Researchers at Berkeley Lab and other institutions are seeking
industrial partners to join a consortium to advance the development
of PHENIX (Python-based Hierarchical EnviroNment for Integrated
Xtallography) software for automated macromolecular crystallography.
The basis for the software, the Python system, provides a
powerful object-oriented scripting language.
This novel software is expected to permit all tasks required
for the computation of phases, automated map interpretation,
model building and refinement to be integrated with newly-developed
procedures for automated decision-making. Eventually, PHENIX
is expected to take X-ray diffraction data and rapidly produce
minimally-biased atomic coordinates with little or no human
intervention. At present, the need for continual, manual intervention
makes rapid, minimally-biased structure solution extremely
difficult. Human intervention is required to obtain initial
phases for the electron density map, build the initial model,
and complete the model with refinement. As a result, the time
required to solve a structure after the data have been collected
is often on the order of weeks or months. The PHENIX system
is expected to significantly decrease this time and therefore
provide a valuable tool to increase throughput for all crystallographers.
For expert users, a flexible interface to the broad array
of methods available in PHENIX will facilitate the solution
of even the most difficult crystallographic problems. Berkeley
Labs new system for automated crystallography is being
built on a strong foundation that can accommodate current
plans and future developments. Researchers are developing
a toolkit that will provide an environment for integrating
crystallographic tasks and automated decision-making. A fundamental
feature of the toolkit is that the entire history of the structure
solution, along with all the structural information generated,
will be stored in the Project History database. This design
allows the various tasks involved in the structure solution
process to communicate information exclusively via the database.
Complicated interfaces for the communication between tasks
are avoided and new ideas can be rapidly implemented and tested.
We are seeking industrial partners to join our existing industrial
consortium to speed the development of the PHENIX software
program. For technical information, please visit http://cci.lbl.gov.
For information on a software program for rapid in-house processing of x-ray diffraction images go to:
LABELIT – Software for Macromolecular Diffraction Data Processing, IB-1960