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ePMV: INTERFACE GLOSSARY
by Graham Johnson and Fabian de Kok-Mercado
possible by Ludovic Autin, Graham
Johnson, David Goodsell, Michel Sanner & Arthur Olson
Download free, install, tutorials, gallery, forum
Get a Molecule:
1. Browse: Use to load ProteinDataBank (PDB) files from your computer
2. Fetch: Directly download PDB file variants with 4-character
code and an internet connection
a. PDB: Protein
Data Bank, pdb.org. This archive
contains 3D coordinates and detailed information about the structures of
molecules (proteins, nucleic acids, and macromolecular assemblies) that have
been experimentally determined by researchers using x-ray crystallography,
Nuclear Magnetic Resonance, homology modeling and hybrid methods.
b. TMPDB: Trans-Membrane
Protein DataBank, tmpdb.hu, files
from the PDB that are computationally determined by the website’s algorithm to
be membrane proteins. A TMPDB protein’s transmembrane region is centered at the
origin and pointed outward along -X, thus the YZplane connotes the center of
the lipid bilayer and “outward” depends on the compartment, but always points
from the deeper towards more superficial membrane-bound compartments to the
c. OPM: Orientations
of Proteins in Membranes database, opm.org.
Similar to the TMPDB, OPM takes transmembrane orientation one step further by
performing a TM molecular dynamics relaxation on the molecule before posting it into the database. An OPM
protein’s transmembrane region is centered at the origin and pointed outward
along +X, thus the XY plane connotes the center of the lipid bilayer. These
files also come with the hydrophobic boundaries of the particular membrane
shown as red (outer) or blue (inner) spheres. Not all membrane-associated
proteins fully cross the membrane (integral) so only one membrane indicator may
be shown for non-integral transmembrane PDBs. (red = superficial, blue = deep)
d. CIF: Crystallography
Open Database, aims to gather all available inorganic, metal-organic, and small
organic molecule structural data.
e. PQS: Protein
Quaternary Structure Query, makes coordinates available for likely quaternary
states for structures contained in the PDB.
1. Current selection: pulldown list of available selections.
Imported molecules are available by default. A user can access saved selections
of any type here as well. The state of the molecule (or selection) will update
the rest of the GUI to correspond. GUI actions only
work on the current selection!
a. Save as PDB: Save the current selection as a PDB file to your harddrive.
2. Add selection set using string or <keywords> :
subselections of the current selection can be made from the pulldown list of
provided keywords or by typing PMV selection syntax into the box. Sophisticated
selections can be made quickly and easily once familiar– asyntax glossary is
available at: ePMV.scripps.edu/documentation/epmv-overview
click on the instructions
link under Advanced Features
The overriding hierarchy is Molecule:Chain:Residue:Atom, for example, 1XYZ:B:ALA:CA,
will select all of the a-carbons
(CA) of all of the Alanines (ALA), in chain B, of loaded molecule 1XYZ.
Keywords provide common yet powerful shortcuts that can be used alone or
incorporated into more complex selections.
a. Picked: A
special keyword worth noting. Picked
scripts a selection set from atoms selected in the host hierarchy
(ObjectManager in C4D)
3. Save set: The selection string and state of the GUI that is
operating on the current selection can be saved and later accessed under the Current
a. Rename set: Rename a selection set that was saved with Save Set.
b. Delete set: Delete a selection set that was saved with Save
Set. The actual atoms won’t be deleted, but the selection set will no
longer be available under Current
Selection. Helps to cleanup the pulldown menu.
4. Delete atoms in the selection set: Always delete ePMV
objects using this button command–deleting from the
C4d object manager will corrupt your current ePMV project and functionality
will be lost. The atoms in the selection set will be deleted from the
ePMV object. Objects like MSMsurfaces will need to be rebuilt to see the
effect, but atoms will be updated immediately.
1. Lines: Redundant
menu item runs a script that checks the Lines
radio button with the same result.
2. Licorice: Runs a script that checks the Sticks radio button and sets the Stick Ratio to 1 to
create thick/rounded lines.
3. SpaceFilling: Runs a script that checks the Atoms radio button.
4. Ball+Sticks: Small atoms are connected with covalent bonds
represented as cylinders according to the proper chemistry. The Scale and Ratio
can be adjusted with the sliders.
