftp site <a href="https://ftp.wwpdb.org/" rel="nofollow noreferrer">https://ftp.wwpdb.org/</a> 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.</p>
  <p>By way of some examples, to get all biological units you could do (note the <code>ftp</code> instead of <code>https</code> in front of the URL):</p>
  <pre><code>wget ftp://ftp.wwpdb.org/pub/pdb/data/biounit/PDB/all/*
  </code></pre>
  <p>or to get a version organized in directories:</p>
  <pre><code>wget ftp://ftp.wwpdb.org/pub/pdb/data/biounit/PDB/divided/*
  </code></pre>
  <p>Note that this would take a few days to download everything, though. After the first download, you can add a <code>-N</code> to the <code>wget</code> command to just download new files.</p>
  <p>For getting just one file:</p>
  <pre><code>wget ftp://ftp.wwpdb.org/pub/pdb/data/biounit/PDB/divided/00/100d.pdb1.gz
  </code></pre>
  <p>Hope this helps.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-30T23:17:19.863Z
Answers.LastActivityDate: 2021-07-30T23:17:19.863Z
Answers.UserDisplayName: Nate
Body: <p>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.</p>
  <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-11T15:04:52.353Z
Comments.Text: 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.
Comments.UserDisplayName: marcin
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-12T09:15:19.560Z
Comments.Text: 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.
Comments.UserDisplayName: Jacob
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-12T18:46:31.360Z
Comments.Text: 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 ...](https://gemmi.readthedocs.io/en/latest/utils.html#convert) or from [Python](https://gemmi.readthedocs.io/en/latest/mol.html#assembly). I suppose that BioJava, cctbx, PyMOL, etc also have such a capability.
Comments.UserDisplayName: marcin
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-15T19:18:37.083Z
Comments.Text: Thanks a lot, I'll give that a try.
Comments.UserDisplayName: Jacob
Tags: <protein-structure><pdb>
Title: PDB: Download all biological assemblies
ThreadText: # PDB: Download all biological assemblies
  
  (Asked by: username_0 on 2021-02-11)
  
  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.
  
  **Tags:** protein-structure, pdb
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_0**: 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.  
  > **username_1**: 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 ...](https://gemmi.readthedocs.io/en/latest/utils.html#convert) or from [Python](https://gemmi.readthedocs.io/en/latest/mol.html#assembly). I suppose that BioJava, cctbx, PyMOL, etc also have such a capability.  
  > **username_0**: Thanks a lot, I'll give that a try.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-07-30. Score: 3
  
  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.
  
  
  ---
  
  