There are four different stages of
YASARA for Linux, Windows, Mac OS X and Android, aimed
at increasingly complicated fields
of application. A certain stage contains the features of all the
previous stages, plus a number of additional functions to tackle a
wider range of scientific questions. Features with unique properties
which you will not find in other programs are marked with orange
View - Molecular graphics and analysis, freely
Model - Everything above, plus molecular modeling
Dynamics - Everything above, plus molecular simulations
Structure - Everything above, plus structure prediction and
NMR Module - NMR structure determination
IF Twinset - Extensive structure validation (PDBReports) and WHAT
tablets and smartphones that can run interactive MD simulations
starting at 175 EUR.
stereoscopic molecular modeling lab for 250 EUR, and a cave for 700 EUR.
Read more about the
philosophy behind YASARA.
System requirements: None, please download the free YASARA View to
verify that YASARA runs on your computer (and please contact us if you encounter problems).
||Stage I: YASARA View -
is available for free and contains all the functions you need to
explore a macromolecular structure interactively. As a bonus, you get
YASARA's innovative 3D engine,
which is up to 10 times faster than what you usually know from OpenGL (see
benchmarks), you can load multiple structures at the same time,
create publication-quality ray-traced images including labels, and
program your own macros and Python plugins. Included is YASARA Movie, a player for
multimedia presentations and tutorials created with any of the higher
stages, as well as the YASARA Python module to simply 'import
yasara' in your Python scripts.
- Cross-platform and easy installation: Windows, Linux and Mac OS X in the same
directory, run directly from USB stick.
molecular graphics with full-scene antialiasing: up to 10 times faster
than other OpenGL based solutions, even the ribosome rotates
in CPK mode.
- Support for the latest GPU shader features like
hardware tessellation, where the GPU increases the geometric details of
polygon meshes (e.g. surfaces and secondary structure).
- Parallel (orthographic) and perspective
- Interactive box, freehand/lasso or sphere selection tools.
- Support for over 70 molecular fileformats
- Download PDB files from the RCSB or the re-refined and improved version from
- Optimal depth perception thanks to real-time shadows and ambient lighting, even on
- All common graphics styles: CPK, balls
& sticks, sticks, traces, tubes, ribbons, cartoons, labels, arrows.
- Interactive secondary structure morpher, which
seamlessly interpolates between a realistic (close to Calpha) and an
idealistic (perfectly straight strands and helices) secondary structure
display, which can additionally be configured in countless ways to
match your favorite secondary structure styling.
- Create alternative views of the scene, and switch between them using tabs at the top.
- Ray-tracing for
quality graphics at
resolutions, interactively move the lightsource, adjust shadows.
- Color any PDB file by sequence conservation and
(automatically mapped from HSSP/PDBFinder2).
- Superpose structures and
structure ensembles, calculate proper RMSDs
(minimized by flipping equivalent atoms).
- Align multiple proteins
based on their structure or sequence, using a variety of methods.
Identify related structures in the PDB.
- Measure distances, angles, dihedrals.
- Build atoms, residues,
peptide chains and mutate amino acids.
contacts, hydrogen bonds,
and hydrophobic/pi-pi/cation-pi interactions.
- Create realistic 3D structures from nonsense, 1D or 2D molecules,
and convert them back to 2D
- Automatic assignment of fractional
bond orders and missing hydrogen atoms, graph-theory
based typing of hetero-polycycles.
- Analyze and change atomic B-factors
occupancies, rename and renumber atoms and residues.
- Extremely fast
algorithms to show and update Van
Waals, molecular and solvent accessible surfaces in real-time.
- Extend YASARA with your own
functions using the Python
- Use YASARA from your Python scripts, simply
- Simple Yanaconda macro
your work and create flexible animations.
- eLearning functions: interactive
provide the knowledge
about molecular structure, modeling and simulations
Click here for free download,
click here for screenshots,
click here for a complete feature list.
||Stage II: YASARA
contains YASARA View and adds all the functions you need to explore,
analyze and model small to macromolecules in a production environment.
includes many features you often miss: unlimited undo/redo, macro
recorder, quad-buffered stereo with shutter
glasses or stereoscopic screens.
You can load
structures at the same time, move them around independently and
create multimedia presentations (YASARA Movies). These movies can be
encoded as MPEGs and pasted into Powerpoint or played back with all
stages of YASARA, including the free YASARA View.
- All the features of YASARA View listed above
are included, no need to keep a separate YASARA View installation.
- Fully immersive OpenGL 3D stereo graphics with sterescopic screens or shutter glasses.