5. RibbonProtein+StickLigand: One step button runs a script
that creates a cartoon ribbon for proteins and nucleic acids and a stick
representation for ligands.
6. RibbonProtein+CPKLigand: One step button runs a script that
creates a cartoon ribbon for proteins and nucleic acids and a spacefilling
representation for ligands.
7. Custom: Saves the state of the current selection as a
8. Save Custom As: Set the name for the custom representation.
1. Atoms: (CPK) Each atomj of a PDB file is represented by a
sphere that approximates the limits of its electron density or Van der Waals
radii. This spacefilling
representation gives viewers a better feeling of shape and space occupied by
the overall molecule, but in general is too visually complex to effectively
represent large molecules or assemblies. Colored by CPK (canonical atom colors)
relative radii of all atoms in the selected chain by scaling the base atom from
default of 1.
2. Sticks: Small atoms are connected with covalent bonds
represented as cylinders according to the proper chemistry. The Scale and Ratio can be adjusted with the sliders. A Ratio > 1 creates a Ball-n-Stick
model. Colored by CPK (by atom type) by default.
a. Scale: Adjusts
the relative radii of all atoms and bonds in the selected chain.
size ratio as baseAtomRadii/bondRadii
3. PointClouds: Each atom is represented as a point in space.
Displays where each atom lies but this shorthand representation shows no
further chemical information. The coordinates can be seen under the C4D Structure menu. You may note here that
the X and Z coordinates are transposed from the PDB file for each atom– this is
because the PDB coordinates are for a right-handed Cartesian coordinate system…
Cinema 4D uses a left-handed system.
4. Lines: Each atom is a point in space connected by covalent
bonds represented as lines. This is the default representation of most
molecular viewers. Useful for efficiently visualizing detailed chemistry at
close range. Rarely used in publication.
Backbone representations connect the a-carbons of each amino acid with
various geometry types– generally different cross-sections swept along a 1.5D
spline, where each anchor connects the a-carbons.
1. Ribbons (Cartoon): Stylized representation of a backbone
model where peptide regions that form α-helices
and β-sheets are widened
into a stylized form. This schematic illustrates the topology of the chain of
proteins and nucleic acids and is essential shorthand for communicating the
folding of biomolecules. Developed by Irving Geis and formalized by Jane
2. BeadedRibbons: A fully customizable ribbon cartoon reminiscent of the Fancy Ribbon style developed by MolScript in the 1990s and
popularized by PyMOL… with lots of bells and whistles
user to customize dozens of parameters in a large palette to create unique
styles that retain correct backbone geometry.
3. Armature: IK Joint
skeletons that can be rigged/bound to model. Use with caution as this feature
makes is very easy to create physically irrelevant structures that will make
content experts cringe.
4. Loft (Will Be renamed Sweep): builds a backbone spline into
a Sweep object to create a backbone worm
representation. The circle may be replaced with any cross-section spline
object. Easily animateable.
4.5 Loft will return in future editions…
temporarily on hold:
Builds a series of cross-section instances at each
alpha carbon from native host splines into a loft object. Will allow for fully
customizable cross-sections for helices, beta strands, turns and coils as well
as smoothly animated transition states.
5. Spline: Builds a spline with an anchor point at each a a-carbon.
A temporary bug requires you to switch from Cubic to Linear, then back to Cubic
in the Attributes Manager to get a smooth spline.
1. MSMSurf: Michel Sanner Molecular Surface. Imagine a rubber
skin wrapped around an Atoms
representation. More accurately, a probe
sphere is rolled around the entire molecule and the MSMsurface is a
resulting mesh that represents the probe’s closest approximation.
a. probe radius:
lower the radius, the tighter the skin is wrapped between the atoms because the
probe can “squeeze” into tighter cavities. A radius of 0.001 can create a
single mesh that approximates a CPK model.
density: Subdivides surface (adds or removes triangles)
2. CoarseMolSurf: Creates “blobby” models of molecules that are
more appropriate for complex mesoscale structures and assemblies such as
a. isovalue: Defines
the contouring threshold
b. resolution: Determines
the radius of the skin in relation to the atom surfaces
c. grid size:
the mesh detail (number of polygons in the mesh polyhedron)
3. Metaballs: Builds an atomic point cloud into a metaball
object to allow 3D animation users to build and adjust a crude surface with
more familiar settings. Future
versions will have color options. For now it can be colored using the APBS
approach on the website or by splitting clouds into atom types and using
proximal shaders with appropriate falloffs. Currently the best option for
smoothly animating surface representation conformation changes.
