Cryo-EM programs developed by Chuan Xiao (River)

In order to do my thesis research of the interaction between picornavirus and their receptors, I wrote many programs for cryo-EM reconstructions. All those programs are also widely used by researchers at Purdue. The purpose of this page is to list the programs and their helps. People can also refer to this page when they used these programs.

Program Description Last Update
Parallelized EMPFT and EM3DR Cryo-EM reconstruction core programs 05-02-2003
JOB and CYCLE Scripts that control the reconstruction 12-31-2001
AUTOSELECT Automatic selection of particles by sigma value 11-06-2001
AUTOSEPERATE Automatic seperation of particles for resolution calculation 12-08-2001
MAPFFT and IMGFFT FFT synthesis and and analyze programs for PIF map and images 02-05-2003
EMRESOL Calculate the Fourier Shell Corelation to estimate the resolution 05-02-2002
PIF2ASC Coversion program between PIF (image or map) and SPIDER,X-Plor,EM ASCII 08-28-2002
CTFEST CTF defocus value automatic estimation program 12-03-2002
CUTPIFMAP Soft cut the density of the protein shell of virus from a PIFMAP 11-13-2003
EMFOM Use FOM as a filtration for map improvement 09-10-2001
REALALIGN Real space alignment of focal pair images 01-06-2003
ROTBCRD Rotate box coordinates of focal pair images 01-31-2003
REBOX Generate re-centered coordinates file from initial PFT search 01-31-2003
FP_BRIEF Determine the initial matrix of focal pair 01-31-2003
RIVEM Radial Interpretation of Viral Electron density Maps 05-26-2006

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