- Quick start
- Data input
- Graphical 2D representation
- Variability measurements
- Identification of contacts
- Integration with POLYVIEW-3D
- Tips and tricks
POLYVIEW-MM (Molecular Motion) enables animation of
trajectories generated by Molecular
Dynamics and related simulation techniques, as well as
visualization of alternative conformers, e.g., obtained
as a result of protein structure prediction methods or
small molecule docking, using an intuitive web-based interface.
The server integrates high quality animation with structural
annotation of molecular motions, and allows both
qualitative and quantitative analysis of the results of
macromolecular simulations. In order to facilitate
structural analyses, POLYVIEW-MM combines:
interactive view and scripting-based conformational
analysis using Jmol and its tailored extensions;
versatile annotation and publication quality animation
using PyMol / POLYVIEW-3D;
motion-at-a-glance using customizable 2D summary plots of
changes in secondary structure states and relative solvent
accessibility of individual residues in proteins;
distance plots and analysis of intra- and
In addition, POLYVIEW-MM integrates
visualization with various structural annotations, including
automated mapping of known interaction sites from
structural homologs, mapping of cavities and ligand
binding sites, transmembrane regions, and protein
Abbreviations used in this document
SS - secondary structure; SA - solvent accessibility; RSA - relative
solvent accessibility; MD - molecular dynamics; PDB -
protein data bank; NR - nuclear magnetic resonance; DSSP
- dictionary of protein secondary structure (software).
- Specify a coordinate file with multiple models of the molecule,
e.g., PDB code for a NMR structure with multiple
models or a user generated file with MD trajectory snapshots
- Select the type of motion analysis; currently available options
include: MD or other trajectory; Morphs or distortions
along normal modes; Protein-protein/DNA docking models;
Protein-ligand docking models (for the latter,
DLG or another PDB file with ligand poses needs to be specified)
- Submit request to the server
At present, POLYVIEW-MM accepts the coordinate file in the PDB
format with multiple models; trajectory files in the
DCD format (used by NAMD and CHARMM), as well as the TRR format
(GROMACS). DCD and TRR coordinate files are supposed
to be accompanied by the structure definition files
(PSF and GRO, respectively).
For the analysis of small
molecule docking, the DLG format used by the popular
AutoDock program is accepted as well.
Coordinate files derived from other MD programs
should be converted to PDB or DCD or TRR files beforehand using, for example,
The file size should not exceed 50MB limit, otherwise the request
will be rejected.
To reduce upload time, coordinate files can be submitted
compressed by ZIP, GZIP, or BZIP2 (file extensions zip,
gz, and bz2, respectively).
Trajectory analysis requires more computational resources and
CPU time, so these requests will be sent to the cluster and
queued. However, once analysis is concluded, further
operations with images are processed interactively.
Optionally, an e-mail address can be specified to receive a link
to view the results once the job is completed.
Multiple models are supposed to be defined using the PDB cards
MODEL/ENDMDL (see example below).
ATOM 1 N VAL A 1 0.965 0.298 -0.467 1.00 1.00 N
ATOM 2 CA VAL A 1 1.811 0.250 -1.701 1.00 1.00 C
ATOM 3 C VAL A 1 3.290 0.400 -1.320 1.00 1.00 C
ATOM 4 O VAL A 1 3.628 1.053 -0.346 1.00 1.00 O
ATOM 407 HG23 ILE A 29 10.152 9.942 -22.140 1.00 0.00 H
ATOM 408 HD11 ILE A 29 10.543 11.167 -18.839 1.00 0.00 H
ATOM 409 HD12 ILE A 29 9.594 10.221 -17.693 1.00 0.00 H
ATOM 410 HD13 ILE A 29 11.306 10.511 -17.391 1.00 0.00 H
TER 411 ILE A 29
ATOM 1 N VAL A 1 0.740 0.226 -0.858 1.00 1.00 N
ATOM 2 CA VAL A 1 1.662 0.223 -2.037 1.00 1.00 C
ATOM 3 C VAL A 1 3.117 0.317 -1.561 1.00 1.00 C
ATOM 4 O VAL A 1 3.411 0.923 -0.545 1.00 1.00 O
ATOM 407 HG23 ILE A 29 10.809 10.803 -20.297 1.00 0.00 H
ATOM 408 HD11 ILE A 29 11.414 10.731 -16.815 1.00 0.00 H
ATOM 409 HD12 ILE A 29 10.441 12.035 -16.132 1.00 0.00 H
ATOM 410 HD13 ILE A 29 10.422 10.438 -15.385 1.00 0.00 H
TER 411 ILE A 29
POLYVIEW-MM provides insights into molecular motion by enabling a quick
analysis of conformational changes in terms of
SS, SA/RSA (Figure 1),
Phi/Psi angles (plain text only),
as well as intra-molecular contacts (Figure 2).
