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PHENIX workshop at ICSG 2011, Toronto, May 10, 2011
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Introduction to PHENIX for beginning to advanced crystallographers
May 10, 2011
8:30 AM - 4:00 PM
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab
Tel: 1-510-486-4225, Fax: 1-510-486-5909
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.
Tom Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Tel: 1-505-667-0072 Fax: 1-505-665-3024
Mail Stop M888
Los Alamos NM 87545
Li-Wei Hung
Los Alamos National Laboratory
Tel: (510)486-7688
BLDG 4-0221, Lawrence Berkeley Laboratory
1 Cyclotron Road
Berkeley, CA 94720, USA
Description of the workshop
The purpose of the workshop is to train both beginning and advanced crystallographers in the use of the PHENIX software for macromolecular structure determination. The workshop will benefit the crystallographic community by making this software accessible to a broader group of crystallographers, by teaching crystallographers when and how to use the software properly, and by teaching crystallographers how to get the most out of the software.
The workshop will have two overall parts. The morning session will introduce PHENIX and the core algorithms that it uses. The afternoon session will be a group hands-on tutorial for beginning and intermediate users concurrent with individual tutorials for advanced users.
The morning session will begin with an overview of PHENIX that introduces what the PHENIX software can do, how it is organized, and how it is used. Then the core automation in PHENIX will be presented along with the key algorithms used in structure solution by MIR/MAD/SAD, density modification and model-building. Next the PHENIX refinement system will be described with emphasis on the core algorithms used. Then the extensive validation available during and after structure determination with PHENIX will be described. Finally the attendees will learn how to use the PHENIX GUI to carry out all the methods used in PHENIX.
During the morning break the attendees that do not already have PHENIX will install PHENIX on their computers. This process takes about 5 minutes with Linux or Mac OSX operating systems. For users with Windows machines self-booting DVD's will be provided that contain the Ubuntu operating system and PHENIX pre-installed. These can be used directly to run PHENIX.
In the afternoon there will be three group tutorials. The first will focus on data analysis (twinning, space groups, structure factor statistics) and structure solution (finding an anomalous substructure in a MAD or SAD dataset). The second tutorial will focus on model-building and ligand fitting. The third will cover refinement and validation. Concurrent with the tutorials, advanced users will have individual tutorials on their own data.
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PHENIX workshop schedule
| 8:30 AM - 12:30 PM |
PHENIX lectures |
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| 8:30 AM |
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PHENIX Overview (Paul Adams) |
| 9:00 AM |
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Automation of Structure Determination in PHENIX (Tom Terwilliger) |
| 10:00 AM |
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Refinement and Validation in PHENIX (Paul Adams) |
| 10:30 AM |
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Break and set-up of PHENIX on individual computers |
| 11:00 AM |
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Refinement and Validation in PHENIX (continued, Paul Adams) |
| 11:45 PM |
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Molecular Replacement and Ligand Fitting (Li-Wei Hung) |
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| 12:305 PM |
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Lunch |
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| 1:30 - 4:00 PM |
Tutorials and individual sessions |
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| 1:30 PM - 2:15 PM |
Hands-on Tutorial -- Data analysis and Structure solution |
| 2:15 PM - 3:00 PM |
Hands-on Tutorial -- Model-building and Ligand Fitting |
| 3:00 PM - 4:00 PM |
Hands-on Tutorial -- PHENIX Refinement and Validation |
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