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courses:public:vmd [2016/06/22 08:36] stank [Create Graphics representations] |
courses:public:vmd [2019/04/08 16:37] (current) 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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| * 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> | ||