Several types of
customizable 2D plots can be generated as described below.
The initial view of SS/RSA changes includes the following elements: residue
numeration, amino acid sequence, corresponding variability
measure, and SS states (or SA/RSA bins) encoded by
colors. On top of it, a grid is placed for the easy tracking
of changes along the extended trajectories. Each cell of
represents 10 residues in 10 consecutive models. Any
element of the image mentioned above can be removed using a
web-form accompanying the image. See examples in
Figure 1, panels A-F.
For initial visualization, all eight SS states are used
(G, H, I, T, E, B, S, and C), but they can be optionally
reduced down to three states (H, E, and C). See example
in Figure 1, panel G.
|Capturing changes in SS states
|Capturing changes in RSA states
Figure 1. Examples of the different views of protein
motion based on the ensemble of 25 NMR models (PDB code
A and I. Annotations produced with default settings
after the initial data submission.
B-F. Resulting images
after hiding individual annotation elements described
in the text above.
G. View of motion after reducing
the number of SS states (in particular, T and S were
converted into C).
H. Image after switching the
variability measure to 8 states entropy.
in terms of SA changes, with variability measured by RSA and
SA variances, respectively.
|Capturing changes in contacts
Figure 2. Examples of different views of inter- (panels A, B) and
intra-molecular (panel C) contacts.
A. Analysis of
the contacts between protein and ligand. The models were
produced using a docking simulation. Files containing
structures of the receptor and ligand poses are
available for download from here (
), as well as from the home page of POLYVIEW-MM.
As can be seen from the contacts summary, while the majority
of poses were found energetically favourable near the
residues 373-377 (NDLQT), one binding mode (model 5)
indicates an alternative location of the ligand binding
with low estimated energy (residues 335-337, TQT).
B. Analysis of the interchain contacts for the first
chain of a protein-protein complex obtained using a protein docking
simulation. Example of the docking models is available
as well as from the server home page. Frequency bars
allow the user to quickly identify the residues of one chain most
frequently observed in contact with the second chain.
C. Analysis of the distance fluctuation between
residues 1047 and 1151 (alpha carbons; atom IDs 2 and
1596, respectively) in the NMR-derived 3D structure of
the nucleotide binding domain of the human Menkes
protein (PDB ID: 2kmv). The chart shows high flexibility
of the extended loop, as the distance from the tip of the loop
(D1151.CA) to the N-terminus (S1047.CA) varies between 5.4 and
Pictorial definitions used in POLYVIEW-MM for protein representation
||Amino acid residue numeration
||Indicator of variability (for SS/RSA)
||0 - the least variable (rigid),
||9 - the most variable (flexible)
||Frequency of contacts
||0 - least observed in contact,
||9 - most frequent in contact
||Relative solvent accessibility (RSA)
||0 - completely buried (0-9% RSA),
||9 - fully exposed (90-100% RSA)
Secondary structure color codes
| G || 3-turn helix|
| H || 4-turn helix|| |
| I || 5-turn helix|
| E || extended strand|| |
| B || residue in isolated β-bridge|
| C || unstructured loop, coil|| |
| T || hydrogen bonded turn|
| S || bend|
| X || gap in structure|
SS and SA are calculated using the DSSP program.
To collect statistics on structural changes, eight (G, H,
I, T, E, B, S, and C) and three (H, E, and C) SS states
are used as
defined in DSSP.
RSA for a residue at a given position is SA normalized by the
maximal value of the solvent exposed surface area for a
given type of amino acid. Thus, RSA adopts values between
0 and 100%, with the latter corresponding to a fully
Per-residue variability of the abovelisted characteristics throughout trajectory is
measured using the following statistics.
