Body: <p>I want to read a PDB file and display/render the atoms using a graphics engine.</p>
  <p>If I consider each residue in the protein as a solid sphere, what would be the radius of the sphere?</p>
  <p>How can I calculate it? Or, is there any database for that?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-27T12:23:45.633Z
Comments.Text: You may want to check how existing molecular viewers (PyMOL, Jmol, Chimera, web-based viewers on RCSB, PDBe and PDBj websites) render it.
Comments.UserDisplayName: marcin
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-27T12:30:30.877Z
Comments.Text: @marcin, I am developing my own software for learning ourposes.
Comments.UserDisplayName: user366312
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-27T12:36:14.607Z
Comments.Text: Van der Waals radii are used to construct a special kind of molecular model called a space-filling model. These models are constructed by drawing each atom as a van der Waals sphere with the atom’s nucleus at the center of the sphere. taken from https://www.reed.edu/chemistry/ROCO/Geometry/space_filling.html not sure how to expand it to a full residue
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-27T12:39:30.323Z
Comments.Text: @pippo1980, thanks! good information. :)
Comments.UserDisplayName: user366312
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-27T12:40:43.353Z
Comments.Text: try this paper not sure why 5A radius is choosen https://www.researchgate.net/figure/Each-protein-is-modeled-as-a-union-of-spheres-of-radius-5-A-one-sphere-per-amino-acid_fig2_8614866 the picture seems OK to me tough
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-27T12:44:15.470Z
Comments.Text: ok full article is for free; it states: "....However, it has been suggested that the 5 Å radius is appropriate to model the hydration shell around the protein
  [19]. The problem of computing
  r for such a model reduces
  to computation of the distance to the surface of each sphere,
  and taking the minimum over all spheres.... " Worth to notice article 19 its about globular protein, no idead if 5A rules could be extended to other kind of protein too
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-27T12:57:36.493Z
Comments.Text: The protein is
  represented as a union of spheres, each of radius 5 Å, and
  centered on the C
  a atom of each amino acid residue
Comments.UserDisplayName: pippo1980
Tags: <protein-structure><pdb>
Title: How can I calculate the radius of a residue?
ThreadText: # How can I calculate the radius of a residue?
  
  (Asked by: username_0 on 2022-06-27)
  
  I want to read a PDB file and display/render the atoms using a graphics engine.
  
  If I consider each residue in the protein as a solid sphere, what would be the radius of the sphere?
  
  How can I calculate it? Or, is there any database for that?
  
  **Tags:** protein-structure, pdb
  
  > **Comments:**
  > **username_1**: You may want to check how existing molecular viewers (PyMOL, Jmol, Chimera, web-based viewers on RCSB, PDBe and PDBj websites) render it.  
  > **username_0**: @username_1, I am developing my own software for learning ourposes.  
  > **username_2**: Van der Waals radii are used to construct a special kind of molecular model called a space-filling model. These models are constructed by drawing each atom as a van der Waals sphere with the atom’s nucleus at the center of the sphere. taken from https://www.reed.edu/chemistry/ROCO/Geometry/space_filling.html not sure how to expand it to a full residue  
  > **username_0**: @username_2, thanks! good information. :)  
  > **username_2**: try this paper not sure why 5A radius is choosen https://www.researchgate.net/figure/Each-protein-is-modeled-as-a-union-of-spheres-of-radius-5-A-one-sphere-per-amino-acid_fig2_8614866 the picture seems OK to me tough  
  > **username_2**: ok full article is for free; it states: "....However, it has been suggested that the 5 Å radius is appropriate to model the hydration shell around the protein [19]. The problem of computing r for such a model reduces to computation of the distance to the surface of each sphere, and taking the minimum over all spheres.... " Worth to notice article 19 its about globular protein, no idead if 5A rules could be extended to other kind of protein too  
  > **username_2**: The protein is represented as a union of spheres, each of radius 5 Å, and centered on the C a atom of each amino acid residue  
  
  ---
  
  ## 0 answers
  
  