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. Solution for 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 Target Model % seq no. mols Solved 1n5b 1k6z 97 4 Yes
1nio
1ggp_A 1
1cv7
1gfl 96
1k6d
1o91 2
1mzr
1a80 51
1h5q
1v18a 34 12 No

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

6. PART 2 Construction of “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 D , (2004)

7. Chainsaw Template Target Action >= Serine Prune to CG Alanine
Prune to CB
Glycine
Prune to CA
>= Alanine
Add CB

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