WK.03  Introduction to PHENIX for Beginning and Advanced Crystallographers

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 the use of 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 components. The morning session will introduce the PHENIX system and the core algorithms that it uses. The afternoon session will be a 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, molecular replacement, density modification and automated model-­‐building.   Next the algorithms for structure refinement will be described with emphasis on the core concepts. Then the extensive validation available during and after structure determination with PHENIX will be described. Finally the attendees will learn how to use the GUI to carry out all the methods used in PHENIX.


During the morning break the attendees that do not already have the software will install PHENIX on their computers. This process takes about 5 minutes with Linux, Mac OSX, and Windows operating systems.


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 molecular replacement, 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.

Tentative schedule

8:30 AM                     PHENIX Overview (Paul Adams)

8:45 AM                     Automation of Structure Determination (Tom Terwilliger)

9:30 AM                     Molecular Replacement (Paul Adams)

10:00 AM                   Break and set-­‐up of PHENIX on individual computers

10:30 AM                   Refinement in PHENIX (Pavel Afonine)

11:15 AM                   Model Validation (Paul Adams)

11:45 AM                   The PHENIX GUI (Billy Poon)

12:15PM                    Discussion

12.30PM                    Lunch

1:30-­4:30 PM            Individual tutorials for advanced users and group tutorials for beginning and intermediate users

1:30PM-2:30 PM      Hands-­‐on Tutorial - Data analysis and Structure solution

2:30PM-3:30PM       Hands-­‐on Tutorial - Molecular Replacement, Model-­‐building and Ligand Fitting

3:30PM-4:30PM       Hands-­‐on Tutorial - PHENIX Refinement and Validation

4:30PM                    Workshop Survey and wrap­‐up


The registration fee $130 for everyone and includes lunch. Preregistration is mandatory and should be included with your meeting registration.



Paul Adams

Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence

Berkeley Lab

Tel: 1-­‐510-­‐486-­‐4225, Fax: 1-­‐510-­‐486-­‐5909

Lawrence Berkeley Laboratory

[email protected]