WK.01 Joint Neutron and Xray Structure Refinement using Joint Refine in PHENIX

This half-day workshop is intended as a somewhat informal and handson tutorial. We will have 4 organizers/hosts with extensive knowledge and experience in neutron crystallographic refinement. There has been a resurgence in macromolecular neutron diffraction over the last decade in the USA, starting with the construction of the LANL Protein Crystallography Station in ~2001. Since the early 2000s we now have another diffraction instrument, Imagine at ORNL, with a third, MaNDi at ORNL, being commissioned in 2014. This increase reflects the massive user demand for neutron diffraction instrumentation and while beam time and data collection is becoming more routine, there has been a lack of computational programs to handle the nontrivial refinement approach to dealing with explicit H and D atoms. The current incarnation Joint refinement in PHENIX is expected to be heavily used by a crystallographic community that is rapidly shifting to PHENIX for most refinements. Theintroductory lecture will frame the context of the workshop.This will explain the "why" of joint Xray and neutron refinement for neutron studies, as well as some of the technical "how". The bulk of the workshop will focus on all the steps after neutron data collection: from preparing an appropriate PDB (is your protein hydrogenous, H/D exchangedor fully deuterated) to the finer nuances of a proper neutron/Xray refinement. There will also be a focus on careful model building in Coot, taking proper hydrogen bonding and chemistry into account.


Participants will be asked to bring their own laptops with the latest version of PHENIX installed. This can be found at:


We will encourage participants that have their own neutron and isomorphous Xray data sets, to bring those and work with us. We also have a high quality neutron data set of crambinto very high resolution if participants do not have their own data. This is the ideal learning data set for participants new to neutron techniques or for participants that are new to PHENIX Joint refine.


Tentative Schedule

08:30 - 09:00

Set up, help participants install PHENIX, distribute practice neutron and Xray data sets


09:00 - 09:30

Brief introduction on PHENIX Joint Refine, philosophy and approach, what's new and improved over previous versions


09:30 - 10:45

Participants work on PDB preparation, initial refinement parameters, making nuclear and electroni density maps for Coot, interpreting maps


10:45 - 11:00

Coffee break


11:00 - 12:30

Continue refinement and model building, finish structure, Q&A.





Pavel Afonine, Lawrence Berkeley National Lab



Marat Mustyakimov , Oak Ridge National Laboratory

mustaykimov[email protected]ornl.gov


Zoë Fisher, Los Alamos National Laboratory



Andrey Kovalevsky, Oak Ridge National Laboratory



Workshop fee:

Registration fee (regular) $100.00

Registration fee (student) $75.00