You are here: start » courses » public » vmd

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
courses:public:vmd [2016/06/20 13:32] – [Visualization of electrostatic potentials] richtercourses:public:vmd [2019/04/08 16:37] (current) – wade
Line 1: Line 1:
-===== 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.
Line 57: Line 57:
     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:
Line 78: Line 77:
   *  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>
Line 112: Line 111:
 //**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.
Line 136: Line 135:
   - 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>
 +  * In the VMD Main window select the molecule of 1yer and right click on it to save its coordinates.
 +    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>
Line 143: Line 144:
  
 <code> <code>
-  * Use the aligned Proteins from the previous section.  +  * Start VMD again and use the aligned Proteins from the previous section (load the previously saved coordinates).  
-  * Right click on each molecule and save its coordinates  +    The proteins should show up as aligned entities. 
-    (only save the protein part  "not (protein or water)") in a file called 1YER_aligned.pdb and 2yer_aligned.pdb +  * Go to the PDB2PQR webserver: http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/ 
-  * Go to the PDB2PQR webserver:  +  * Upload one of the aligned coordinate files.  
-{{http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/|http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/}} +    Choose the force field (AMBER) and naming scheme (AMBER), and click ’Submit’. 
-  * Choose the force field (AMBER) and naming scheme (AMBER), and click ’Submit’.+  * Save the output files (xxxx_aligned.in, xxxx_aligned.propka and xxxx_aligned.pqr) on disk. 
 +  * Press "Run APBS" -> Launch 
 +  * Again, save the output files, espcially the *.dx.gz grid files.  
 +    You might want to look at the program output and error logs if there are errors or warnings. 
 +  * Repeat for both structures and unpack the *.dx.gz file.
 </code> </code>
 +In the respective pqr files, what are the net charges for the two proteins[[courses:hidden:vmd#Alignment of proteins|_?_]] 
 +<code>
 +  * To visualize the electrostatic potential, select in the vmd main window the molecule 1yer.
 +  * Go to File-> Load data in molecule. Select the corresponding dx grid file from your apbs output Press Load.
 +  * In Graphics Representation, change the standard representation to New Cartoon.
 +  * Create a new representation, Color by ID (blue), Select drawing method Isosurface. Select an Isovalue of 3 
 +    and draw as Solid surface.
 +  * Again Create a new representation. Color by ID (red), Select again drawing method Isosurface with an Isovalue of -3.
 +    also draw as Solid surface.
 +  * Repeat the steps with the other molecule. 
 +</code>
 +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:visualizationstatealigment.zip|Visualizationstate alignment}}+{{:courses:hidden:hsp90_aligned_electrostatics.zip|Visualization state alignment and electrostatics}}
  
-[[courses:hidden:visualizationstateselectrostaticsvmdtutorial.zip|Visualization state from electrostatics tutorial]] 
  
  
  

Trace:

Navigation
Print/export