Differences
This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Last revision Both sides next revision | ||
courses:public:vmd [2016/06/21 09:29] stank [Visualization of electrostatic potentials] |
courses:public:vmd [2017/03/21 11:35] richter [Inspecting Protein Structure: The Ramachandran Plot] |
||
---|---|---|---|
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 172: | Line 171: | ||
{{courses:hidden:visualizationstatesbasicvmdtutorial.zip|Visualization states from basic tutorial}} | {{courses:hidden:visualizationstatesbasicvmdtutorial.zip|Visualization states from basic tutorial}} | ||
- | {{:courses:hidden:hsp90_aligned_electrostatics.zip|Visualizationstate alignment and electrostatics}} | + | {{:courses:hidden:hsp90_aligned_electrostatics.zip|Visualization state alignment and electrostatics}} |