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courses:public:vmd [2016/06/21 08:38] – richtercourses:public:vmd [2019/04/08 16:37] (current) – wade
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-===== Molecular Visualization using VMD (Visual Molecular Dymanics) =====+===== Molecular Visualization using VMD (Visual Molecular Dynamics) =====
  
 VMD, a molecular graphics program, is developed in the Theoretical and Computational Biophysics group (Univ. of Illinois) together with other software (eg. NAMD) to simulate molecular systems. The group is lead by Klaus Schulten. VMD, a molecular graphics program, is developed in the Theoretical and Computational Biophysics group (Univ. of Illinois) together with other software (eg. NAMD) to simulate molecular systems. The group is lead by Klaus Schulten.
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     to Backbone (protein backbone will be rendered in green and the      to Backbone (protein backbone will be rendered in green and the 
     side chains in blue)     side chains in blue)
-  * Replace 'protein' by 'resname NAG' in the Selected_Atoms field  +  * Click on Create_Rep button and replace 'protein' by 'resname NAG' in the Selected_Atoms field 
-    and click on Create_Rep button+
   * Change the Drawing_Method from Surf to Licorice and the Coloring_Method    * Change the Drawing_Method from Surf to Licorice and the Coloring_Method 
     from Backbone to Name, and answer the following question:     from Backbone to Name, and answer the following question:
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   *  In VMD_Main window, go to Extensions -> Analysis -> Ramachandran Plot   *  In VMD_Main window, go to Extensions -> Analysis -> Ramachandran Plot
   *  In the Molecule menu select 1HEW.pdb   *  In the Molecule menu select 1HEW.pdb
-  *  Note that several points (on the left side of the graph) fall outside of the allowed conformational region+  *  Note that several points (on the right hand side of the graph) fall outside of the allowed conformational region
   *  Click on these points (yellow squares) to identify these residues and answer the following question:   *  Click on these points (yellow squares) to identify these residues and answer the following question:
 </code> </code>
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 //**Goal: Compare structures from different organisms or different folds**// //**Goal: Compare structures from different organisms or different folds**//
 <code> <code>
-    * Sometimes similar proteins exist in different species - they may perform the same function  +    * Sometimes similar proteins exist in different species - they may perform the same function, 
-      but have different sequence. It is useful to compare structures of these proteins. +      but have different sequences. Therefore, it is useful to compare structures of these proteins. 
       To do that, one needs to align the proteins based on their sequence        To do that, one needs to align the proteins based on their sequence 
       and sometimes also taking the structure into account.       and sometimes also taking the structure into account.
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   - What region displays largest difference between the two structures[[courses:hidden:vmd#Alignment of proteins|_?_]]    - What region displays largest difference between the two structures[[courses:hidden:vmd#Alignment of proteins|_?_]] 
 <code> <code>
-  * Right click on each molecule and save its coordinates  +  * In the VMD Main window select the molecule of 1yer and right click on it to save its coordinates. 
-    (only save the protein part  "Chain A") in a file called 1YER_aligned.pdb and 2yer_aligned.pdb+    Choose only the protein part (chain A) in 'Selected Atoms' and save it in a file called 1YER_aligned.pdb and repeat these steps also for the other molecule 2ior_aligned.pdb
   * Close the VMD program    * Close the VMD program 
 </code> </code>
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 <code> <code>
-  * Use the aligned Proteins from the previous section (load the previously saved coordinates). +  * Start VMD again and use the aligned Proteins from the previous section (load the previously saved coordinates). 
     The proteins should show up as aligned entities.     The proteins should show up as aligned entities.
   * Go to the PDB2PQR webserver: http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/   * Go to the PDB2PQR webserver: http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/
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   * Repeat for both structures and unpack the *.dx.gz file.   * Repeat for both structures and unpack the *.dx.gz file.
 </code> </code>
-In the repective pqr files, what are the net charges for the two proteins[[courses:hidden:vmd#Alignment of proteins|_?_]] +In the respective pqr files, what are the net charges for the two proteins[[courses:hidden:vmd#Alignment of proteins|_?_]] 
 <code> <code>
   * To visualize the electrostatic potential, select in the vmd main window the molecule 1yer.   * To visualize the electrostatic potential, select in the vmd main window the molecule 1yer.
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   * Repeat the steps with the other molecule.    * Repeat the steps with the other molecule. 
 </code> </code>
-What are the differences between the electrostatic potentials of the two proteins? What species are the respective proteins from[[courses:hidden:vmd#Alignment of proteins|_?_]] +What are the differences between the electrostatic potentials of the two proteins? From which species are the respective proteins from[[courses:hidden:vmd#Alignment of proteins|_?_]] 
 ==== Tutor only ==== ==== Tutor only ====
  
 {{courses:hidden:visualizationstatesbasicvmdtutorial.zip|Visualization states from basic tutorial}} {{courses:hidden:visualizationstatesbasicvmdtutorial.zip|Visualization states from basic tutorial}}
  
-{{:courses:hidden:hsp90_aligned_electrostatics.zip|Visualizationstate alignment and electrostatics}}+{{:courses:hidden:hsp90_aligned_electrostatics.zip|Visualization state alignment and electrostatics}}
  
  
  
  

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