Pymol User Interface

PyMOL User Interface

Upper Control Window The Upper Control Window is where the main drop down menus are located. These menus control files, settings, and tools. Other points of interest in this window are the Ray button in the top right and the command line entry point along the bottom.

PyMOL Viewing Window Object Control Menu

The Object Control Menu is used to control atoms/molecules (called objects), and sets of atoms/molecules (called selections). This menu and its many pop-up menus allow a lot of control Z Axis over how objects are represented in the PyMOL Viewing Window.

X and Y Axes A=Action S=Show H=Hide L=Label C=Color

Mouse Controls In the PyMOL Viewing Window molecules can be viewed and directly interacted with. In this window, the camera PyMOL’s mouse controls for moving the and molecules can be moved and rotated, sets of atoms Zoom camera in the PyMOL Viewing Window can be selected directly by clicking on the molecule or by Rotate utilizes a virtual track ball. Holding the clicking in the Sequence Viewer located at the top, scenes left mouse button while the pointer can be changed and updated via the scene buttons in is inside the molecule will cause the the lower left hand corner, movies can be controlled with camera to rotate along the X and Y axes. Translate If however the pointer is outside the the movie bar controller in the bottom right, and model and Clip representation of individual atoms can be changed by molecule, the camera will rotate along right-clicking on the molecule to call up pop-up menus. the Z axis. Common Operations in PyMOL Loading Molecules Representations Display and Settings Programmed Movies

Upper Control Window: PyMOL has many options when it comes Many display options and other effect settings PyMOL is a very powerful moviemaker with many File > Open > to representing molecules many of which can be controlled from the Display and Setting sophisticated options, however there are also can be controlled from the Object Control drop down menus located in the Upper Control several pre-programmed movie options available Plugin > PDB Loader Service Menu via the single letter pop-up menus Window. for the beginner to use. and can be applied to both Command Line: objects and selections. Example Commands: Example Commands: load “file name” Display > Sequence Movie > Program > Camera Loop > Example commands: fetch “pdb_code” starts up the Sequence Viewer Y-roll-> 4 sec > as > cartoon Display > Background > White creates a movie that rotates 360˚around shows a cartoon representation only the Y-axis in 4 seconds Mouse Controls sets the background color white > sticks Movie > Program > Scene Loop > Left button: Setting > Transparency > Surface > 50% adds sticks to the current representation Nutate > 4 sec Hold: rotate sets transparency of all surfaces to 50% > waters creates a movie that loops through stored Setting > Rendering > Shadows > None Click: select (residues by default) hides waters from the current scenes and oscillates them for 4 seconds representation turns off shadows during ray tracing Right button: > preset > ball and stick Setting > Edit All... Saving and Exporting Files Hold: zoom brings up a new window with all settings classic ball and stick representation Click: pop-up menu It is important to save your work and very easy to > residue Scene Control export your figures and movies. Center button: labels residues with three letter code and Example Commands: Hold: translate number Scenes are snapshots of the PyMOL viewing area that include all of the representation information File > Save Session As... > blues > marine Click: center on atom as well as the camera position. Changing and saves the entire contents of your PyMOL Scroll: adjust clipping plane colors the representation marine updating scenes is very easy from the PyMOL session Viewing Window if you turn on the Scene Buttons. Click , then Selections File > Save Image As > PNG... Example Commands: exports a ray traced image Selections in PyMOL are sets of atoms and are differentiated from objects by Scene > Append the use of ( ) in the Object Control Menu. The default selection is (sele) which Movie > Ray Trace Frames, then is automatically created upon selecting any atom or residue. To start a second stores a new scene File > Save Movie As > MPEG/QuickTime selection, rename (sele) and deselect it, then start a new selection. Scene > Buttons exports the current movie and ray traces every toggles the interactive scene buttons in the frame Creating selections: PyMOL Viewing Window Left mouse button Further Help Clicking on the molecule will select/deselect resides by default Measurement Wizard PyMOL has a diverse and active community, and much of PyMOL’s functionality can be learned Sequence Viewer PyMOL has a built-in measurement tool, for from community-sponsored resources and distances, angles, dihedrals, and neighbors. Display-> Sequence professional support. Left click and drag on sequence to select/deselect large portions of the Wizard > Measurement molecule starts the measurement wizard visit www.pymol.org/support (distance by default) Renaming a selection: Click to toggle measurements > > rename selection > delete and retype new name pick atoms as directed