High quality GPU accelerated anaglyph stereo mode for red/cyan glasses,
that tricks the brain into seeing full color and enables stereo also on
notebooks. Red/cyan glasses are included.
- Create the fanciest
rotations, movements, zooms, text
in 3D letters, texture
mapping of PNG/JPG images and conversion to 3D objects.
- Encode animations in MPEG format, paste them
Powerpoint presentations. Export Alias Wavefront objects for use by
3DStudioMax and others.
- Import OpenOffice Impress and Microsoft
presentations, add molecular animations to the slides.
- Work with thousands of structures at the same
- Extensive coordinate manipulation: center,
fragments (e.g. loops) or replicate them (e.g. domains).
- Analyze contacts, hydrogen bonds,
hydrophobic/pi-pi/cation-pi interactions and protein
- Align small molecules like ligands
automatically, by superposing
them on the largest common fragment.
- Measure distances, angles and dihedrals between
groups of atoms like helices or planar side-chains.
- Change distances, angles and dihedrals
- Choose a default pH from 0 to 14 when assigning
fractional bond orders and adding hydrogens.
- Show and calculate Van
solvent accessible surfaces, distinguish between outer and inner
surfaces, calculate volumes. Analyze and show cavities formed by
- Create multiple
interactive cut-planes to look inside surfaces and other objects.
- Identify cis-peptide bonds and wrong
- Store the results of your analysis in tables,
- Record macros or write them with a text
- Support for special input devices like
glove (currently Linux only).
- Unlimited undo/redo.
contains YASARA Model and adds support for molecular simulations.
In addition to YASARA's own force fields (NOVA, YAMBER) you can
use other well known MD force fields like AMBER, and run accurate
MD simulations in aqueous solution with Particle Mesh Ewald longrange
Dynamics is not a "black box" with input and output files, but
shows the MD simulation in real-time on screen. You can fully interact
with the scene, pull atoms or whole molecules around and finally do the
type of molecular modeling that Cyrus Levinthal already pioneered back
in 1966 ("..do the same type of pulling and pushing in the computer
that we can do with our hands while building actual models. ",
cited from an article in Scientific American).
- All features listed for YASARA View and
above are included, no additional purchase needed.
- Prepare a simulation: clean proteins, predict
protonation states, fill the simulation cell with water.
- Fastest molecular dynamics algorithms for CPU and GPU (see benchmarks), energy minimizations in non-periodic or periodic &
triclinic crystal cells.
- AMBER and newly developed force fields (NOVA, YAMBER) included,
define your own force fields.
- Accurate treatment of long-range electrostatic
with the Particle Mesh Ewald approach.
- Parallel and reproducible simulations on multiple CPUs and CPU cores with
close to ideal speedups.
- Constrain bond lengths and water molecules with
LINCS and SETTLE to reach large timesteps.
- Calculate energies, binding energies and solvation
energies using Poisson-Boltzmann or PME methods.
- Manipulate a simulation interactively: pull
molecules around, fix and free atoms, add restraints, toggle force
- Calculate the
electrostatic potential using Poisson-Boltzmann or PME methods,
visualize the results as densities, contours or surfaces.
- Run simulations at the touch of a button even
in the presence of ligands, thanks to fully
automatic force field
parameter assignment for the General Amber Force Field (GAFF).
Semi-empirical QM point charges are calculated using either AM1BCC or
AutoSMILES, a newly developed approach for hi-speed assignment of RESP
- Run simulations of
membrane proteins at the touch of a button.
- Automatic correction of cis-peptide bonds or
stereoisomeres for homology model refinement.
- Geometry optimization and analysis with
semi-empirical MNDO/AM1/PM3 quantum chemistry using YAPAC, a built-in
derivative of MOPAC.
trajectories for conformational changes, calculate time averages,
RMSDs, RMSFs, RDFs and dynamic cross-correlation matrices.
- Read and write trajectories in SIM or XTC
oligosaccharides interactively, with stepwise energy minimization.
contains YASARA Dynamics and adds all the functions needed to predict
and validate macromolecular structures, including ligand docking and
accurate force fields with knowledge-based potentials. If you already
own one of the other YASARA stages, you can upgrade easily, just contact us for a quote.
- All features listed for YASARA View, YASARA
above are included, no additional purchase needed.
- Small-molecule docking at the touch of a
button, using tuned versions of AutoDock and
automatic setup, receptor flexibility and multi-CPU support.
Additional support for Fleksy, an induced
fit docking program based
on FlexX, developed at Organon/Schering-Plough.
