Introduction to PMV
Note: This is the print view with all the tutorial pages on one page. The paginated version is available here, if you prefer that.
Before we start
First of all, you don't need to know Python in order to use Python
Molecular Viewing (PMV). However we do recommend to have PMV installed
so that you can follow this step-by-step tutorial. PMV is distributed
with MGLTools and we assume that you have downloaded
and successfully installed MGLTools. If not, click on the Download
tab and follow installation instructions. Once
MGLTools is installed, start PMV either by clicking on the PMV
icon () or by running the pmv script. The default startup configuration has the Menu, Toolbar and 3D Viewer
shown in the screenshot on the left.
This tutorial covers most commands in the Menu and Toolbar; click Next to get started.
| Download 1KES.pdb, click on
PMV currently supports reading these file formats: pdb, mol2, pdbq, pdbqs, pdbqt, cif, pqr. Click on ‘-‘ in file browser widget to list all supported file extensions.
When molecules are loaded, by default, PMV displays white lines drawn between bonded atoms. You can directly interact with the molecules in the PMV Viewer with your computer’s mouse or touchpad.
Press N on the keyboard to bring current object to the center of the screen.
Press D to toggle depth cueing.
Press R to reset (i.e. undo all previous transformations).
Mac users: make sure that middle button is set to "Button 3" in Apple → System Preferences ... → Keyboard & Mouse. You can also emulate three button mouse by going to X11 → Preferences ...
Coloring by atom type
To that end, click on
Hydrogens (H) - cyan
Carbons (C) - gray
Nitrogens (N) - blue
Oxygens (O) - red
Sulfurs (S) - yellow
Phospors (P) - magenta
All others - green
You could change PMV preferences so that all new molecules are colored by atom type. This is done by usingSince hydrogens are difficult to resolve with X-ray, we are going to add them using
Click OK to add missing hydrogens.
Distance and Shift-click on any atom of interest. A yellow sphere should appear on underlying atom. Now, Shift-click on another atom to measure the distance between these two atoms. Similarly, you can use
Torsion to measure angles or torsions.
Changing material properties
Click on button off the Toolbar to open DejaVu GUI. DejaVu uses scene-graph to organize objects in the scene and you can use the GUI to control different properties of the objects. Click on + to navigate object hierarchy and select MSMS-MOL geometry. To change opacity of the surface, click on Front button next to Material. This opens Front Material Editor shown below where you can control opacity by moving Opacity slider. You can also alter front polygon mode by clicking on Front button next to Polygon mode and selecting one of the options (point, line, outlined, etc. ).