Some color types don’t affect certain representations.
Ribbons are not yet fully colorable by gradient options– each secondary
structure polyhedron will receive the color of the first amino acid in that
region. Many of the default colors can be altered via the color-coding palette–
Edit>ColorPalettes. After changing a color in the palette, the ColorBy:
dropdown must be reapplied to glue it to the current selection
1. Atoms Using CPK:
2. Atoms DG (polarity/charge): Colors hydrogen atoms the same
as the atom to which they are bonded. It also changes carbon to white, and uses
pastel shades for oxygen and nitrogen that do not carry a formal charge. Fully
saturated reds carry a negative charge and fully saturated blues carry a
positive charge. It highlights the shape of the molecule and also reveals
carbon-rich amino acids that interact with the cellular membrane. Go under
options>color palette to see color coding.
3. Per residue: Amino Acids or Nucleotides color coding scheme.
Change defaults with color-coding palette– Edit>ColorPalettes. This is
something PyMol requires a plugin for.
4. Per residue shapely: Residues color scheme derived from
5. Secondary structure: Color codes amino acids as belonging to
α-helices (default is pink),
random coils (white), and Turns (blue). Change defaults with the color-coding
palette– Edit>ColorPalettes. To color atoms/bonds/surfaces by secondary
structure, you must first build a standard ribbon
representation to the scene (it need not be visible, you can just build it once
then uncheck the box.)
Chains: Colors each amino acid chain differently. Change defaults with
color-coding palette– Edit>ColorPalettes. Works on all representations
except line and point.
7. Custom color: Click the color
box to define a color then apply it to your current selection.
8. Rainbow for N to C: Rainbow gradient from the N-Terminus
(translation start of protein) to the C-Terminus (end of protein/amino acid
chain). ROYGBIV in reverse (N=blue, C=Red) Communicates tertiary structure
associations and domain localization of relative regions of the linear peptide
sequence at a glance.
9. Temperature Factor: Spectral color scheme based on protein
anisotropic temperature (B factor). Used to describe attenuation of x-ray
scattering or coherent neutron scattering caused by thermal motion. (blue=cold,
10. sas area:
1. Create Texture Mapping for: Type the name of the ePMV
molecular object (name found in the ObjectManager hierarchy), that you’d like
to texture. Must be a polygonal
2. Using: Select the method you’d like to use to unwrap the
a. unwrapped mesh UV:
b. regular disposed triangle:
3. Create: Type the path to your current C4D file and give the
material a name, then click [Create]
Be Patient, large meshes can
take several minutes.
1. Overview: The Data
Player window is a context-sensitive scroll bar that allows you to do
things like efficiently play through multiple 3D conformations of a protein as
if in a movie, regardless of the representation style, or to adjust relevant
parameters, like the isosurface value of a volumetric 3D map file to create a
•Files that have multiple states of a PDB built into them
with the MODEL # syntax, e.g. NMR files, that get loaded into Get Molecule, will automatically appear
in the Data Player pulldown to allow
a user to scroll through all of the conformations.
•Other files that refer to a compiled data trajectory file,
for example, require you to load one state of the molecule as a PDB file, then
to load a trajectory file second. The PDB and the trajectory file must have the
exact same number of atoms in the exact same order and with the exact same atom
names- to ensure this, you should save a single PDB state from your MD program
or viewer at the same time you export your .xtc or .trj file. For example, on
our tutorial page, you can Get Molecule 1bta.pdb to build any representation of
the protein, and load 1bta.xtc in the Data Player to scroll through 1000
conformations of the protein that resulted from a molecular dynamics simulation
performed by Ludovic Autin using GROMACs.
We recommend using the lines representation for fast scrolling, but they
all work (be careful scrolling with a surface representation.) You need to
rebuild ribbons after you stop scrolling to see the updated conformation.
As of July 2011, you must first load any PDB file before
you can load a 3D map file to trigger the necessary libraries into action.
