Differences

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

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Next revision Both sides next revision
courses:public:vmd [2016/06/20 14:01]
richter [Visualization of electrostatic potentials]
courses:public:vmd [2016/06/22 08:36]
stank [Create Graphics representations]
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 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 ​sequenceIt is useful to compare structures of these proteins. ​+      but have different ​sequencesTherefore, 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>​
-  * 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  "​not ​(protein or water)"​) in a file called 1YER_aligned.pdb and 2yer_aligned.pdb+    ​Choose ​only the protein part (chain Ain '​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 145: Line 144:
  
 <​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.
   * 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/​
-  * Choose the force field (AMBER) and naming scheme (AMBER), and click ’Submit’.+  * Upload one of the aligned coordinate files.  
 +    ​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.   * Save the output files (xxxx_aligned.in,​ xxxx_aligned.propka and xxxx_aligned.pqr) on disk.
   * Press "Run APBS" -> Launch   * Press "Run APBS" -> Launch
-  * Again, save the output files. You might want to look at the program output and error logs if there are errors or warnings. +  * Again, save the output files, espcially the *.dx.gz grid files.  
-  * Repeat for both structures and unpack the .dx.gz file.+    ​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]] 
  
  
  
Navigation
Print/export