IMPORTANT
NOTE TO
THOSE WHO HAVE USED OLDER OR OTHER VERSIONS OF PFT2
AND EM3DR2
(EMPFT, EM3DR, etc.)
The convention of the OMEGA angle was changed for PFT2 and
EM3DR2. OMEGA(new) = OMEGA(old) + 90 deg. This was done to
make the angle consistent between the projections of the 3D model and
the 2D images. If you use the old convention in EM3DR2, the
output reconstruction will be corrupted (and should be obviously
wrong). Also, the STAR format (see discussion
of parameter-file format on the PFT2 page) is
required for the input of particle and other parameters. To
convert to the new convention do the following four steps (you may also
use a utility that will
convert from the older PFT data files [e.g.
*.DAT file] to the STAR format and vice versa and can do the
changes mentioned below in 1-3):
1) Add 90 deg. to OMEGA. Use a utility or the following
Bsoft
command: "bstar -floatscale _particle.omega 1.0,90 -output
out.star in.star". (Note: If you used an older version of
PFT that already had the OMEGA convention changed [typically named
PFT_DMB*], you should ignore this step.)
2) Remove commas from the spaces between the parameter values.
Then add the "loop_" structure to the beginning of each block of
particle parameters.
3) Make a data block for each micrograph. Parameters such as
units, voltage, and pixel size go here.
4) Check the output reconstruction
for consistency to the previous
reconstruction--especially the handedness. If the handedness is
opposite, you may have subtracted 90 deg. instead of adding 90 deg.
2 Dec 2006
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