AMPLE (CCP4: Unsupported Program)


AMPLE - automated de novo search model generation for molecular replacement


Utilises programs like Rosetta to generate ab initio models to be used in molecular replacement: [-h] [-ROSETTA ROSETTA_path] [-RDB ROSETTA_database] [-fragsexe path to] [-Rosetta_cluster path to Rosettas cluster] [-fasta fasta_file] [-name priotein name] [-NProc NoProcessors] [-RunDir run_directory] [-SCWRL path to scwrl] [-LGA path_to_LGA dir] [-MAX Maxcluster exe] [-THESEUS Theseus exe required] [-MTZ MTZ in] [-MODELS folder of decoys] [-MakeModels Do the modelling] [-ROSETTA_DIR Rosetta_dir] [Command line options]


AMPLE has three main parts:

  1. For a given target sequence, calls Rosetta for the ab initio modeling of protein decoys, or reads in a set of pre-made models
  2. Preparation of decoys into search ensembles for molecular replacement
  3. Running molecular replacement using these search ensembles and inputting MR results into SHELX


Before AMPLE can be used, the following dependencies should be installed on the local system.



Input structure factor file for target structure. Must include a FreeR flag column.


Fasta of the target, followed by a new line.

Intermediate Output files

Generated models will output to the "Models" directory.

The models are clustered and the clustered models are output to the "clusters" directory.

Ensembles are made and places in the "ensembles" directory. 

MRBUMP will run in the "MRBUMP" directory.

SHELX will run in each MRBUMP run directory

Final Output files

Potential solutions will be placed in the "RESULTS" directory


optional arguments:

Using the GUI

Input Files

HKLIN: mtz file. The flags F, SIGF and FREE must be set.
number of processors: int for parallel running for speed
Fasta: must have a new line char at end of sequence
work directory: where all run files are generated

Models Import

Make Models: if you want Rosetta to make the models locally, specify "True". If you have models already made specify "False" and give a path to a folder containing them.
Models Path: specify "none" to make them locally. give a path if importing.

Rosetta Quick

Rosetta Install Directory: Install folder of Rosetta will try to find paths of the executables.

Rosetta Full Pathways

for a non standard install, the paths may be different. So give the following paths:
AbinitioRelax.linuxgccrelease (executable)
rosetta_database (folder pathway) (executable)
cluster.linuxgccrelease (executable)

3rd Party Locations

For some functions some 3rd party executables are needed, give the pathways if not in PATH:
maxcluster (executable)
Scwrl4 (executable)
theseus (executable)




Jaclyn Bibby, University of Liverpool, UK 


Daniel Rigden, Martyn Winn, Olga Mayans.

AMPLE Program References

Any publication arising from use of AMPLE should include the following reference:

AMPLE: a cluster-and-truncate approach to solve crystal structures of small proteins using rapidly computed ab initio models

In addition, authors of specific programs should be referenced where applicable:


R.M.Keegan and M.D.Winn (2007) Acta Cryst. D63, 447-457


Collaborative Computational Project, Number 4. (1994), "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763


W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85, 2444-2448


A.A.Vagin & A.Teplyakov (1997) J. Appl. Cryst. 30, 1022-1025


McCoy, A.J., Grosse-Kunstleve, R.W., Storoni, L.C. & Read, R.J. (2005). "Likelihood-enhanced fast translation functions" Acta Cryst D61, 458-464


G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method" Acta Cryst. D53, 240-255