Welcome to 2015

James Fraser
02 January 2015

##Moving on up

We finished 2014 by moving to our new lab space up on the fourth floor of Genentech Hall. The two years we spent next to the Von Zastrow, Mostov, and Bivona Labs were absolutely fantastic. I became great friends with all the PIs (and Henry Bourne, our cluster office mate) and will miss the energy of all the students, postdocs, and staff on the floor. But, it was time to move to a labspace with a bit more room to spread out. We are excited to share equipment, space, and good times with the Frost, Thomson, Cheng, and Douglas labs!


In keeping with the traditions of Genentech Hall, we removed our old lab photos on the second floor and added some new ones to the display on the fourth floor.

Fourth Floor Photos

We went with a new theme surrounding Jennifer Li’s excellent cartoon of the lab. If you can’t tell what we are going for, you should stop by for a closer look!

Creepy Photo Bombs


We are welcoming Erin Poss (CCB) and Evan Green (iPQB/Biophysics) to the lab for the winter quarter. Apparently, even after PUBS they couldn’t get enough of me and Ben, who was their TA on team DUBSTEP.


We celebrated submitting two of Andrew’s papers at the same time as our lab-warming party. The Frost lab is new to the area too, and we are located on the same wing of our neighbourhood: the FR* wing!

After submitting the articles, we decided to post them on BioRXiv, a free online archive and distribution service for unpublished preprints in the life sciences, as well. The two manuscripts can be enjoyed together and continue Andrew’s work to exploit diffuse scattering to improve macromolecular models emerging from crystallography. We had great help from collaborators on this project (and the work on the second manuscript is primarily from Sacha and Pavel). As I wrote in the cover letter:

The first manuscript, “Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles”, describes a prediction of the diffuse scattering features created by TLS refinements. When combined, the two manuscripts outline a powerful strategy for validating X-ray models that include TLS refinement. Different TLS models have equivalent agreement with Bragg data (judged by Rfree), but different agreement with diffuse data (judged by the correlation coefficients of anisotropic diffuse intensities). Our results point the way forward for using more of the recorded scattering to improve models and generate new biological insights about the role of correlated motions in protein function.

The second manuscript, “From deep TLS validation to ensembles of atomic models built from elemental motions”, describes a new tool that can convert TLS matrices to multi-model (ensemble) PDB files that in particular are required for the project described in the first manuscript. This enables easier visualization and interrogation of the correlated motions proposed by TLS refinement. This algorithm discusses that, on the top of well-known conditions that the T and L matrices must be positive definite to be interpretable by such motions, there are other conditions that are usually ignored. Ignoring these conditions creates an unusual situation: although the final ellipsoids define real atomic motions, the TLS matrices imply imaginary correlated movements of rigid bodies.

Happy New Year - and we look forward to more papers and preprints in 2015!

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