- Side-chain rotamer prediction combining graph-theory and dead-end elimination with
accurate treatment of electrostatics, solvation and subtle packing
- Knowledge-based loop
modeler with a compressed index of the PDB, peptide segments
spanning selected anchor residues can be located within a fraction of a
second, while considering sequence and secondary structure preferences.
Loops can be optimized together with surrounding side-chains,
considering all energy components including solvation.
- New force fields
(YASARA and YASARA2) with multi-dimensional knowledge-based components
for highly accurate refinement simulations to aid protein structure
determination and prediction.
- Homology modeling at the touch of a button:
select the target sequence and get a
homology model, combined from multiple templates, refined in explicit
solvent, as well as a detailed
scientific report describing how the model was built, including
extensive validation with figures and quality plots. Check the CASP results.
- pH dependent hydrogen
bonding network optimizer, that automatically considers ligands and
determines ambiguities in X-ray density.
- Built-in BLAST and
PSI-BLAST, with automatically updated SwissProt, UniRef90, PDB
and PDBC sequence databases, the latter augmented with WHAT_CHECK/
validation data to rank PDB structures sharing the same sequence.
- Secondary structure prediction with PsiPred and
- Extensive structure validation to judge the
quality of experimental structures and models, based
on a new combination of force field energies and Z-scores, that yields
results not only for proteins, but for all organic molecules. This
allows to validate for example protein-ligands interactions, an
important aspect in drug design.
- Perform twisted structural alignments, where the protein is bent and wound to
maximize the number of structurally aligned
residues, for example to create sequence profiles for homology
- Prediction and
visualization of ion binding sites using valence scanning.
||The WHAT IF /
is a customized joint-distribution of WHAT IF and YASARA
Dynamics (Linux and Windows, not MacOSX) or YASARA Structure (Linux
only). Since YASARA Dynamics is just a subset of YASARA Structure, Windows
users of YASARA Structure do not need an extra YASARA Dynamics
license. With over 3000 citations, WHAT IF is a widely
program for structure validation and modeling. In the Twinset, WHAT IF
inherits YASARA's user interface, graphics engine, macro language,
undo/redo etc, so that WHAT IF functions become easily accessible.
The Twinset is freely
available for academic use and costs 1500 € / 1650 $ for
unlimited commercial use per building (this fee is waived if you own a
group leader license of YASARA Dynamics or Structure). In addition, you
for YASARA Dynamics or Structure and also WHAT IF. Click here for WHAT IF license details, and note that the academic WHAT IF version is now shareware. Customers in Austria have to add 20% VAT.
To order the Twinset, just
place a normal order for YASARA
or YASARA Structure and then
Twinset upgrade from .
If you already own YASARA,
email us your YASARA serial number.
Commercial users need to send their WHAT IF license number too.
molecular modeling lab for 250 EUR
Stereoscopic 3D molecular
modeling hardware has
become easily affordable, so that
entire classrooms can enjoy this unique experience. The image
on the right shows the easiest and cheapest solution: 3D
vision is provided using 'passive stereo', where the images for left
and right eye are shown in odd and even pixel lines and separated using
flicker-free polarized glasses. The first popular screens with this
feature were the Zalman ZM-M215W, ZM-M220W and ZM-M240W, costing around
200 EUR. Unfortunately it appears that Zalman discontinued this product
line, so they are now mostly available as refurbished second hand
models. But there are many follow up products, googling for passive stereo odd even
finds e.g. the LG D2342P, the HP 2311x, the AOC e2352Phz or the
Viewsonic V3D231. The big advantage is that this type of display is
directly supported by
YASARA with any graphics card
and any operating system (no
expensive Quadro/FireGL cards or special video drivers are needed). You
can move your molecules
through 3D space using the Connexion
3D SpaceNavigator with six degrees of freedom. Order
now for 50 EUR.
ZM-M220W has a resolution of 1680×1050 pixels. The polarized glasses
ensure that the left eye sees only the odd pixel lines, while the right
eye sees the even lines. So the resolution is reduced to 1680×525
pixels per eye as soon as the glasses are put on. This is hardly
noticeable when looking at molecules, but becomes apparent when looking
at characters. Text is therefore harder to read than with alternative,
more expensive stereo solutions. Without glasses, the screen behaves
just like any other screen and can be used for everyday work. It has a
quite glossy surface, reflections can be a problem in bright rooms, but
are hardly noticeable in somewhat darker 'molecular modeling caves'. At
least YASARA Model is required.
||The 3D modeling showcase: a huge 3DTV for 380 EUR
If you want to demonstrate 3D modeling on a large screen,
we recommend passive 3DTVs like the LG 42LB620V shown on the right. With a diagonal of 42" (107 cm), two polarized
3D glasses and a price of 380 EUR, this 3DTV is an excellent deal that will please your audience.
