Sextant MR
SextantMRbeta
Molecular replacement · by Echo Life Sciences
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Molecular replacement in the browser

Place a search model in your crystal's unit cell: a six-dimensional search split into a rotation function and a translation function, scored against your measured intensities on the GPU.

Ready
1Model intensity grid
2Rotation function
3Translation & packing
4Rigid-body refinement
Load your diffraction data (MTZ) and a search model (PDB or mmCIF) on the right, then press Run molecular replacement. When the search finishes you can refine the solution at the bottom of the page.

Solution

CopyVerdictRFZTFZCCClashesEuler α β γ (°)Position (frac.)

The report is the complete record of the job: inputs, parameters, data analysis, every rotation and translation candidate, the solution, phasing statistics and the difference-density blobs. "Download all" packs it with the PDB, the phased MTZ and your input files.

Rotation function

How often each Z-score occurs over every sampled orientation (log scale). Noise piles up near zero; marks above the histogram are the refined peaks taken forward. A correct rotation usually sits clear of the rest.

Translation function

Section through the search grid at the chosen peak, coloured by Z-score. A single sharp maximum, ringed, is what a correct solution looks like.

Crystal packing

Cα trace of every placed copy (solid) and its symmetry mates (faint), wrapped into one unit cell. Look for continuous contacts without overlaps and for solvent channels that fit the Matthews estimate.

Log


    


    

      
Electron density
from the phased MTZ

      

        

        

          
          

          
          

          
The maps appear here once the phased MTZ is ready.

        

        
Drag to rotate · shift-drag to pan · wheel to zoom · shift-wheel to change the 2mFo−DFc contour · double-click an atom to centre on it.

        

        

          

            
            
1.2 σ

          

          

            
            
3.0 σ

          

          

            
            
10 Å

          

          
          

            
Positive difference blobs

            
Connected mFo−DFc density above +3σ, ranked by integrated density. Blobs beside incomplete residues or on top of model atoms are flagged; the view opens on the strongest unmodelled blob, the most likely spot for a ligand or ion.

            
Waiting for maps…

          

        

      

    


    

      
Refinement

      

        
Run molecular replacement first. The placed model and your data are then filled in here, ready to refine.

        

          

          

          
B-factors (ADP)
            

          

        

        

        

          
          
        

        
        
        

        
        
        
Refinement log 

        
Sextant Refine: maximum-likelihood amplitude target, bulk solvent and anisotropic scaling, geometry restraints, isotropic, mixed or anisotropic B-factors with an R-free test. Not yet included: occupancies, riding hydrogens, TLS, NCS restraints and twinning. The restraint library is derived from GeoStd, Copyright (c) 2009, The Regents of the University of California, through Lawrence Berkeley National Laboratory, used under its BSD licence.