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Both sides previous revision Previous revision Next revision | Previous revision Last revision Both sides next revision | ||
courses:public:vmd [2016/06/21 08:02] 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: | ||
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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> | ||
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//**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. | ||
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- 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> | ||
- | * Right click on each molecule and save its coordinates | + | * In the VMD Main window select the molecule of 1yer and right click on it to save its coordinates. |
- | (only save the protein part "Chain A") in a file called 1YER_aligned.pdb and 2yer_aligned.pdb | + | 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> | ||
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<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/ | ||
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* Repeat for both structures and unpack the *.dx.gz file. | * 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]] | ||