LAFIRE : an automatic refinement software


LAFIRE (Local-correlation-coefficient-based Automatic FItting for REfinement) is an automatic refinement system for protein crystallography. The system starts with an initial model (approximate or partial model) and finishes with the final structure including water molecules. LAFIRE uses the refinement programs CNS (v. 1.2 or 1.3) , Refmac5, phenix.refine or autoBUSTER.

At first step, LAFIRE confirms amino residues of the initial model based on the sequence file that may be provided by the program user, and displaces the incorrect amino residues of the model.

In the refinement loop, the program first builds the parts that are missing in the model or seriously misfitted to the electron density map calculated from the observed phases or to the 2fo-fc, fo-fc maps. Then, correlation coefficient is calculated for each residue, and if the correlation is not good enough, the corresponding residue is subjected to the refitting routine.

LAFIRE also writes out the file of Rfree/Rwork factors and Ramachandran plot for the current model in order to monitor the progress of refinement. The Rfree/Rwork factor plot and Ramachandran plot can be viewed easily using graphics program Lafire_moleview. (Lafire_moleview is only for SGI version.)

From v. 4.0, the new programs NAFIT and NABUILD for automated nucleic acid refinement were included.

<Past and actual situation>

The beta-version of LAFIRE has been released on May, 1, 2004. Since then, LAFIRE was debugged and improved several times. The current version is 4.0:
June 30, 2013 : version 4.0
The new features in v. 4.0:
  1. Fitting and building programs for automated nucleic acid refinement are added (NAFIT & NABUILD).
  2. Besides REFMAC5 and CNS supports, phenix.refine and autoBUSTER can be chosen for refinement.
  3. LAFIRE_FBDD, a pipeline for Fragment Based Drug Design is introduced.
  4. Debug.


For profit users LAFIRE is charged. They are requested to E-mail to the address below.

<Download (nonprofit use only)>

(All users who has only registered for beta-version of LAFIRE, need to be registered again as a new user for over version 1.0.)
If this is the first time to download LAFIRE, please do registration first.
If you are already registered, please choose "Download".
For installing LAFIRE, please see "LAFIRE manual"

Registration for an account and password to download Lafire (for the first time)
Download (if you are already registered)


  1. "LAFIRE: software for automating the refinement process of protein structure analysis".
    YAO M., ZHOU Y., AND TANAKA I., Acta. Cryst., D62, 189-196
  2. "New algorithm for protein model building: extending partial model in map segment".
    ZHOU Y., YAO M., AND TANAKA I., J. Appl. Cryst., 39, 57-63
  3. "New model-fitting and model-completion programs for automated iterative nucleic acid refinement"
    YAMASHITA K., ZHOU Y., TANAKA I., AND YAO M. Acta Cryst., D69, 1171-1179


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