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Visualizing the Secondary Structure of a Protein





Working of PyMol and Loading the .pdb file


Installation instructions and the links to download the software or the data can be obtained through the simulator tab 


When the molecule is loaded into PyMol the molecule can be controlled by mouse, with three buttons, left, middle (push able ball), and right. The left button is used to rotate the molecule. Middle button is used to move the molecule and the right mouse button is used to move the molecule in z axis that is to zoom in and out.


Load the downloaded PDB file into PyMol (Figure 1).




 Figure 1: Screenshot of standard file chooser of PyMol to load the PDB file


File →open →choose the PDB file where it is actually located. User can also load the file through command line using the command load <file path>

E.g., “load C: Downloads1UBQ.pdb”

By default, the loaded PDB file structure will be shown with line representation in PyMol (Figure 2).




 Figure 2: Screenshot of PyMol with a loaded molecule


We can see two rows on the right side of Figure 8, labeled as ‘all’ and ‘1UBQ’ where we can change individual appearance of a molecule as well as all molecules together. If there are multiple molecules, user can also select every molecule or object at same time.


User  can also see A,S,H,L and C labels in the two rows as different columns, these alphabets implies, Action , Show , Hide , Label and Color respectively. We can use these GUI elements or the user can give commands to get performed actions (Figure 3).




 Figure 3: Screenshot of the Internal GUI buttons


Viewing the image or structure in an interpretable manner is good, so that the user can understand the structure easily, which helps to find the active binding sites in a protein molecule. 

Representing protein structure in lines is not interpretable, to view or highlight secondary structures of a protein. There are other representations to view the model as stick, ribbon, and cartoon (Figure 4).




 Figure 4: Screenshot of the molecule with lines, ribbon and cartoon representation


To view these different representations 

  1. Select the object or molecule in internal GUI on the right side.
  2. Select the molecule or object by clicking left mouse button (in this case 1UBQ).
  3. Select ‘S’ labeled button, we can select (show →as →stick).
  4. Similarly for other representations.


From the Figure 8 we can see the structure represented in cartoon could be easily interpreted for secondary structure. It can differentiate the helices (coiled like structures), beta sheets (strands with arrow marks), and loops (strings). 

Make a color representation of the protein based on secondary structure. So that user can easily identify the structure of a protein (Figure 5).



Figure 5: Screenshot of the protein molecule to color based on the secondary chain


The red coiled like structures are alpha helices, yellow strands which are anti-parallel in direction are beta-strands, and the two beta strands are connected by green loops or turns.

User can save the image of a protein structure in ‘png’ formatted image file, with a higher resolution of 2400, 2400 using the command “ray” (Figure 6).



Figure 6: Screenshot of the object which has been rendered to a 2400, 2400 resolution image


 The user can save the image file by the file menu option, file →save image (Figure 7).



Figure 7: Screenshot to save the image



Figure 8: The saved image of the protein 


 When the user wants to continue the work after some break, the user can save his work by saving into a session file. The file menu chooser has an option to save the session, user can select file menu → save session, and can save that session file (Figure 9).




 Figure 9: Screenshot to save the session


(Note: all these representations can also driven through command line)





 This experiment uses :The PyMOL Molecular Graphics System, Version Schrödinger, LLC.



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