text: user1847: I'm using R and its Rpdb package to work with PDB files. I use the read.pdb function but, nevertheless, I couldn't find the argument which will allow me to view the SEQRES section and the full amino-acid sequence of the protein.
  For example, I want to find which amino-acid is in the 17th position of the sequence and I want to extract it from the 'SRQRES' section in the PDB file (the original length of the sequence was reduced for the sake of the example):
  SEQRES   1 A  390  GLU PRO GLU TRP THR TYR PRO ARG LEU SER CYS GLN GLY          
  SEQRES   2 A  390  SER THR PHE GLN LYS ALA LEU LEU ILE SER PRO HIS ARG          
  SEQRES   3 A  390  PHE GLY GLU ALA ARG GLY ASN SER ALA PRO LEU ILE ILE          
  SEQRES   4 A  390  ARG GLU PRO PHE ILE ALA CYS GLY PRO LYS GLU CYS LYS          
  SEQRES   5 A  390  HIS PHE ALA LEU THR HIS TYR ALA ALA GLN PRO GLY GLY          
  SEQRES   6 A  390  TYR TYR ASN GLY THR ARG GLU ASP ARG ASN LYS LEU ARG          
  SEQRES   7 A  390  HIS LEU ILE SER VAL LYS LEU GLY LYS ILE PRO THR VAL          
  SEQRES   8 A  390  GLU ASN SER ILE PHE HIS MET ALA ALA TRP SER GLY SER          
  SEQRES   9 A  390  ALA CYS HIS ASP GLY ARG GLU TRP THR TYR ILE GLY VAL          
  SEQRES  10 A  390  ASP GLY PRO ASP SER ASN ALA LEU ILE LYS ILE LYS TYR          
  
  ...   
  The original file can be found here 1a4g.pdb.
  Any ideas on how to accomplish that?
  
  user150: I have not used Rpdb but I have used, and would recommend, bio3d.
  To read the PDB file 1A4G:
  library(bio3d)
  pdb1a4g <- read.pdb("1a4g")
  
  To get the SEQRES information, there are two options. Get it from the pdb object directly:
  seq1a4g <- pdb1a4g$seqres
  
  Or call pdbseq:
  seq1a4g <- pdbseq(pdb1a4g)
  
  Using the second method, the 17th position (note this is not the same as the 17th position of the original protein sequence):
  seq1a4g[17]
   92 
  "Q" 
  
  
original_text: 1847: <p>I'm using R and its Rpdb package to work with PDB files. I use the <code>read.pdb</code> function but, nevertheless, I couldn't find the argument which will allow me to view the <code>SEQRES</code> section and the full amino-acid sequence of the protein.</p>
  
  <p>For example, I want to find which amino-acid is in the 17th position of the sequence and I want to extract it from the 'SRQRES' section in the PDB file (the original length of the sequence was reduced for the sake of the example):</p>
  
  <pre><code>SEQRES   1 A  390  GLU PRO GLU TRP THR TYR PRO ARG LEU SER CYS GLN GLY          
  SEQRES   2 A  390  SER THR PHE GLN LYS ALA LEU LEU ILE SER PRO HIS ARG          
  SEQRES   3 A  390  PHE GLY GLU ALA ARG GLY ASN SER ALA PRO LEU ILE ILE          
  SEQRES   4 A  390  ARG GLU PRO PHE ILE ALA CYS GLY PRO LYS GLU CYS LYS          
  SEQRES   5 A  390  HIS PHE ALA LEU THR HIS TYR ALA ALA GLN PRO GLY GLY          
  SEQRES   6 A  390  TYR TYR ASN GLY THR ARG GLU ASP ARG ASN LYS LEU ARG          
  SEQRES   7 A  390  HIS LEU ILE SER VAL LYS LEU GLY LYS ILE PRO THR VAL          
  SEQRES   8 A  390  GLU ASN SER ILE PHE HIS MET ALA ALA TRP SER GLY SER          
  SEQRES   9 A  390  ALA CYS HIS ASP GLY ARG GLU TRP THR TYR ILE GLY VAL          
  SEQRES  10 A  390  ASP GLY PRO ASP SER ASN ALA LEU ILE LYS ILE LYS TYR          
  </code></pre>
  
  <p>...   </p>
  
  <p>The original file can be found here <a href="https://files.rcsb.org/download/1A4G.pdb" rel="nofollow noreferrer">1a4g.pdb</a>.</p>
  
  <p>Any ideas on how to accomplish that?</p>
   150: <p>I have not used <code>Rpdb</code> but I have used, and would recommend, <a href="http://thegrantlab.org/bio3d/index.php" rel="nofollow noreferrer">bio3d</a>.</p>
  
  <p>To read the PDB file 1A4G:</p>
  
  <pre><code>library(bio3d)
  pdb1a4g &lt;- read.pdb("1a4g")
  </code></pre>
  
  <p>To get the SEQRES information, there are two options. Get it from the <code>pdb</code> object directly:</p>
  
  <pre><code>seq1a4g &lt;- pdb1a4g$seqres
  </code></pre>
  
  <p>Or call <code>pdbseq</code>:</p>
  
  <pre><code>seq1a4g &lt;- pdbseq(pdb1a4g)
  </code></pre>
  
  <p>Using the second method, the 17th position (note this is not the same as the 17th position of the original protein sequence):</p>
  
  <pre><code>seq1a4g[17]
   92 
  "Q" 
  </code></pre>
  