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iMODFIT specifications


Unique identifier OMICS_26705
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data A fitted atomic structure and a score file to check for convergence and a used command log.
Output format PDB+TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
Computer skills Advanced
Version 1.44
Stability Stable
Maintained Yes




No version available


  • person_outline Pablo Chacon

Additional information

Publication for iMODFIT

iMODFIT citations


Robo1 Forms a Compact Dimer of Dimers Assembly

PMCID: 5807052
PMID: 29307485
DOI: 10.1016/j.str.2017.12.003

[…] 1 ECDa was then fitted as one rigid body using the ‘fit-in-map’ module of Chimera. Following this, the density corresponding to a Robo1 monomer was extracted, and flexible fitting was performed using iMODFIT (). For the flexible fitting, all individual domains were fixed, and only the linker regions: Ig1-Ig2, Ig4-Ig5, Ig5-Fn1, and Fn1-Fn2 were allowed to move. This monomeric model (B) was then doc […]


Diversity of Nicotinic Acetylcholine Receptor Positive Allosteric Modulators Revealed by Mutagenesis and a Revised Structural Model

PMCID: 5767682
PMID: 29196491
DOI: 10.1124/mol.117.110551

[…] sed cross-correlation coefficient of 0.82) clearly following the density shape. In the third stage, the model containing the refined loop was used as input for normal mode-based flexible fitting with iMODFIT () into the density maps of both closed and open conformations of the Torpedo nAChR (EMD-2071 and EMD-2072, respectively) (). In the final stage, the open and closed models produced by iMODFIT […]


Tools for the cryo EM gold rush: going from the cryo EM map to the atomistic model

Biosci Rep
PMCID: 5715128
PMID: 28963369
DOI: 10.1042/BSR20170072

[…] fore, the battery approach is useful to confer modeling confidence to identify local regions that are likely to fit well. A similar conclusion was made with other flexible methods as well: flexEM and iMODfit [] (). Not only did they derive the same conclusion, but also they improved the fit by using both of these flexible fitting methods (first they identified poorly fitted region by comparing res […]


Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase

Sci Adv
PMCID: 5544394
PMID: 28798962
DOI: 10.1126/sciadv.1701726
call_split See protocol

[…] , respectively) were used to model the pore loops disordered in other crystal structures. Initial rigid body fitting of the monomers in the map was manually done in Chimera using the Fit in Map tool. iMODFIT () was used for fitting involving large domain motions. Flex-EM () was then used for refinement of secondary structures and loops in the map. Energy minimization to fix geometry was performed […]


The Structure of the R2TP Complex Defines a Platform for Recruiting Diverse Client Proteins to the HSP90 Molecular Chaperone System

PMCID: 5501727
PMID: 28648606
DOI: 10.1016/j.str.2017.05.016
call_split See protocol

[…] tomium thermophilum) and 2C9O (human RUVBL1). The atomic model was initially fitted using the rigid body approach available in UCSF Chimera (), and further refined using the flexible fitting software iMODFIT (). EM maps and atomic models were visualized using UCSF Chimera (). Fitting of crystal structures of the CS domain of Pih1p bound to Tah1p (PDB 4CGU) and the N-terminal PIH domain of Pih1p (P […]


Regulatory coiled coil domains promote head to head assemblies of AAA+ chaperones essential for tunable activity control

PMCID: 5699869
PMID: 29165246
DOI: 10.7554/eLife.30120.036
call_split See protocol

[…] onomers were generated using Phyre2 (). They were modelled based on the B. subtilis atomic structures (PDBcode: 3pxi). Each protomer was rigidly fitted manually using USCFChimera () and refined using iModFit (). For the ClpC resting state structure, real-space refinement in Phenix and Rosetta was performed trying to optimise as much as possible the model geometry and giving less weight to the map. […]


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iMODFIT institution(s)
Department of Biological Physical Chemistry, Rocasolano Physical Chemistry Institute, CSIC, Madrid, Spain
iMODFIT funding source(s)
Supported by BFU2009-09552, CAM S2010/ BMD-2353 and by the Human Frontier Science Program – RGP0039/2008.

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