Pymol/VMD - Switch to atomic level - (Aug/30/2012 )
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!
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.org/index.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.edu/Training/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