![]() ![]() VMD will automatically recognize the file type to be loaded. New Molecule allows a new molecule to be loaded, Load Data into Molecule allows appropriate data like the psf file or the trajectory file to be loaded. 5Ħ Menu File All options are available once any loaded molecule is highlighted. vmd console The vmd console is an information window (Fig. Vmd OpenGL window with atom, bond, angle and dihedral labels shown. ![]() For more options please see menu Mouse below. The other option is to use Main menu Graphics Labels please see below. ![]() Note: to hide atom, bond, angle and dihedral labels it is enough to click again on appropriate atoms. Information about the selected atoms will appear also at the vmd console window. The cyan green label for the selected atoms and additionally the cyan label with the angle (in degs) will appear (Fig. To switch-on the selection mode press 4 on the keyboard and then click on any four atoms. 8) Select and measure the dihedral between selected atoms. The green label for selected atoms and additionally the yellow label with the angle (in degs) will appear (Fig. To switch on the selection mode press 3 on the keyboard and then click on any three atoms. 7) Select and measure the angle between selected atoms. The green label for selected atoms and additionally the white label with the distance (in Å) will appear (Fig. To switch-on the selection mode press 2 on the keyboard and then click on any two atoms. 6) Select and measure the distance between two atoms. This will state the molecule id, trajectory frame, atom name, atom type, atom index, 3Ĥ residue name, residue id, chain name, segment name and x, y, z coordinates of the selected atom. Simultaneously additional information at the vmd console will appear. The green label containing residue name, number and atom type will appear (Fig. To switch-on the selection mode press 1 on the keyboard and then click on any atom. If you come back to the rotation mode you will see that now the protein rotates around the chosen atom. To switch-on the center mode press c on the keyboard and then click left on the chosen atom. Scaling is also possible in the rotation or translation mode by rolling the middle mouse button. To switch-on the translation mode press s on the keyboard and then press the mouse left key and translate. To switch-on the translation mode press t on the keyboard and then press the mouse left key and translate. Usually the rotation mode is the default 2) Translate the protein. If it does not work press r on the keyboard to switch-on the rotation mode. In the VMD OpenGL display window the user can: 1) Rotate the protein. VMD OpenGL The VMD OpenGL (Fig.3) is the main graphic window in which the molecule is displayed. If the trajectory is loaded, this window allows the user to play, stop and pause the trajectory, to select a particular frame number to be displayed, to choose if the trajectory should be played once or in a loop or to change the speed (how fast the trajectory is played). To change T, A, D and F it is enough to double-click on them. Each molecule has its ID, T (Top), A (Active), D (Displayed) and F (Fixed) options, the information about number of atoms in the structure and the number of Frames loaded is given. 2) is a VMD control window, which contains all sub-menus and also shows all loaded molecules. ![]()
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