Body: <p>I'd like to use protein structure data from PDBs visualized by Chimera to do two things.
  I'd be happy to learn the appropriate tools and methods.</p>
  <p>・Mapping information about amino acids present on protein surfaces to sequences</p>
  <p>・Find the charges of exposed amino acids on the surface and apply color gradations to the amino acid molecules according to their values</p>
  <p>The second one in particular looks like it could be done with Chimera's &quot;Coulomb surface coloring&quot;. But I'm not sure what kind of value to enter underneath the color and how to find it, which is needed to add a gradient.</p>
  <p>Sorry for my bad English ...</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-10T04:51:46.273Z
Comments.Text: Hi @farinelli what is sospecial about Chimera? For example, PyMol can be used following a surface charge calcuation
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-14T09:52:01.140Z
Comments.Text: Finding solvent accessibility of residues is straightforward, however, the charge of a residue is trickier. An atom has a formal charge and a partial charge (Gasteiger-Marsili charge). Protons are not seem in protein crystals, so which protonation state a surface residue has needs to be calculated. The Advanced Poisson-Boltzman Solver for example is implemented in several tools, such as PyMOL or pdb2pqr.
Comments.UserDisplayName: Matteo Ferla
Tags: <protein-structure><pdb><3d-structure>
Title: Extract only the amino acid residues on the surface of protein structure data
ThreadText: # Extract only the amino acid residues on the surface of protein structure data
  
  (Asked by: username_0 on 2020-07-10)
  
  I'd like to use protein structure data from PDBs visualized by Chimera to do two things.
  I'd be happy to learn the appropriate tools and methods.
  
  ・Mapping information about amino acids present on protein surfaces to sequences
  
  ・Find the charges of exposed amino acids on the surface and apply color gradations to the amino acid molecules according to their values
  
  The second one in particular looks like it could be done with Chimera's "Coulomb surface coloring". But I'm not sure what kind of value to enter underneath the color and how to find it, which is needed to add a gradient.
  
  Sorry for my bad English ...
  
  **Tags:** protein-structure, pdb, 3d-structure
  
  > **Comments:**
  > **username_1**: Hi @username_0 what is sospecial about Chimera? For example, PyMol can be used following a surface charge calcuation  
  > **username_2**: Finding solvent accessibility of residues is straightforward, however, the charge of a residue is trickier. An atom has a formal charge and a partial charge (Gasteiger-Marsili charge). Protons are not seem in protein crystals, so which protonation state a surface residue has needs to be calculated. The Advanced Poisson-Boltzman Solver for example is implemented in several tools, such as PyMOL or pdb2pqr.  
  
  ---
  
  ## 0 answers
  
  