Differences
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| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
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courses:public:vmd [2016/06/21 09:42] stank [Visualization of electrostatic potentials] |
courses:public:vmd [2016/06/22 08:36] stank [Create Graphics representations] |
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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: | ||
| Line 147: | Line 146: | ||
| * Start VMD again and 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/ |
| * Upload one of the aligned coordinate files. | * Upload one of the aligned coordinate files. | ||
| Choose the force field (AMBER) and naming scheme (AMBER), and click ’Submit’. | Choose the force field (AMBER) and naming scheme (AMBER), and click ’Submit’. | ||
