title: Using MDAnalysis to extract coordinates in an array from pdb
body: <p>I have a pdb file that is a subset of a much larger system. This pdb is special because I have some vectors based on this file's coordinate system. I want to draw these vectors and the basis vector of that system onto the pdb. Eventually I would like to visualize the vector and basis vectors as it moves through some MD simulation where I an update the vector position based on the trajectory over time.</p>
  <p>To start, I would like to read a pdb that has coordinates that define the basis vectors that further define the other vectors I want to visualize. Right now I'm using this class in MDAnalysis:
  <a href="https://docs.mdanalysis.org/1.0.0/_modules/MDAnalysis/coordinates/PDB.html#PDBReader" rel="nofollow noreferrer">https://docs.mdanalysis.org/1.0.0/_modules/MDAnalysis/coordinates/PDB.html#PDBReader</a></p>
  <pre><code>molecule=mda.coordinates.PDB.PDBReader('molecule.pdb')
  </code></pre>
  <p>This works and it reads the pdb just fine, but returns with this variable type</p>
  <pre><code>coordinates.PDB.Reader
  </code></pre>
  <p>I suppose this isn't a surprise, but I want to be able to print this variable and get some array of coordinate positions and atom types. I'd love to see the bonds as well but that's not necessary. Now when I print I get</p>
  <pre><code>&lt;PDBReader molecule.pdb with 1 frames of 60 atoms&gt;
  </code></pre>
  <p>I want something that would look like</p>
  <pre><code>[atomtype1,x1,y1,z1]...[atomtypen,xn,yn,zn]
  </code></pre>
  <p>Thank you,</p>