Answers.Body: <p>Molecular structures are 3D.
  The records (lines) in the PDB files are in so-called fixed column format.<br />
  The fields don't need to be separated with blank characters, but they must be in specified columns. For example, the X coordinate is in columns 31-38.
  Here is the specification of the ATOM record from <a href="https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM" rel="nofollow noreferrer">PDB v3.3</a>.</p>
  <pre><code>COLUMNS        DATA  TYPE    FIELD        DEFINITION
  -------------------------------------------------------------------------------------
   1 -  6        Record name   &quot;ATOM  &quot;
   7 - 11        Integer       serial       Atom  serial number.
  13 - 16        Atom          name         Atom name.
  17             Character     altLoc       Alternate location indicator.
  18 - 20        Residue name  resName      Residue name.
  22             Character     chainID      Chain identifier.
  23 - 26        Integer       resSeq       Residue sequence number.
  27             AChar         iCode        Code for insertion of residues.
  31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
  39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
  47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
  55 - 60        Real(6.2)     occupancy    Occupancy.
  61 - 66        Real(6.2)     tempFactor   Temperature  factor.
  77 - 78        LString(2)    element      Element symbol, right-justified.
  79 - 80        LString(2)    charge       Charge  on the atom.
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-04-02T09:53:11.870Z
Answers.LastActivityDate: 2021-04-02T09:53:11.870Z
Answers.UserDisplayName: marcin
Body: <p>Is there a way we can get 2d/3d structural coordinates like in (x/y/z) manner from a pdb file.</p>
  <p>I have looked a believe that the coordinates are in below line:</p>
  <pre><code>ATOM   1067  NH1 ARG A 141     -10.147   7.455  -6.079  1.00 23.24           N  
  </code></pre>
  <p>but i am unable to make a sense from it as i don't know which one is (x/y/z) in (2d/3d) coordinate system.</p>
  <p>If anyone describe it, that'll be a great help.</p>
  <p>Thanks</p>
  
Tags: <proteins><protein-structure><pdb>
Title: How to get 2d/3d structural coordinates from a PDB file?
ThreadText: # How to get 2d/3d structural coordinates from a PDB file?
  
  (Asked by: username_0 on 2021-04-01)
  
  Is there a way we can get 2d/3d structural coordinates like in (x/y/z) manner from a pdb file.
  
  I have looked a believe that the coordinates are in below line:
  
  ```
  ATOM   1067  NH1 ARG A 141     -10.147   7.455  -6.079  1.00 23.24           N  
  
  ```
  
  but i am unable to make a sense from it as i don't know which one is (x/y/z) in (2d/3d) coordinate system.
  
  If anyone describe it, that'll be a great help.
  
  Thanks
  
  **Tags:** proteins, protein-structure, pdb
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-04-02. Score: 3 | Accepted answer
  
  Molecular structures are 3D.
  The records (lines) in the PDB files are in so-called fixed column format.  
  The fields don't need to be separated with blank characters, but they must be in specified columns. For example, the X coordinate is in columns 31-38.
  Here is the specification of the ATOM record from [PDB v3.3](https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM).
  
  ```
  COLUMNS        DATA  TYPE    FIELD        DEFINITION
  -------------------------------------------------------------------------------------
   1 -  6        Record name   "ATOM  "
   7 - 11        Integer       serial       Atom  serial number.
  13 - 16        Atom          name         Atom name.
  17             Character     altLoc       Alternate location indicator.
  18 - 20        Residue name  resName      Residue name.
  22             Character     chainID      Chain identifier.
  23 - 26        Integer       resSeq       Residue sequence number.
  27             AChar         iCode        Code for insertion of residues.
  31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
  39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
  47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
  55 - 60        Real(6.2)     occupancy    Occupancy.
  61 - 66        Real(6.2)     tempFactor   Temperature  factor.
  77 - 78        LString(2)    element      Element symbol, right-justified.
  79 - 80        LString(2)    charge       Charge  on the atom.
  
  ```
  
  
  ---
  
  