AMPLE (CCP4: Unsupported Program)

NAME

AMPLE - automated de novo search model generation for molecular replacement

SYNOPSIS

Utilises programs like Rosetta to generate ab initio models to be used in molecular replacement:

ample.py [-h] [-ROSETTA ROSETTA_path] [-RDB ROSETTA_database] [-fragsexe path to make_fragments.pl] [-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]

DESCRIPTION

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

DEPENDENCIES

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

• SCWRL (version 4.0) available from: Rosetta (tested with versions 3.2 and 3.3) Rosetta
• Theseus (ver. 1.4.3) Theseus
• Maxcluster (ver 0.6.6) (as a replacement for LGA) Maxcluster
• SHELX (Beta version of shelxe)
• phenix (optional)

INPUT AND OUTPUT FILES

HKLIN

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

FASTA

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

COMMAND LINE INPUT

optional arguments:

• -h, --help     show this help message and exit

• -ROSETTA ROSETTA_path     path for Rosetta AbinitioRelax

• -RDB ROSETTA_database     path for Rosetta database

• -fragsexe path to make_fragments.pl     location of make_fragments.pl

• -Rosetta_cluster path to Rosettas cluster     location of rosetta cluster

• -fasta fasta_file     protein fasta file. (required)

• -name priotein name     name of protien in the format ABCD

• -NProc NoProcessors     number of processers (default 1)

• -RunDir run_directory     directory to put files (default current dir)

• -SCWRL path to scwrl     pathway to SCWRL exe

• -LGA path_to_LGA dir     pathway to LGA folder (not the exe) will use the 'lga' executable

• -MAX Maxcluster exe     Maxcluster exe

• -THESEUS Theseus exe (required)     Theseus exe

• -MTZ MTZ in     MTZ in

• -MODELS folder of decoys     folder of decoys

• -MakeModels Do the modelling     run rosetta modeling, set to False to import pre-made models (required if making models locally default True)

• -ROSETTA_DIR Rosetta_dir     the Rosetta install directory

• -F Flag for F

• -SIGF Flag for SIGF

• -FREE FreeR flag

• -CLUSTER True if using a cluster, false if a multi-core PC 

• -percent percent of the model to truncate at each interval 

• -NumShelxCyc number of shelxe cycles to perform?|

• -NoShelx will not run shelx, will only run MRBUMP?|

• -TRYALL if True will try all ensembles, if False will exit at the first success?|

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)
make_fragments.pl (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)

EXAMPLE USAGE

PROGRAM OUTPUT

AUTHORS

Jaclyn Bibby, University of Liverpool, UK 

ACKNOWLEDGEMENTS

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:

MrBUMP

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

CCP4

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

FASTA

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

MOLREP

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

PHASER

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

REFMAC

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