2. Browse: Browse your harddrive(s) to load a data file of one
of the types listed under the <e.g.> pulldown.
a. e.g.: A list
of the different file types you can load (not all are perfectly functional as
of July 2011 beta)
3. Apply: Applies the step
value associated with the trajectory or map file to the data selected in
this pulldown, e.g., you can have more than one trajectory file loaded for a
molecule but the one selected here will be applied to the current selection
(assuming the atoms matched as described in the Data Player Overview above.
4. Step/Value: A context sensitive value displayed and
adjustable here will alter a relevant parameter specific to your filetype as
described in the Data Player Overview
above. It will automatically adjust to display a relevant range (e.g. .map
files have negative reals and .trj files have only as many positive integers as
are in the file.)
1. Open: Open an existing python command that comes installed
2. Save: Modify an existing command or type your own and save
it to disk here.
3. Command line: Type Python commands you want to execute here.
This command box is the same as the default command line, but offers more space
and syntax color for easier coding.
4. Exec: Click to execute the python script visible in the
ePMV: TOP MENU
by Graham Johnson and Fabian de Kok-Mercado
possible by Ludovic Autin, Graham
Johnson, David Goodsell, Michel Sanner & Arthur Olson
1. Recent Files:
2. Open PDB:
3. Save PDB: Allows user to save a pdb file modified in the
host, does not save ePMV settings, only atomic
coordinates. To save the ePMV settings, just save your host file using
File>SaveAs in the host GUI menu. In
August 2011, you’ll be able to rebuild the exact connection and ePMV GUI state
of your host molecules.
4. Open Data: Same as the Data
Player [Browse] button
a. Center Molecule:
Translates the atoms from the crystallographic coordinates to position the
molecule’s center of mass at the origin of the host scene upon loading
b. Femove Water:
Deletes waters from the ePMV instance of the PDB file upon loading.
realtime: Enables changes that a user or function makes to atom positions
in the host viewport to alter the underlying ePMV instance of he molecule. If
checked, saving a PDB file after moving atomic spheres or points will generate a modified PDB file with
coordinates that reflect the changes. Simulators like Extensions>Modeller
will allow for realtime molecular dynamics in the viewport following user
d. PMV camera:
Adds a host camera to the scene with settings that exactly match the default
camera in the PMV viewport exactly. (PMV is the standalone molecular viewer
that underlies ePMV.)
e. Use progress
bar: Show a progress bar in the host’s native GUI when an ePMV process
takes more than a few seconds to let you know that ePMV is still calculating
f. Split bonds:
Generate two bond instances at each bond (one from each covalent participant)
instead of one bond instance that has a gradient color. By default, this would
create a grey and a red cylinder meeting in the middle of a carboxyl bond which
could add geometry and cause issues when rendering stick models with
downloading on Fetch: If you fetch different instances of molecules with
the same name as one that still exists in the PMVdownloadedMoleculeCache, the
cached version of the molecule will be used. This is faster but causes an issue
if you want to, for example, load the PDB, TMPDB, and OPM version of a
transmembrane protein (they have the same name from each database e.g.,
1xyz.pdb) into the same scene to compare the different files. Unless this box is checked, the version
of the molecule first fetched would be used each time. Forcing download will
import the molecule desired from the correct database regardless of the
molecules name at the database or in cache.
h. PMV light:
Adds a host light (or sun) to the scene with settings that exactly match the
default light in the PMV viewport exactly.
i. Use Modeller:
When checked, if a PDB file is loaded from the harddrive (won’t work if
Fetched), a new Modeller-specific version of the PDB file will be generated in
the same directory with cleanups needed by Modeller to perform MD simulations. For example, with Use Modeller checked, ePMV will save 1crn.pdb, when loaded to a new
file 1CRNm.pdb in the same directory and 1CRNm.pdb will be loaded instead of
1crn.pdb as indicated in the Current Selection pulldown name..
j. Use PyMol:
Allows PyMOL geometry to be loaded into ePMV directly, e.g., (Molscript style
beaded ribbons, Caver, relaxed models, Ligand functional group Building, etc.)
k. Center Grid:
Center 3D grids that correspond to molecules or volumetric maps- similar to
Center Molecule as described above.
l. Synchronize data
player to time: When repaired in August, this will allow you to scroll
through the current data player using the host timeline controls to easily set
up keyframes, etc.
