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| Both sides previous revision Previous revision Next revision | Previous revision Last revision Both sides next revision | ||
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courses:public:vmd [2016/06/20 13:30] richter [Visualization of electrostatic potentials] |
courses:public:vmd [2017/03/21 11:35] richter [Inspecting Protein Structure: The Ramachandran Plot] |
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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 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 112: | Line 111: | ||
| //**Goal: Compare structures from different organisms or different folds**// | //**Goal: Compare structures from different organisms or different folds**// | ||
| <code> | <code> | ||
| - | * Sometimes similar proteins exist in different species - they may perform the same function | + | * Sometimes similar proteins exist in different species - they may perform the same function, |
| - | but have different sequence. It is useful to compare structures of these proteins. | + | but have different sequences. Therefore, it is useful to compare structures of these proteins. |
| To do that, one needs to align the proteins based on their sequence | To do that, one needs to align the proteins based on their sequence | ||
| and sometimes also taking the structure into account. | and sometimes also taking the structure into account. | ||
| Line 136: | Line 135: | ||
| - What region displays largest difference between the two structures[[courses:hidden:vmd#Alignment of proteins|_?_]] | - What region displays largest difference between the two structures[[courses:hidden:vmd#Alignment of proteins|_?_]] | ||
| <code> | <code> | ||
| + | * In the VMD Main window select the molecule of 1yer and right click on it to save its coordinates. | ||
| + | Choose only the protein part (chain A) in 'Selected Atoms' and save it in a file called 1YER_aligned.pdb and repeat these steps also for the other molecule 2ior_aligned.pdb | ||
| * Close the VMD program | * Close the VMD program | ||
| </code> | </code> | ||
| Line 143: | Line 144: | ||
| <code> | <code> | ||
| - | * Use the aligned Proteins from the previous section. | + | * Start VMD again and use the aligned Proteins from the previous section (load the previously saved coordinates). |
| - | * Right click on each molecule and save its coordinates | + | The proteins should show up as aligned entities. |
| - | (only save the protein part "not (protein or water)") in a file called 1YER_aligned.pdb and 2yer_aligned.pdb | + | * 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/|http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/}} | + | * Upload one of the aligned coordinate files. |
| + | Choose the force field (AMBER) and naming scheme (AMBER), and click ’Submit’. | ||
| + | * Save the output files (xxxx_aligned.in, xxxx_aligned.propka and xxxx_aligned.pqr) on disk. | ||
| + | * Press "Run APBS" -> Launch | ||
| + | * Again, save the output files, espcially the *.dx.gz grid files. | ||
| + | You might want to look at the program output and error logs if there are errors or warnings. | ||
| + | * Repeat for both structures and unpack the *.dx.gz file. | ||
| </code> | </code> | ||
| + | In the respective pqr files, what are the net charges for the two proteins[[courses:hidden:vmd#Alignment of proteins|_?_]] | ||
| + | <code> | ||
| + | * To visualize the electrostatic potential, select in the vmd main window the molecule 1yer. | ||
| + | * Go to File-> Load data in molecule. Select the corresponding dx grid file from your apbs output Press Load. | ||
| + | * In Graphics Representation, change the standard representation to New Cartoon. | ||
| + | * Create a new representation, Color by ID (blue), Select drawing method Isosurface. Select an Isovalue of 3 | ||
| + | and draw as Solid surface. | ||
| + | * Again Create a new representation. Color by ID (red), Select again drawing method Isosurface with an Isovalue of -3. | ||
| + | also draw as Solid surface. | ||
| + | * Repeat the steps with the other molecule. | ||
| + | </code> | ||
| + | What are the differences between the electrostatic potentials of the two proteins? From which species are the respective proteins from[[courses:hidden:vmd#Alignment of proteins|_?_]] | ||
| ==== Tutor only ==== | ==== Tutor only ==== | ||
| {{courses:hidden:visualizationstatesbasicvmdtutorial.zip|Visualization states from basic tutorial}} | {{courses:hidden:visualizationstatesbasicvmdtutorial.zip|Visualization states from basic tutorial}} | ||
| - | {{:courses:hidden:visualizationstatealigment.zip|Visualizationstate alignment}} | + | {{:courses:hidden:hsp90_aligned_electrostatics.zip|Visualization state alignment and electrostatics}} |
| - | [[courses:hidden:visualizationstateselectrostaticsvmdtutorial.zip|Visualization state from electrostatics tutorial]] | ||
