VMD Software Tutorial

1. Delete the molecule that has been loaded into the window

First: Select the molecule in "VMD main", then in "VMD Main", Molecule—Delete

Second: In "VMD Main", Extentions - Tk Console, then in "VMD TkConsole", type mol delete all, and then press Enter, on to delete it.

2. Display atomic names, key lengths, key angles, dihedral angles.

  • At first, open a molecule in VMD and put the mouse into openGL Display, the mouse is still an arrow.
  • How to pick an atom in open GL: In VMD Main, select pick, at this point in open GL, the mouse will become a cross, at this point you can select the atom by clicking on it, click on it, and it will be displayed in the command line: Info) User Pick: mol0 atom: 1249. (Note: When picking, the Mouse must be in Rotate Mode.
  • In openGL, mark atom, key length and key angle dihedral angle, etc.: In VMD Main, Mouse - Lable and select it. (Length unit is A, angle is degree).

3. When loading two molecules at the same time, how to show the two molecules with different colors?

Load two molecules into VMD at the same time.

  • In VMD Main, Graphics-----representations, adjust the selected molecules to change the coloring methods of both molecules to Molecule.
  • In VMD Main, Grapics---Colors---categories, change to Molecule, then select different molecules in Names and change their colors respectively.

4. How to create a different Rep and represent it in a different form?

  • Click on Create Rep and one will be created exactly like the existing one.
  • Next, let the shadow be placed on the newly created Rep, delete all in the section Selected Atoms, and enter the new one. For example, you can enter resname HEM; resname SO4 CO; or enter resid 93 64, etc. Remember to press enter after entering, otherwise it will not take effect.
  • Modify the respective Drawing Methods, for example, resname HEM can use Licorice, resname SO4 CO can use VDW, resid 93 64 can use CPK.

5. Display the structure of the protein, and display the color according to the secondary structure.

  • After loading in the protein, in Graphical Representations, change Selected atom to backbone and press enter, then all proteins except the protein skeleton will disappear.
  • In Graphical Representations, select NewCartoon, then in Coloring Methods, select Secondary Structure, and color the skeleton according to the secondary structure.

6. How to save HD pictures?

  • File --- Render... Open File Render Controls, then select Render the current scene using: as Tachyon, the two text boxes below are the default values.
  • Click on Start Rendering, at this point there will be an additional vmdscene.dat.tga file in the working directory.

7. With respect to the Selected atoms in the Representations section of Graphics, it can be described as follows:

  • Atoms within 10A of a residue: First create a rep, then enter within 10 of resid 94, which selects atoms within 10A of this residue.
  • x>5 selects all atoms whose x coordinate is greater than 5
  • mass>12 and mass<14 selects all atoms with masses larger than 12 and smaller than 14.

8. Calculate the rmsd of two molecules

  • First load the two molecules into VMD, for example, the IDs of the two molecules are 0 and 1 respectively
  • Then open TKConsole and enter:

1 set sel1 [atomselect 0 "backbone"]
2 set sel2 [atomselect 1 "backbone"]
3
4 measure rmsd $sel1 $sel2

Related Links

Applications of Visual Molecular Dynamics Software

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