LOOS / News: Recent posts

There is an issue with building LOOS and Boost 1.52 and greater. We will address this in the next release of LOOS. In the interim, we recommend building with the Boost that is installed by your package manager, or with no version of Boost more recent than 1.51 for MacOS (or manual installs).

This version of LOOS addresses a few bugs including a potential issue with the SVD tool for MacOS 10.6 (intel) and corrects how ATLAS is linked in, in principal giving a performance boost for linux machines. There are new tools as well as a new suite of tools for analyzing hydrogen bonding, and order_params has been updated to work with both the 1- and 3- residue per lipid formats. For more details, see the change log...

This release of LOOS includes several improvements and bug fixes.
First, the build system has better support for other linux
installations (i.e. Ubuntu and SUSE). An issue with SCons trying to
invoke doxygen, even though the built docs are bundled with the
release, has been fixed. A missing definition on Debian systems that
afflicted the parser has also been fixed. Improvements include a much
faster algorithm in the contact-time tool, support for user-defined
HCA parameters in the ENM tools, and special handling when the spring
constants go negative in the ENM tools. For more details, see the
ChangeLog in the distribution.

This new release of LOOS includes several new tools, including one to merge new dcd's into an already merged trajectory (faster than concatenating all with subsetter), a tool for computing the Vibrational Subsystem Analysis ENM for a model, and a tool for computing contacts between selections over time. Also included are a few minor bug fixes. See the ChangeLog for more details.

This is a maintenance release of LOOS addressing issues with reading Amber restart files. A bug affecting the "segname" keyword for atom selections has also been fixed. In addition, the eigenvalues from the principal axes result are now scaled by the number of atoms used. Please see the change log file (or in the Doxygen documentation) for more details.

A bug in the install target was discovered. The "trr.hpp" header file was not copied into the install directory. This bug is fixed in the current release. Alternatively, manually copy the "trr.hpp" file into the "include" directory where you installed LOOS.

We're pleased to announce version 1.5.0 of LOOS. What's new and notable in this release is support for Gromacs files (.gro, .trr, and .xtc). This support has not been as rigorously tested as other formats, however, so it should be considered experimental. Please report any problems either using the tracker here on SourceForge, or to us directly.

There are a number of largely internal changes and improvements (such as support for hybrid-36 PDB files) as well as a few bug fixes. Please see the release notes or the bundled ChangeLog for more details.

We would love to hear feedback about your experiences with LOOS. If you download and use it, please drop us a note (loos-maintainer@urmc.rochester.edu) to let us know that and a little bit about what you are doing with it. This information is important to the continued development of LOOS.

Similarly, feature requests, usability concerns, and definitely bug notices are welcome to. We can be reached either through the forums/tracker system here at Sourceforge, or by emailing us directly at loos-maintainer@urmc.rochester.edu .

This release includes a number of new analysis tools such as calculating ramachandran plots over a trajectory, rotameric states, distances between groups, as well as the principal axes of a group. In addition, subsetter can now automatically sort the input trajectory filenames making merging of trajectories easier. Several tools geared towards elastic network models are now included as well, along with a tool for creating "porcupine" plots from either ENM or SVD/PCA results. There have been several internal changes as well as bug fixes (in subsetter, averager, and rmsds). See the full documentation at http://loos.sourceforge.net/Docs/ for more details.