- Entropy of SS:
S = −K · ∑ pi · log(pi),
where K is a normalization factor K = 1 / log(N);
N - number of SS states (8 or 3);
pi - probability of i-th state.
This measure provides the insight as to how many SS states a
given residue was involved in through the trajectory.
- Counts of hoppings between SS states
This measure indicates how often a given residue changed its
SS state through the trajectory.
- Variance of SA and Variance of RSA:
s² = 1/(n−1) · ∑(yi − mean(y))²,
where n is the number of conformations in trajectory; y -
respective SA and RSA observed at the sequence position
i; mean(y) - the average value of SA (or RSA) for the i-th
amino acid across all structural models. The first
measure is more sensitive to minor changes in SA compared
to variance of RSA.
- Frequency of contacts
When analysis of protein-protein, protein-DNA, or
protein-ligand docking models are requested, per-residue
frequencies of being in intermolecular contact are computed
throughout the models.
All measures are normalized to the corresponding
maximums observed across all residues in one protein
chain. All computed
statistics are used in visualization and available for
download in the plain text format.
Following previous studies, we define protein-protein interaction
sites based on the RSA change upon complex formation, i.e.
RSA difference between an unbound and bound (complex)
structure of an individual chain. The procedure and thresholds
used to assign an amino acid residue as an interaction site
can be found in the
Protein-protein interaction interfaces
can be characterized in terms of the surface area buried upon
complex formation, amino acid properties, and the presence of
conserved hot spots, facilitating analysis of protein docking
simulations, for instance.
Protein-ligand contacts are
determined using the respective procedure adopted in
and subsequently in the
FirstGlance in Jmol
server (FGiJ) that accounts for hydrogen bonds, water and salt
bridges, hydrophobic and aromatic ring interaction, and
different types of metals binding. For the corresponding bond
distance definitions, the reader is referred to the
Mapping specific residues in contact with the
ligand in alternative poses of protein-ligand complexes can be
used to assess the results of docking simulations. Consistency
of interacting sites observed in protein-protein or
protein-ligand docking models is measured by computing
frequency of being in contact with the interacting co-factor.
Interactive 3D visualization is provided using the Jmol java applet. It
allows the user to animate a trajectory at different rate and access to a specific
model. High quality animation is available via the link to
POLYVIEW-3D provided at the resulting page. The images produced
can be placed into PowerPoint slides or other electronic
resources. No additional installation necessary
for using both Jmol and POLYVIEW-3D. Figure 3 provides links to
animations generated using different types of molecular simulations
and deposited to the
Click on each thumbnail to view a full sized animation.
Figure 3. Examples of the different types of molecular
A. Animation showing the ensemble of NMR
models for calmodulin indicates likely extent of
conformational changes in solution. Backbone of the
protein is rendered and colored according to SS states it
B. MD trajectory for a resilin-like elastomeric
peptide with Tyrosine side chains shown to underscore
their propensity to be in contact.
C. Alternative poses of the fucose ligand with
respect to a Norovirus capsid protein obtained from the
ligand docking simulation.
For the interactive analysis of conformational changes using Jmol, the
following options are provided in addition to those built-in
the Jmol applet and accessible via right-mouse click on the
Browse models The user can review the
structural models successively by using the buttons
Prev on the form. It is also
possible to jump to a specific model by typing its number in
the text field and pressing the button
Jump to. The order number of the currently
presented model is reflected at the Jmol pane at the top left
corner. In addition, all models can be viewed
simultaneously using the button
Animate models Available conformations of the
submitted macromolecular structure can be visualized as
animation using a single run through all models
Once), endless loop starting each time
from the first model (
Loop), and endless
reversible loop when models enumerated from the first to the
last and backward, from the last to the first
Reversible Loop), with additional
pauses at the terminal models. The rate of animation can be set
in terms of
frames per second (fps) using the
corresponding text field.
Custom Jmol commands The user can
manipulate Jmol in order to change/improve the
structure rendering. Multiple commands separated by semicolon
can be specified in the corresponding text field and then
applied using the
The same can be achieved from
the Java console, which is available from the context menu of
the Jmol pane (right-mouse click). The syntax of the commands
can be found in the
Highlighting Residues can be highlighted
using colors with side chains rendered as sticks as opposed to
the ribbon rendering of the overall atructure.
Available colors are
red, green, blue, cyan,
magenta, and yellow. Colors are specified
by their corresponding first characters.
