Welcome to the sas rigid project!

Here you will find some proof of concept software: Can rigid body modeling with small-angle scattering data be done using a scan of discrete movement parameters? Find out yourself!

Description

sas rigid is a modeling package designed to enable efficient rigid body modeling based on small angle scattering (SAS) data. In principle both data types, X-ray and neutron / SAXS and SANS, can be processed. The package provides fast and easy access to rigid body modeling with molecules of arbitrary symmetry. In order to speed up modeling the package enables the user to perform a Monte Carlo based "rough" modeling followed by a systematic search in a confined parameter range.

There are also basic facilities for manipulating or preparing PDB-files for better handling for the purpose of rigid body modeling.

News

Development has ceased? Sadly true, but snapshots / bug fixes will be released from time to time.

Contents

Currently you will find the following content on these project pages:

• a download section including source files
• a brief tutorial (Please note that extensive documentation is included in the download.)
• and, last not least, you can browse the source code and follow the development

Bug Reports & Feature Requests

Unfortunately Origo up to now only allows registered users to report issues. If you are / want to be registered, please don't hesitate to use the issue tracker. If you don't want to become registered, but you still feel like there is some burning issue, there is an email address in the download. Any feedback is appreciated!

Publications & Supplementary Material

Papers

• A "citable" paper with all algorithm descriptions appeared in Computational Biology and Chemistry. (Please look at the PDF, only. The web version of that paper is with wrong equations.) If your institution does not allow to download a copy, request one from the authors. Thank you.
• The first publication on this software can be found in the conference proceedings book from the CBSB08 conference: NIC series, Volume 40, 2008, ISBN 978-3-9810843-6-8.
• Yet another conference paper, this one only web based. The paper was written within the frame of the EuroSciPy conference 2009. Please note, that it never appeared in a peer-reviewed journal.

Conference Slides

• Slides from a lightning talk given at the Euro Scipy 2008 conference in Leipzig (Germany).
• Slides from a real talk given at the Euro Scipy 2009 conference in Leipzig (Germany).

Conference Posters

• You can find a brief description of the software on a poster presented at the CBSB08 conference on the poster.

Acknowledgments

• Bruno Pairet & Thorsten Schweikardt (currently no link) helped a lot during the initial stages of the project.
• Anja Rabenhorst (currently no link) for reference data.
• Borries Demeler was the first to give input on the [1]. His ideas are reflected from the 0.4 release onwards.
• Graeme O'Keefe gave permission to use his implementation of a NNLS routine.
• Prof. Decker & Prof. Jaenicke and Alexandra Beusch (currently no link) for continuous support during the early development stages.

• The entire project was coded at the Institute of Molecular Biophysics in Mainz, Germany, within project D4 of the SFB 490 in the years 2007-2008. Currently I'm working as a protein specialist at the private Aesku.Kipp Institute in Wendelsheim, Germany.

Contact information

In case of questions please contact the main author of this project. You will find detailed contact information in the download of the source. And please don't hesitate to ask!

Other software developed by me

• yamas a meta-analysis software for genome wide association studies.
• Not to forget the recently started splot project for light scattering data analysis.

Bugs & Issues

Unfortunately bugs and issues can only be reported, if logged in into Origo. You can either create an account or contact the main developer (email in the download): In this case issues will be reported on your behalf.

Do not hesitate to report any issue / feature request you might have. Thank you!