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Commits (2)
# MotionCor2 Installation
1. Download MotionCor2 manually from https://emcore.ucsf.edu/ucsf-motioncor2
2. Update files/variants
3. Run `./build <version>`
4. Move all executables to /opt/psi/EM/MotionCor2/$VERSION/bin
5. Move user manual to /opt/psi/EM/MotionCor2/$VERSION/
6. Fix permissions: chmod 755 /opt/psi/EM/MotionCor2/$VERSION/bin
## Cuda versions
| MotionCor2 | Cuda Versions |
|------------+---------------|
| 1.0.5 | 8.0 9.1 |
| 1.1.0 | 8.0 9.0 9.1 |
| 1.2.0 | 8.0 9.1 9.2 |
| 1.2.6 | 8.0 9.2 10.1 |
| 1.3.0 | 8.0 9.2 10.1 |
#!/usr/bin/env modbuild
# Binary distribution with manual installation. See README.md
pbuild::add_to_group 'EM'
pbuild::prep() {
cp $BUILDBLOCK_DIR/files/LICENSE $PREFIX/
}
pbuild::configure() {
:
}
pbuild::compile() {
:
}
pbuild::install() {
:
}
UCSF MotionCor2 Non-Commercial Software License Agreement
This license agreement ("License"), effective today, is made by and between you
("Licensee") and The Regents of the University of California, a California
corporation having its statewide administrative offices at 1111 Franklin Street,
Oakland, California 94607-5200 ("The Regents"), acting through its Office of
Technology Management, University of California San Francisco ("UCSF"), 3333
California Street, Suite S-11, San Francisco, California 94143, and concerns
certain software known as "MotionCor2," a software for correction of electron
beam-induced sample motion in cryo-electron microscopy, for research purposes
and includes executable code, source code, and documentation ("Software"). The
Software was developed by the Keck Advanced Microscopy Laboratory and by Dr.
David Agard at UCSF while Dr. Agard was an employee of Howard Hughes Medical
Institute (“HHMI”).
1. General. A non-exclusive, nontransferable, perpetual license is granted to
the Licensee to install and use the Software for academic, non-profit, or
government-sponsored research purposes. Use of the Software under this License
is restricted to non-commercial purposes. Commercial use of the Software
requires a separately executed written license agreement.
2. Permitted Use and Restrictions. Licensee agrees that it will use the
Software, and any modifications, improvements, or derivatives to the Software
that the Licensee may create (collectively, "Improvements") solely for internal,
non-commercial purposes and shall not distribute or transfer the Software or
Improvements to any person or third parties without prior written permission
from The Regents. The term "non-commercial," as used in this License, means
academic or other scholarly research which (a) is not undertaken for profit, or
(b) is not intended to produce works, services, or data for commercial use, or
(c) is neither conducted, nor funded, by a person or an entity engaged in the
commercial use, application or exploitation of works similar to the Software.
3. Ownership and Assignment of Copyright. The Licensee acknowledges that The
Regents hold copyright in the Software and associated documentation, and the
Software and associated documentation are the property of The Regents. The
Licensee agrees that any Improvements made by Licensee shall be subject to the
same terms and conditions as the Software. Licensee agrees not to assert a claim
of infringement in Licensee copyrights in Improvements in the event The Regents
prepares substantially similar modifications or derivative works. The Licensee
agrees to use his/her reasonable best efforts to protect the contents of the
Software and to prevent unauthorized disclosure by its agents, officers,
employees, and consultants. If the Licensee receives a request to furnish all or
any portion of the Software to a third party, Licensee will not fulfill such a
request but will refer the third party to the UCSF CryoEM Software web page so
that the third party's use of this Software will be subject to the terms and
conditions of this License. Notwithstanding the above, Licensee may disclose any
Improvements that do not involve disclosure of the Software.
4. Copies. The Licensee may make a reasonable number of copies of the Software
for the purposes of backup, maintenance of the Software or the development of
derivative works based on the Software. These additional copies shall carry the
copyright notice and shall be controlled by this License, and will be destroyed
along with the original by the Licensee upon termination of the License.
5. Acknowledgement. Licensee agrees that any publication of results obtained
with the Software will acknowledge its use by an appropriate citation as
specified in the documentation.
6. Disclaimer of Warranties and Limitation of Liability. THE LICENSEE AGREES
THAT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. THE REGENTS MAKES NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE
WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT. IN NO EVENT SHALL THE
REGENTS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
7. Termination. This License is effective until terminated by either party.
Licensee's rights under this License will terminate automatically without notice
from The Regents if Licensee fails to comply with any term(s) of this License.
Licensee may terminate the License by giving written notice of termination to
The Regents. Upon termination of this License, Licensee shall immediately
discontinue all use of the Software and destroy the original and all copies,
full or partial, of the Software, including any modifications or derivative
works, and associated documentation.
8. Governing Law and General Provisions. This License shall be governed by the
laws of the State of California, excluding the application of its conflicts of
law rules. This License shall not be governed by the United Nations Convention
on Contracts for the International Sale of Goods, the application of which is
expressly excluded. If any provisions of this License are held invalid or
unenforceable for any reason, the remaining provisions shall remain in full
force and effect. This License is binding upon any heirs and assigns of the
Licensee. The License granted to Licensee hereunder may not be assigned or
transferred to any other person or entity without the express consent of The
Regents. This License constitutes the entire agreement between the parties with
respect to the use of the Software licensed hereunder and supersedes all other
previous or contemporaneous agreements or understandings between the parties,
whether verbal or written, concerning the subject matter. Any translation of
this License is done for local requirements and in the event of a dispute
between the English and any non-English versions, the English version of this
License shall govern.
MotionCor2/1.0.2 stable
MotionCor2/1.0.4 stable
MotionCor2/1.0.5 stable
MotionCor2/1.1.0 stable
MotionCor2/1.2.0 stable
MotionCor2/1.2.6 unstable
MotionCor2/1.3.0 unstable
#%Module1.0
module-whatis "Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy"
module-url "http://msg.ucsf.edu/em/software/motioncor2.html"
module-license "This software may only be downloaded and used for free by academic and/or non-profit users"
module-maintainer "Spencer Bliven <spencer.bliven@psi.ch>"
module-help "
Correction of electron beam-induced sample motion is one of the major factors
contributing to the recent resolution breakthroughs in cryo-electron
microscopy. Based on observations that the electron beam induces doming of the
thin vitreous ice layer, we developed an algorithm to correct anisotropic image
motion at the single pixel level across the whole frame, suitable for both
single particle and tomographic images. Iterative, patch-based motion detection
is combined with spatial and temporal constraints and dose weighting. The
multi-GPU accelerated program, MotionCor2, is sufficiently fast to keep up with
automated data collection. The result is an exceptionally robust strategy that
can work on a wide range of data sets, including those very close to focus or
with very short integration times, obviating the need for particle polishing.
Application significantly improves Thon ring quality and 3D reconstruction
resolution.
Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan
Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion
for Improved Single-particle Electron Cryo-microscopy, Nature Methods,
submitted. BioArxiv: http://biorxiv.org/content/early/2016/07/04/061960
"