PFT2/EM3DR2 changes as compared
to PFT/EM3DR programs developed by T. Baker lab.
1) A new front end was written in C to be able to use
-command line
arguments
-the generalized parameter format from the Bsoft
package (the STAR format)
-the wide range of image formats supported by
Bsoft
2) As originally implemented, PFT only used amplitude information
in
the Fourier transforms to select the "best" view. Users can now
elect to have the program test multiple candidate orientations for each
particle with phase and amplitude information.
3) Multiple references can be used during a single PFT2 run.
4) The FORTRAN code was modified to be more portable, with the
removal of all POINTER, RECORD, COMMON, STRUCTURE, MALLOC and FREE
keywords. Memory allocation is now done through C wrapper
functions.
5) Numerous changes were made to remove unused variables and fix
small bugs, although the overall philosophy and execution of the data
processing was not changed significantly.
6) New modes of operation were added: origin, brute, theta, phi,
omega, mag, hand, and symmetry modes.
7) Some provisions for use of multiple processors on specific
architectures (primarily Apple and Intel processors).
8) PFT2 and EM3DR2 accept as input orientation parameters either i)
Euler angles, as either {phi, theta, psi} or {phi, theta, omega}, or
ii) View vector and angle. (See the PFT3DR
conventions and 3DEM
Image Conventions websites for more information.)
Other PFT2/EM3DR2 Changes
==============
PFT2 Changes
==============
1) Long option names replaced single letter options
Old New =================== a
select c
ctf f
fom g
allccs h
handedness m
mode n
phaseampl o
output p
outprjpft s
split t
time v
verbose
2) All parameters except particle parameters can be entered on the
command line. This includes (option name in parentheses) binning
(bin), symmetry (symmetry), angle step size (anglestep), radii (radii),
resolution (resolution), 3D input model (map), projections and PFTs
file names (inprjpft), jcut (jcut), and relative magnification
(mag) There is no longer a need to prepare a separate data block
of these general parameters. However, for backwards
compatibility, the program will still take input from such a file or
included data block.
3) Brute mode: This mode searches every possible THETA and PHI
angle and each possible OMEGA angle within each THETA and PHI. An
x,y origin is determined for each (PHI,THETA,OMEGA) view, Each
view is then tested via the chosen figure-of-merit (FOM). Only
FOM options 0, 3, 12, and 20 can be used.
4) Option "nopftresmin" can be used to turn off use of low-resolution
cut-off for PFTCC test (done in modes 1-3).
5) Resolution limits now are used for the PRJCC test in modes
1-3. Option "noprjccres" will turn this test off.
6) Renamed "search" mode in PFT2 to "sphere_search". This change
should help users realize that this mode is only good for spherically
shaped particles.
7) Changed the printing of the general parameters in PFT2. Names
were changed to be more "user-friendly" and the format and comments
were changed. I added some formulas to help users understand, for
example, how the different resolution parameters are calculated.
8) Added back the calculation of the averages of mags, and coefficients
at end of a run. Added explanation of the FOM chosen.
9) Screen mode output in ORIGIN mode is now similar to that in GLOBAL,
SPHERE_SEARCH, and REFINE.
10) Fixed a bug that appeared when multiple maps were used.
Instead of resetting the data to the input parameters
(theta,phi,omega,x,y) for the second, third, etc. map, pft2 used the
values from the previous run. Now values of particle parameters
from the input STAR file are always used as input when multiple maps
are used.
11) Fixed a bug that prevented REFINE mode from ending if the
asymmetric unit included THETA = 180 deg. (e.g. cyclic symmetries).
12) Fixed a bug in which some origins for bin factors > 1 were not
correct. Images binned in PFT are compressed in a way that keeps
the center pixel of the unbinned image also in the center of the binned
image. In addition, binned images are always made to have an odd
size. The problem was that the binning of the origin did not take
into account these two facts. Origins were always measured from
the 0,0 point (first pixel) of the image.
13) Step size for OMEGA is now equivalent to the step size for THETA
and PHI.
14) FOM options were expanded.
15) User now must specify an FOM option that requires R-factors for
them to be computed if the allccs option is chosen.
16) Old STAR tag names for radial parameters are changed to current
names
17) Optimized code for the PRJCC, map projection, and image
interpolation routines was implemented. This code will run
fastest on the PPC and Intel platforms. However, a significant
speed-up should be noticed on other platforms as well.
18) Theta,phi angles were not computed properly in refine mode for
cyclic symmetries (and probably other non-icosahedral symmetries as
well). This problem was fixed.
19) User may keep previous selection values (option "-keepselection")
20) Added octahedral and tetrahedral symmetries
21) User may skip origin refinement in modes 1, 2, 3, and 5,
sphere_search, global, refine, and brute, respectively.
================
EM3DR2 Changes
================
1) Explanation of how to use EM3DR2 to compute multiple maps from a
data set is now in the usage statement
2) 1/2 of map for icosahedral symmetry is now computed.
Previously only 1/4 was Output of 5-fold icosahedral map now
gives a full-size map, not 1/4.
3) Long option names replaced single letter options
Old New =================== 5
fivefold b
bgfile c
ctf l
lgfile m
mode n
numrecons o
output t
minpart v
verbose
4) All parameters except particle parameters can be entered on the
command line. This includes (option name in parentheses) binning
(bin), symmetry (symmetry), high resolution cut-off (resmax), output
resolution (resout), and relative magnification (mag). There is
no longer a need to prepare a separate data block of these general
parameters. However, for backwards compatibility, the program
will still take input from such a file or included data block.
5) Old STAR tag name (_em3dr.output_resolution) is changed to current
name (_em3dr.resolution_output)
6) User can output 3D map in any image datatype supported by Bsoft
(byte, short, float, etc.)
7) Compute multiple maps from selected particles
=================================================================================
"Internal" PFT2 & EM3DR2 Changes (changes that will not be
readily
apparent to the user)
=================================================================================
1) Cleaned up the PFTRAD_LO,PFTRAD_HI,ANN_LO,ANN_HI
"relationship". No longer are the PFTRAD variables changed to
ANN_LO,ANN_HI and then changed to 1 and max. radius.
2) To avoid the long list of parameters that are passed to and from the
FORTRAN functions in PFT2, many general parameters were put into
arrays. The individual values are then called from or put into
the arrays with a get and put function, respectively.
3) Reorganized pft_setup and PFT_CHECK routines.
4) PFTCC calculation revamped
-calculate Jn limits once (for each pixel size)
-some changes after the loops to avoid recalculations
-round to nearest integer instead of up for resmin and
down for resmax
5) Removed +1 indexing of radii in PFTCC and PRJCC calculations.
The conversion to polar coordinates is put into an array that begins
with PFTRAD_LO which equals 1. Therefore, the first radius is R =
1, not R = 0 (see GET_PRJSPFTS) and if a person select the max. radius,
that radius would be run through PFTCC twice (since the index is set to
the min of IR+1 or NANNULI).