UCSD Baker Home Page
Introduction Lab Members Courses Images Publications Computer Programs Procedures Access Scope Facilities

Electron Microscopy Programs

Software To-Do List (password protected)

Production Code of the EM System (purdueEM_v2.20.tar.gz - Feb. 6, 2006)

Documentation for Programs Currently in Use



Last Update

Cuts a 3D MAP based on input of a radius, row, column or section numbers 11-13-03
EM3DR Produces a 3D MAP from a set of particle images 08-24-04
EMCORORG Uses cross-correlation procedures to determine the location of the origin of particles which appear circular in projection 11-14-03
EMICOFV This is a "brute force"program that determines orientations of icosahedral particles. This is the original common lines program at Purdue University that was developed from the MRC FINDVIEW program. 11-14-03
EMICOGRAD Refines the orientation of up to 200 icosahedral particles against each other. EMICOGRAD is usually used following EMICOFV and EMICOORG (origin determination program). 09-15-94
EMMAP3DT Calculates 3D structure factors from a 3D MAP 11-14-03
EMMAPZOOM Magnifies or demagnifies a 3D MAP or a portion of a 3D MAP 11-14-03
EMPFTPRJ Calculate a database of projection and polar Fourier transform data 11-14-03
EMPRJ Produce a series of projection images from a 3D MAP 11-14-03
EMRESOL(html) Calculate the resolution of the EM reconstruction. The function is similar to the EMSF program 11-13-03
EMROTAVG Form aligned average of rotationally symmetric images 11-14-03
EMROTFLT Rotational filtering and power spectrum 11-14-03
EMSF Multipurpose structure factor manipulation program 11-14-03
EMSF3DBT Inverse 3D FFT of 3D structure factor data; produce 3D MAP file 11-14-03
EMSFREF All purpose 2D crystal structure factor data manipulations 7-31-86
FFT(html) Reads 3D Maps and 2D images in the Pif format and calculates FFTs 11-13-03
OOR Determines orientations and origin values for particle images based on a comparison with model data. OOR performs the refinement over a limited search window. 08-18-04
PFTSEARCH Determines orientations and origin values for particle images based on a comparison with model data. PFTSEARCH performs a global search over the entire asymmetric unit. 08-18-04

From High to Low
From High to Low contains information on how you can compute low-resolution density from an atomic model.

ROBEM README(txt file)
How do I get ROBEM to run?

ONED is useful for illustrating in one-dimension the principles of diffraction theory

Procedure for using the Zeiss scanner on electron microscopy data.

System Information



Last Update

EMICO_SYS Contains lists of programs and available documentation, common variables and parameters used in emico programs, and a reference list 1-31-97
EMPROGS Contains a listing and brief description of current and older EM programs, descriptions of file structures, descriptions and declarations of common variables, and other general program information  12-22-97
EMSYSTEM Provides basic information concerning the use and setup of the set of electron micrograph image analysis programs 9-8-89
PIF Contains information regarding the Portable Image Format (PIF) for electron microscopy data 10-29-98

  Older Documentation Archives

Baker Home Page Contact Site Map Search Baker Site Baker Group Calendar