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Pymol/VMD - Switch to atomic level


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#1 Speedies

Speedies

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Posted 30 August 2012 - 05:57 AM

Hello,

I'm trying to figure out the structure of a protein. So I installed the programs Pymol and VMD which can show the 3D-structure of proteins using a pdb-file.

I have the sequence of a protein and would like to check where a certain amino acid is exactly located at in the structure.

Does anyone know how to use those programs?

Thank you very much!

Greetings,
Speedies

Edited by Speedies, 30 August 2012 - 06:05 AM.


#2 ascacioc

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Posted 30 August 2012 - 10:04 AM

Pick one program and learn very well how to use it. If you want to do beautiful pictures for papers, I recommend pymol. If you are doing molecular dynamics simulations, VMD is the tool (Visual Molecular Dynamics)
In Pymol (for which I recommend: http://www.pymolwiki...x.php/Main_Page ):
-open pymol and load your protein from file/open
-go to Display/Sequence and the sequence will appear on the top of the structure window; you have numbers and you can scroll down to your desired residue
-click on the residue and it will be selected in the structure
-left mouse button to rotate the structure and right + drag mouse button to zoom in/out
In VMD (for which I recommend: http://www.ks.uiuc.e...ning/Tutorials/ )
-File/New molecule to load your structure
-Extensions/Analysis/Sequence Viewer to open the sequence window; again select your residue and it will get yellow
-r from the keyboard to activate the rotation mode and rotate with the mouse
-s from the keyboard to activate the scale mode and drag with the mouse for zooming in and out




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