Automated Molecular Replacement

1. Automated Molecular Replacement Part 1: Automating Amore Make Amore as easy to use as Molrep, Phaser. Part 2: Construction of “best” model for Phaser Enable maximum number of structures to be solved using MR.

2. Amore Solution Process 1. Estimate number of molecules in Asymmetric unit (MATTHEWS). 2. Solve for first molecule (AUTO-AMORE) a) Rotation function. Euler angles { (α,β,γ) } b) Translation function. Euler angles + fractional translations { (x,y,z)} c) Fitting = Rigid Body Refinement 3. Solve for additional molecules. Extra translations. (iterative) 4. Final round of fitting 5. Apply rotations and translations to atom coordinates. (PDBSET ) 6.Merge into one pdb file. 7.Check for clashing(DISTANG)

3. Solutionfor n molecules • Take top 5 (distinct) translation solutions from n – 1 molecule solution • Take top 5 (distinct) rotation solutions • Consider all possible combinations • Search for translation solutions for 1 more molecule • Score by summing correlation coefficients over all n molecules • Sort solutions in order of decreasing score

4. Test Results

5. Future developments • Incorporation in Ronan’s pipeline • Model Building using Arp/Warp

6. PART 2 Constructionof “best model” for phaser Apply sequence alignment algorithm PSIBLAST : sequence – profile alignment FFAS : profile – profile alignment Modify template (Chainsaw) If Target R = Template R retain If not … R. Schwarzenbacher et al, Acta Cryst D60 1229, (2004)

7. Chainsaw

8. Future work • Use more sophisticated sequence alignment algorithms • Apply to ensembles