text: user9650: https://alphafold.com/entry/Q9Y499
  Starting at line 918 of the downloadable mmCIF file, it looks like there might be coordinates in x, y,z:
  ATOM 1    N N   . TRP A 1 1   ? 12.549  -2.565  -21.811 1.0 96.06 ? 1   TRP A N   1 Q9Y499 UNP 1   W 
  ATOM 2    C CA  . TRP A 1 1   ? 12.477  -2.290  -20.365 1.0 96.06 ? 1   TRP A CA  1 Q9Y499 UNP 1   W 
  ATOM 3    C C   . TRP A 1 1   ? 11.221  -2.928  -19.812 1.0 96.06 ? 1   TRP A C   1 Q9Y499 UNP 1   W 
  ATOM 4    C CB  . TRP A 1 1   ? 12.469  -0.785  -20.103 1.0 96.06 ? 1   TRP A CB  1 Q9Y499 UNP 1   W 
  ATOM 5    O O   . TRP A 1 1   ? 10.206  -2.922  -20.501 1.0 96.06 ? 1   TRP A O   1 Q9Y499 UNP 1   W 
  ATOM 6    C CG  . TRP A 1 1   ? 13.795  -0.114  -20.270 1.0 96.06 ? 1   TRP A CG  1 Q9Y499 UNP 1   W 
  ATOM 7    C CD1 . TRP A 1 1   ? 14.286  0.508   -21.369 1.0 96.06 ? 1   TRP A CD1 1 Q9Y499 UNP 1   W 
  ATOM 8    C CD2 . TRP A 1 1   ? 14.791  0.098   -19.228 1.0 96.06 ? 1   TRP A CD2 1 Q9Y499 UNP 1   W 
  
  I am a bioinformatics noob (took an intro class in my undergrad CS degree at a Canadian university) but know some Unity game engine with which I want to build a standalone visualization tool for users with VR headsets.
  
  user6322: Don't
  A protein is not only list of atomic coordinates. Bar for a proof of concept (i.e. learn to code in Unity VR), it is an endless spiral of hurt in a field where there is a lot of competition and were you to push a product you'd need to invest more manhours in publicity than in coding...
  Connectivity
  Here is the short of it. Chemistry is classically a graph network: nodes=atoms, edges=bonds. The connectivity of the atoms is dictated by their residue's 3-letter name, which is either
  
  assumed —software know the 20 AAs (and several modifications, eg. SEP, 4x2 bases and some ligands, e.g. HOH— or
  a special entry in the PDB or mmCIF file —in PDB it's a CONECT entry.
  E.g. https://www.rcsb.org/ligand/CFF
  
  AlphaFold2 does not have ligands, AlphaFill does. But scientists (not PR specialists) use PDB entries or run their own modelling. AlphaFold2 from EBI is rarely used: oligomers with ligands is where it's at. Especially if doing a drug discovery campaign (and red biotech can and does afford VR headsets).
  Format
  mmCIF is a deposition standard, PDB is the workhorse standard. mmTF is a cool idea that is not catching on (cf XKCD comic strip about standard proliferation...). Using PDB is easier: https://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
  Representation
  Problems arise when offering representations —everyone has their favourite. See NGL gallery for an array: https://nglviewer.org/ngl/gallery/index.html
  Surface display has additional issues —PyMOL simply and openly reuses the Advance Poisson-Boltzmann Solvation tool as it's tricky.
  Dragons in the minefield
  In a PDB entry not from AF2, you can have disulfides (SSBOND and/or CIZ entry), isopeptide bonds (LINK), missing atoms, the UNK, UNX and UNL residues, alphatraces, insertion sequences, alt. occupancy, gaps, non-standard usages of all of these etc etc. and my favourite implied proximity bonding.
  
