Table 1.

Graphic User Interface (GUI) functions available in ePMV v0.0.2a Related to Figure 3

GUI section	GUI Feature	Descriptive example
Data access	File System browser	Load a local PDB file
	Fetch from web	Download to cache and then load a PDB file from the internet directly from the ePMV GUI without opening a web browser.
	Database pointer	Specify to fetch from a variety of optional databases, e.g., Optimized Membrane Protein or Transmembrane Protein Data bases, or load CIF or PSQ versions of the data.
Selection	Current selection:	Choose a molecule or a previously saved custom selection set
	Add selection set	Make a selection using PMV commands or dozens of provided keywords to make chemistry based selections
	Save, rename, or delete selection sets	Save complicated selections for later access. Rename the defaults to easily track numerous and complex selections. Delete unwanted selection sets without affecting the actual atoms
	Delete the atoms	Remove atoms defined by the current selection set (atoms are deleted from the host view as well as from the underlying model.)
Representation	Choose from preset Representations	A present representation will turn on and adjust parameters of the various appropriate standard representations
	Atoms	Spacefilling or CPK representation with each atom represented as a sphere with van der Waals radii and a single radius scaling slider
	Sticks	Atom and bond representation with a scaling option and an atom/bond radius ratio slider
	Ribbons	Cartoon backbone representation
	Loft	A smoothed cartoon backbone that uses host-based lofting technologies (morphing a smooth skin from one 2D cross-section shape to another) to create a single mesh. Users can access host tools to alter the transverse profiles of coils, helices and sheets independently or universally. Useful for animating transition states to avoid binary flickers in secondary structures while morphing between conformers.
	Armature	A joint/bone technology ubiquitous in hosts allows molecular models to be animated with kinematics rigging techniques and tools.
	Spline	A multipurpose 3D curve drawn between atoms can be used for animating joints and backbones or for creating a smooth worm model backbone or a linear CA trace for example.
	Metaballs	A surfacing technology ubiquitous in hosts that skins clusters of points, splines, or spheres. It can make a smooth skin between disparate geometry types and can be used, for example, to maintain a smooth and continuous mesh surface over a dynamic molecule.
	MSMSurf	Standard “solvent excluded” molecular surface representation with an adjustable probe radius
	CoarseMolSurf	Standard Gaussian-based coarse molecular surface representation with adjustable isovalue and resolution sliders
	Color scheme:	Color representations using a variety of color schemes, e.g., Color By: atom type, residue, secondary structure, temperature factor, etc.
Data Viewer	Disk Browser	Load a variety of data file types such as Molecular Dynamics files (trj, xtc) or Volumetric grid Maps (e.g., mrc, ccp4, map, etc.)
	Apply Data	Select which loaded data file to apply to the current geometry
	Data Player	Context sensitive numeric slider bar will set appropriate ranges and adjust the parameter accessible in the data file. Loading an NMR structure in the Data Access Panel will set the player to a range from 0 to the number of structures in the PDB file and the slider can be used to scroll through them Loading a .ccp4 file will set the data player to adjust the isocontour value.
Script manager	Open	Open a python script from library of premade scripts or from a custom file on the hard drive
	Save (as)	Save a copy of a custom script or save a new version of a modified default script
	Script window	Access the full functionality of PMV and other python applications by typing or pasting script text into this window. For users unfamiliar with PMV’s python syntax, every action performed in PMV has the corresponding command written to a log file, which can be copied and pasted into ePMV.