[proc=<min proc>,<maxproc>] | Number of proceesors to use for parallel processing |
[hard=<maxpr>] | Hard limit for make3d |
[ctfc=<res in A>] | Performs CTF correction filtered to the specified resolution |
[ctfcw=<SF file>] | Performs CTF correction with Wiener filtration using a structure factor specified in a file |
[median] | Specify this when CTF correction is NOT being performed |
[sym=<c2,c4,etc>] | Imposes symmetry on the model |
[mask=<rad>] | Applies an outside mask in several stages of refinement |
[pad=<size>] | Pads the model during Fourier reconstruction |
[classkeep=<sigma coef>] | Classkeep value for <a href=classalignall.html>classalignall</a> |
[classiter=<iter>] | Iterations for <a href=classalignall.html>classalignall</a> |
[precen] | Indicates that raw particles have been accurately precentered |
[imask=<rad>] | Applies an inside mask in several stages of refinement |
[xfiles=<a/pix>,<mass in kd>,<ali to>] | Used to generate 3d models that are easy to evaluate |
[amask=<r>,<thr>,<n iter>] | This applies an automask between steps in a reconstruction. see automask2 in proc3d. REQUIRES xfiles to be used. |
[3dit=<n it>] | After constructing a model with Fourier reconstruction, this runs several iterations of real-space model 'cleansing' |
[3dit2=<n it>] | This is real-space refinement with a special maximum entropy-like feature extraction method |
[euler2] | Reassigns Euler angles to class averages using the same step used by refine. ie - 2 will use ang/2 (see <a href=classesrefs.html>classesrefs</a> |
Description
This program's options parallel refine. 'ttest' options are a
subset of refine's options. ttest is used to perform a fairly robust resolution
determination on a reconstruction. It is run in the same directory as a completed
refine command. Note that the refine command MUST terminate normally. Chances are
good that if refine is interrupted in the middle of a run, ttest will not produce
valid results. ttest splits each cls file into even and odd halves, then proceeds to
build an independent model based on each half of the data. By calculating a Fourier
shell correlation between the two resulting maps, a fairly robust resolution determination
can be made. For a proper determination, the data should be split into 2, 4, 8, etc sets,
then the resolution can be determined by interpolating to the entire data set. The
estimate made by comparing 2 halves of the data is actually slightly underestimating
the final resolution. Due to the rapid nonlinear falloff in signal to noise ratio
at resolution limiting spatial frequencies, this underestimation should be
relatively slight in most cases.
EMAN Manual page, generated Tue Oct 8 21:38:47 2002