MAD Scripts
This page describes the SMB-MC MAD Scripts development project. Beamline users may go to the MAD Scripts Manual for directions on how to use the scripts to solve structures.
Overview
The ultimate way to validate a diffraction data collection experiment is to be able to extract meaningful phases from the data. In the particular case of MAD and SAD experiments, where the approach to structure solution is highly systematic, it should be possible to attempt phasing and model building during experimental beam time. The SSRL SMB-MC in-house MAD scripts are developed to facilitate the many steps required for structure solution, hiding the complexities of the software installation on the Macromolecular Crystallography file server and providing automated input to all the programs in the structure solution pipeline with minimal edits by the user.
Software License
Copyright 2001
by
The Board of Trustees of the
Leland Stanford Junior University
All rights reserved.
Disclaimer Notice
The items furnished herewith were developed under the sponsorship of the U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the Leland Stanford Junior University, nor their employees, makes any warranty, express or implied, or assumes any liability or responsibility for accuracy, completeness or usefulness of any information, apparatus, product or process disclosed, or represents that its use will not infringe privately-owned rights. Mention of any product, its manufacturer, or suppliers shall not, nor is it intended to, imply approval, disapproval, or fitness for any particular use. The U.S. and the University at all times retain the right to use and disseminate the furnished items for any purpose whatsoever. Notice 91 02 01
Work supported by the U.S. Department of Energy under contract DE-AC03-76SF00515; and the National Institutes of Health, National Center for Research Resources, grant 2P41RR01209.
Permission Notice
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Acknowledgements
Author: Ana Gonzalez (SSRL).
Downloading the Scripts
On MC beamline computers, the scripts are located under:
/data/account_name/templates/MAD-scripts.
Or they can be downloaded here:
