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Helixhunter and Foldhunter

software for data interpretation of intermediate resolution structures

Wen Jiang

Matthew Baker

Publication: Bridging the Information Gap: Computational Tools for Intermediate Resolution Structure Interpretation. Journal of Molecular Biology (5, May 2001) Vol 308, No. 5, p1033-1044, doi:10.1006/jmbi.2001.4633

**Individual Programs Implemented Here**
helixhunter	takes intermediate resolution density map and find the possible helices, output the helices in VRML, Open Inventor, COSEC, DejaVu formats. parallelizd with OpenMP
foldhunter	quantitatively fit the partial subunit/domain structure into another larger structure, output the transformed partial structure, a list of candidate transforms in text, csh script, and binary format for a IRIS Explorer module. parallelized with pthreads
symAxisSearch	iteratively search the local rotation symmtry axis. output the symmetry coefficients at different slices and mask out all voxels that are more symmtric than threshold. parallelized with OpenMP
pdb2sse	parses the PDB file to generate DejaVu and COSEC format files for the helices by central axis fitting, only use the definitions of helices in the header
iv2cosec	converts the descriptions of helices from Open Inventor format to COSEC format
iv2dejavu	converts the descriptions of helices from Open Inventor format to DejaVu format
ivTransform	transforms (rotate, translate, mirror) the helices defined in Open Inventor format
ivFit	takes the COSEC result of matched pairs of helices to find the overall rotation and translation needed to fit the two groups of helices
cosec2iv	converts the descriptions of helices from COSEC format to Open Inventor format
dejavu2iv	converts the descriptions of helices from DejaVu format to Open Inventor format
euler2quater	converts the rotation defined with 3 Euler angles (EMAN convention) to the 4 numbered Quaternion format

**Useful Third-party Programs**
ribbons	generates ribbons representation of atomic model from a PDB file
IRIS explorer	a complete visualization package by NAG with extensive custom add-on modules from NCMI
ivview	views Open Inventor files, part of Open Inventor package, available on all SGI computers (example file)
cosmoplayer	views VRML files, available for SGI IRIX and Windows systems (example file 1, example file 2)
kaptain	universal graphical front-end for command line programs. the download source won't compile on SGI because of a bug in the configure script, but I have figured out the bug and compiled it on SGI successfully. Contact me if you are interested to know how it is done.
dejavu	searches for homologous structure at secondary structure level (example file)
cosec	searches for homologous structure using graph theory with vectorized secondary structure elements (example file)
EMAN	single particle reconstruction package, provides file handling programs such as pdb2mrc, proc3d

Sample data files:
A 8Å resolution density map in MRC format: 1BVP-single-8A-density.mrc
The helixhunter result in Open Inventor format: 1BVP-single-8A-hh.iv
The ribbons representation of atomic structure and helixhunter result in Open Inventor format: 1BVP-single-ribbon-hh.iv

Some test results:
helixhunter and foldhunter resolution dependency test results
helixhunter results on the 30 most often occuring folds
foldhunter results for some homologous structures

Download
These programs have been integrated into EMAN package, click here to download.

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