Passive 3DTVs use exactly the same principle as described above for passive 3D computer screens, so they will work with
any operating system and any graphics card, with YASARA running in window or fullscreen mode.
Notes: Make sure to buy a screen with a resolution of 1920×1080 pixels (FullHD). Since the images for
left and right eye are shown in odd and even pixel lines, this leaves an effective resolution of 1920×540 pixels
per eye, and you certainly do not want a lower resolution on such a large screen. Higher resolutions would of course
be even better, but will only be supported by YASARA later this year and also require an advanced GPU with HDMI 2.0
connection. It is essential that the 3DTV supports a display mode where the input signal is shown directly on screen,
without scaling (overscan) and other post-processing (which would destroy the stereo effect). On LG 3DTVs, you can set
this display mode by labeling the input with "PC" (push the "Settings" button on the remote, then go to Input > HDMI1,
push the red button with the single white dot and select the "PC" label). If your graphics card/notebook
only has a DVI output, don't forget to buy a DVI->HDMI adapter and a HDMI cable. Finally, it is noteworthy that
passive stereo screens have a certain viewing volume. On the LG 42LB620V, your head should be located about 2 meters
away, aligned with the bottom of the screen (i.e. you should be sitting or the screen should be hanging high up on the wall).
Inside the viewing volume, the 3D effect is crystal clear, but outside, there can be considerable ghosting.
At least YASARA Model is required, click Window > Stereo > Interlaced to enable stereo. If the stereo is 'inside out', click Window > Stereo > Swap left and right.
||High resolution 3D
modeling for 350 EUR
High resolution 3D stereo
with active shutter glasses is
the next higher level, since it does not suffer from the reduced
resolution of the passive screens above. The probably easiest solution
with the best price/performance ratio is the Viewsonic V3D241wm
shown on the right. The screen with a 24"/60cm diagonal has a
resolution of 1920×1080 pixels and a non-reflective surface, it is thus
well suited for everyday work. It functions with every operating system
and every graphics card (nVIDIA/AMD) that can display quad-buffered
stereo with 100 or 120Hz at a resolution of 1920×1080 pixels. The
shutter glasses are included in the 350 EUR package. A slightly more
expensive but also more commonly used and more flexible solution is nVIDIA's 3D
system, check the guidelines here
and here. Other
suppliers of 3D glasses are eDimensional
graphics card must have a dual-link DVI connector and support quad
buffered OpenGL stereo, a feature which
is normally only available in workstation
products like nVIDIA Quadro
and AMD FireGL. You do not need the very expensive high-end Quadros
with mini-DIN stereo connector, since the shutter glasses are supplied
with the screen and plug into the screen with a cable, neither emitter
nor batteries are required. Only one pair of glasses can be connected,
so this system is for one person only. And
since the monitor does not know the difference between left and right
image, you may have to swap left and right in YASARA on startup. The
aspect ratio of 16:9 is very movie-like, you may have to fiddle with
your desktop settings to avoid windows that are too wide to read. The
screen shows very little ghosting, which becomes noticeable mainly in
the bottom 5cm. At
least YASARA Model is required.
molecular modeling cave for 700 EUR
Recently also specialized 3D beamers, that
previously cost above 10000 EUR, have finally become mainstream
technology. You can now easily build your private molecular modeling
showroom, projecting giant 3D views that measure several meters along
the diagonal. The image on the right shows a 3D beamer from Viewsonic,
costing around 500 EUR. The beamer projects the
images for left and right eye alternatingly with 120 Hz. So you
additionally need shutter glasses to separate the images, the probably
best choice are glasses with DLP-link like the
Viewsonic PGD-250 (~80 EUR) or the XPAND Edux3 (~80 EUR). An
alternative with a less
comfortable infrared emitter are
glasses shown on the right (~200 EUR).
Any beamer that is 3D-ready, features 'DLP-link' and
supports a 120 Hz mode over VGA or DVI cable should work with YASARA, to see
click here, then select 'Supported 3D projectors'.
have been done in Linux, where you need to add a 120Hz modeline to your
xorg.conf. Other operating systems work too if they allow you to choose
a 120Hz video mode in their display settings. Additionally, your
graphics card must support quad buffered OpenGL stereo, a feature which
is normally only available in workstation
products like nVIDIA Quadro
and AMD FireGL. These cards often also have a mini-DIN connector for
the shutter glasses, which is however not needed if you chose glasses
with DLP-link (see above). The only disadvantage of DLP-link glasses is that
you sometimes need to manually flip left and right image. At least YASARA Model is required to display stereo.