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courses:public:vmd [2016/06/21 09:29]
stank [Visualization of electrostatic potentials]
courses:public:vmd [2019/04/08 16:37]
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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 {{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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