original_text: 9650: <p><a href="https://alphafold.com/entry/Q9Y499" rel="nofollow noreferrer">https://alphafold.com/entry/Q9Y499</a></p>
  <p>Starting at line 918 of the downloadable mmCIF file, it looks like there might be coordinates in x, y,z:</p>
  <pre><code>ATOM 1    N N   . TRP A 1 1   ? 12.549  -2.565  -21.811 1.0 96.06 ? 1   TRP A N   1 Q9Y499 UNP 1   W 
  ATOM 2    C CA  . TRP A 1 1   ? 12.477  -2.290  -20.365 1.0 96.06 ? 1   TRP A CA  1 Q9Y499 UNP 1   W 
  ATOM 3    C C   . TRP A 1 1   ? 11.221  -2.928  -19.812 1.0 96.06 ? 1   TRP A C   1 Q9Y499 UNP 1   W 
  ATOM 4    C CB  . TRP A 1 1   ? 12.469  -0.785  -20.103 1.0 96.06 ? 1   TRP A CB  1 Q9Y499 UNP 1   W 
  ATOM 5    O O   . TRP A 1 1   ? 10.206  -2.922  -20.501 1.0 96.06 ? 1   TRP A O   1 Q9Y499 UNP 1   W 
  ATOM 6    C CG  . TRP A 1 1   ? 13.795  -0.114  -20.270 1.0 96.06 ? 1   TRP A CG  1 Q9Y499 UNP 1   W 
  ATOM 7    C CD1 . TRP A 1 1   ? 14.286  0.508   -21.369 1.0 96.06 ? 1   TRP A CD1 1 Q9Y499 UNP 1   W 
  ATOM 8    C CD2 . TRP A 1 1   ? 14.791  0.098   -19.228 1.0 96.06 ? 1   TRP A CD2 1 Q9Y499 UNP 1   W 
  </code></pre>
  <p>I am a bioinformatics noob (took an intro class in my undergrad CS degree at a Canadian university) but know some Unity game engine with which I want to build a standalone visualization tool for users with VR headsets.</p>
   6322: <h2>Don't</h2>
  <p>A protein is not only list of atomic coordinates. Bar for a proof of concept (i.e. learn to code in Unity VR), it is an endless spiral of hurt in a field where there is a lot of competition and were you to push a product you'd need to invest more manhours in publicity than in coding...</p>
  <h2>Connectivity</h2>
  <p>Here is the short of it. Chemistry is classically a graph network: nodes=atoms, edges=bonds. The connectivity of the atoms is dictated by their residue's 3-letter name, which is either</p>
  <ul>
  <li>assumed —software know the 20 AAs (and several modifications, eg. <code>SEP</code>, 4x2 bases and some ligands, e.g. <code>HOH</code>— or</li>
  <li>a special entry in the PDB or mmCIF file —in PDB it's a CONECT entry.
  E.g. <a href="https://www.rcsb.org/ligand/CFF" rel="nofollow noreferrer">https://www.rcsb.org/ligand/CFF</a></li>
  </ul>
  <p>AlphaFold2 does not have ligands, AlphaFill does. But scientists (not PR specialists) use PDB entries or run their own modelling. AlphaFold2 from EBI is rarely used: oligomers with ligands is where it's at. Especially if doing a drug discovery campaign (and red biotech can and does afford VR headsets).</p>
  <h2>Format</h2>
  <p>mmCIF is a deposition standard, PDB is the workhorse standard. mmTF is a cool idea that is not catching on (cf XKCD comic strip about standard proliferation...). Using PDB is easier: <a href="https://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html" rel="nofollow noreferrer">https://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html</a></p>
  <h2>Representation</h2>
  <p>Problems arise when offering representations —everyone has their favourite. See NGL gallery for an array: <a href="https://nglviewer.org/ngl/gallery/index.html" rel="nofollow noreferrer">https://nglviewer.org/ngl/gallery/index.html</a>
  Surface display has additional issues —PyMOL simply and openly reuses the Advance Poisson-Boltzmann Solvation tool as it's tricky.</p>
  <h2>Dragons in the minefield</h2>
  <p>In a PDB entry not from AF2, you can have disulfides (<code>SSBOND</code> and/or <code>CIZ</code> entry), isopeptide bonds (<code>LINK</code>), missing atoms, the <code>UNK</code>, <code>UNX</code> and <code>UNL</code> residues, alphatraces, insertion sequences, alt. occupancy, gaps, non-standard usages of all of these etc etc. and my favourite implied proximity bonding.</p>
  