Differences
This shows you the differences between two versions of the page.
| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| courses:public:vmd [2016/06/21 09:43] – [Visualization of electrostatic potentials] stank | courses:public:vmd [2019/04/08 16:37] (current) – wade | ||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ===== Molecular Visualization using VMD (Visual Molecular | + | ===== Molecular Visualization using VMD (Visual Molecular |
| 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 | + | * Click on Create_Rep button and replace |
| - | 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: | ||
| </ | </ | ||
