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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 09:18] stank [Alignment of proteins] |
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 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. | 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/ | ||
| Line 156: | Line 155: | ||
| * Repeat for both structures and unpack the *.dx.gz file. | * Repeat for both structures and unpack the *.dx.gz file. | ||
| </code> | </code> | ||
| - | In the repective pqr files, what are the net charges for the two proteins[[courses:hidden:vmd#Alignment of proteins|_?_]] | + | In the respective pqr files, what are the net charges for the two proteins[[courses:hidden:vmd#Alignment of proteins|_?_]] |
| <code> | <code> | ||
| * To visualize the electrostatic potential, select in the vmd main window the molecule 1yer. | * To visualize the electrostatic potential, select in the vmd main window the molecule 1yer. | ||
| 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}} |