1. Steps every: Take this many time steps…
2. Frames: …
per this many host-timeline frames.
2. Color palettes
a. atoms type: refers
to Atoms Using CPK
b. atoms polarity
type: refers to Atoms DG
c. residue type: refers to Per residue
d. residue shape
type: Refers to Per residue shapely
structure: refers to Secondary
f. chains: refers
g. reset to: reset
all colors to the PMV defaults
h. set color: apply the colors you altered to the vector based and independent materials
3. Delete water: Remove all water molecules from the ePMV instance of the PDB file
hydrogens: Remove all hydrogens from the ePMV instance of the PDB file
b. add hydrogens: Build hydrogens onto the current selection obeying rules of chemistry.
3. Biological unit: Many molecular structures exist in quaternary conformations in cells that are
different from the quaternary conformations revealed in the crystallized state.
The default download for 2plv.pdb (polio virus capsid protein, for example,
does not look like a spherical (icosohedral) capsid that you see representing
the infamous biological state of this molecule. The protein data bank provides
two mechanisms that allow molecular viewer software to show biologically
relevant version. On the PDB website, you have the option of downloading the
Asymmetric unit or the biological unit(s). The biological unit and asymmetric
unit are often the same, for example, in 1crn.pdb (you can toggle back and
forth between static representations of them in the PDB image view at pdb.org.)
You have the option of downloading the biological unit (sometimes there is
more, which in the case of 2plv.pdb will be a file 60x larger than the
asymmetric unit. The other choice is to download a properly formatted, modern
version of the asymmetric unit and to construct the other biological units from
a list of matrix transformations found in the newer versions of the files
(REMARK 350 lines).
Edit>Biological Unit does this for you.
a. Edit>Options: Uncheck Center Molecule
Edit>Biological Unit: Copy and paste the name of the ePMV representation
that you want to instance into the box, hit run, and wait. If there are BIOMT coordinates in the
REMARK 350 lines of the file, a new parent will appear with the appropriate
number of instances below. Some
molecules will have only one representation that fits over the original exactly
(i.e., the asymmetric unit = the biological unit), Some will have a simpler
molecule (i.e., the biological unit is smaller than the asymmetric unit), and
some will be larger, a dimer, a trimer, a multimer, with certain viruses having
several hundred copies of the asymmetric unit in the Biological unit.
transformation: PDB model elements moved by the user (such as changing the
position of an atom(s), will be applied to the underlying PMV model.
a. From: Picks which modified elements to send back to the
1. Cpk: Send
coordinate changes of Atom from viewport to the model
2. Lines: Send
coordinate changes of PointCloud under lines from viewport to the model
3. Bones: Send
coordinate changes of bones to associated atoms to the model
4. Splines: Send coordinate changes of viewport splines to associated atoms
Up to date descriptions of third party modules that extend
ePMV functionality and installation instructions can be found under the
Extensions button on the wiki at http://ePMV.scripps.edu Although the following menu items exist
in the default install, some of them require the installation of additional
python software as instructed on the website.
Electrostatics (plugin): Allows any geometry with a UV coordinate tag to be
colored by an electrostatic potential map that is either imported or generated
directly from a model in the scene. The user can, for example, import a
molecule, generate an APBS color grid based on the atoms in that model,
generate a host sphere, convert the sphere to polygons, and map the
intersecting colors from the grid onto the sphere
d. normal offset
e. std scale
f. geometry color
c. type of score
d. Display label
e. Real time
f. Color Rec
h. Color LIg
3. Add an Extension
THIS SECTION IS INCOMPLETE- Please check back in late August 2011!
1. About ePMV:
useful to see the current version and contributing authors and any licensing or
copyright needs as they come up.
documentation: links to the current user manual and reference files on the
epmv.scripps.edu wiki website
3. Check for Update:
As of version 0.3.2, this button will offer you a chance to automatically
update your ePMV software. It provides the option to archive your current
version in case you prefer to revert by hand. You can opt to keep up with the
latest experimental build that may change daily, or to retain the stable
version of the software until the next stable release is avaialbe- either way
you can update in one click with this menu item.
Information: Several contributing algorithms need to be cited if you plan
to publish a modified version of the software or refer to it in a paper. We ask that images made with ePMV,
especially journal covers, additionally cite ePMV- for example, Cover image created by John Doe with ePMV…