ARCIMBOLDO LITE

Simple, user friendly implementation for straightforward cases

ARCIMBOLDO_LITE runs on all cores of a single machine, without requiring a grid, supercomputer or database. The executable binary for LINUX and for MAC OS can be downloaded here

Latest update: January 2016

The same ARCIMBOLDO_LITE binary can run using a local or remote grid. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER are now also distributed as binaries and support both standalone or grid modes.

arcimboldo


1. Download the program

Register and download the ARCIMBOLDO_LITE binary.



2. Third party programs

PHASER and SHELXE have to be available on the machine running ARCIMBOLDO. These programs have separate licenses and need to be obtained from their developers if not already installed:

In addition, Python 2.6 or higher must be installed.



3. Running ARCIMBOLDO_LITE

Once these requirements are fulfilled, you will need:

  1. An .mtz file containing the reflection data in CCP4 format
  2. An .hkl file containing the reflection date in SHELX format
  3. A .bor file containing the input for ARCIMBOLDO.

The following is an example of a .bor configuration file

[CONNECTION]:
distribute_computing: multiprocessing
#NOTE: You need to configure the following parameter
#only if you are using the mode local_grid or remote_grid
#setup_bor_path: /path/to/setup.bor

[GENERAL]:
working_directory= /path/to/workdir
mtz_path: %(working_directory)s/data.mtz
hkl_path: %(working_directory)s/data.hkl

[ARCIMBOLDO]
name_job: example
molecular_weight: 
f_label: F
sigf_label: SIGF
number_of_component: 1
fragment_to_search: 2
helix_length: 14

[LOCAL] 
path_local_phaser: /path/to/local/phaser
path_local_shelxe: /path/to/local/phenix

[CONNECTION]

This section defines the connection to remote or local grids if needed. Default in ARCIMBOLDO_LITE is multiprocessing on a single machine. The setup.bor file path is only required if a grid is used (further information).


[GENERAL]

This section defines paths to the working directory and data files.


[ARCIMBOLDO]

This section declares the ARCIMBOLDO_LITE search parameters. For a full list of possible parameters, run ARCIMBOLDO_LITE with -b option


[LOCAL]

This section contains the absolute paths to the PHASER and SHELXE executables required for single machine use.



Execution

  1. Interactively:

    ARCIMBOLDO_LITE  input.bor 
  2. In background:

    ARCIMBOLDO_LITE input.bor >& log & 
    


Output

On the working directory, there is an .html file with an echo of the input parameters, a table with the results and map and trace files from the best solution produced, if possibly solved (CC>25 %).



References

  1. Phaser crystallographic software. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007) J Appl Cryst. 40, 658-674.
  2. Extending molecular-replacement solutions with SHELXE. Thorn, A. & Sheldrick, G. M. (2013) Acta Cryst. D69, 2251-2256.
  3. Exploiting tertiary structure through local folds for ab initio phasing. Sammito, M., Millán, C., Rodríguez, D. D., M. de Ilarduya, I., Meindl, K., De Marino, I., Petrillo, G., Buey, R. M., de Pereda, J. M., Zeth, K., Sheldrick, G. M. & Usón, I. (2013) Nat Methods. 10, 1099-1101.

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