In case of macromolecules with multiple chains, a chain label for residues of
interest needs to be specified as well.
Numbers of residues to be highlighted should be enumerated with
comma delimitation (white spaces are ignored). The use of dashes
to define a range of numbers is also supported.
The syntax of the string used to specify residues to be
highlighted is the following:
[Chain_label:]Residue_number[:Color], where '[ ]'
denotes optional parts of the string. Capital letters R, G or B
are used to highlight a residue in both color and bold font
style, whereas lower case characters result in highlighting by
the corresponding color only.
Below are several examples:
A:145:r - highlight the 145th residue in chain A using red
C:5-10 - highlight residues from 5 through 10 in chain C
using sticks to show their side chains
14-17,25-30,43:b - highlight residues 14, 15, 16, 17, 25,
26, 27, 28, 29, 30 in the first chain by showing side chains and blue
color for a residue 43
A:3,A:10-20,A:35,B:15-20,B:25,B:40 - highlight residues
3, 10-20, 35 in chain A and residues 15-20, 25, 40 in chain B by
showing their side chains.
To facilitate the conversion of the residue list to the required
format, a separate web-form is provided via the link
Converter on a resulting page.
Contact analysis This set of options appears
only when Jmol successfully loads the macromolecular
structure. The user can type in or click on a pair of atoms of
interest to review the distance fluctuation between these
atoms throughout the trajectory. Distance can be measured in
angstroms, nanometers, and picometers. Distance fluctuation
for a given pair of atoms can be retrieved either as a chart
or in the plain text format. If multiple atom pairs were
chosen, the data are retrieved for the last selected pair only.
Integration with POLYVIEW-3D
POLYVIEW-MM allows to display trajectories and multiple conformers
using interactive animations and static views in Jmol, coupled
with tailored selection and annotation options. These can be
subsequently imported into POLYVIEW-3D in order to generate
publication quality static pictures and animations using the PyMol
rendering. The POLYVIEW-MM resulting page contains a link to POLYVIEW-3D
that passes to the latter the coordinate file, current
orientation of the structure in Jmol pane, and zooming factor.
All movies and plots generated by the server can be
deposited with user-defined annotations to an image library as a
mechanism to document and share data with colleagues.
Details regarding the use of POLYVIEW-3D to generate high quality
images and animations can be found in the POLYVIEW-3D
Tips and tricks
Below are some tips that help make some tricks with
the interactive Jmol view and images of protein annotations:
To apply new rendering and color settings in Jmol to all
conformations (frames), there are two ways:
(1) For less
experienced users, make right mouse click on the Jmol
pane, choose item
Model and click on
All. When all
models appear, apply any rendering/coloring options using
the popup menu. Then, select some specific model via popup
menu, or use
Jump to button on the
page, which makes visible only specific model while
keeping all changes made for other models.
(2) For more
advanced users, open Jmol/Java console or use text field
Custom Jmol command to type in and apply any
rendering command using Jmol scripting language that will
be applied to all models at the same time.
To accelerate the upload of the trajectory, use the file
compression. Accepted formats are ZIP, GZIP, or BZIP2
(file extensions zip, gz, and bz2, respectively).
To convert a trajectory coordinate file to one of the accepted
formats (DCD, TRR, or multi model PDB), use some convert
utility, such as
Additional documentation on the use of CatDCD can be found
To get an image in publishable format click on the tool
Get as in the corresponding Image processing
toolbar next to each image. You will be prompted to save a PS or TIFF file
to a disk.
If a TIFF formatted image looks tiny, when embedded in a
document, scale it to the desirable size, quality will not get
All images generated by the POLYVIEW-MM server can be FREEly saved,
printed, and distributed by means of any media without our written
permission for academic and non-commercial purposes. However, the use
of POLYVIEW-MM's pictures SHOULD be acknowledged by
a reference to the server.
The use of the POLYVIEW web site and server is at your own risk and no
liability is accepted for any loss or damage arising through the use
of the web site and graphical representations generated by the server.
For citation, please use the following references:
A. Porollo, J. Meller (2010)
POLYVIEW-MM: Web-based Platform for Animation and Analysis of
Nucleic Acids Research, 38, W662-W666.
Contact us and submit your feedback here.
Last update of the document: May, 2010
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