Frealign

I was testing frealign_v8_mpfftw with 4 CPUS as I wrote my earlier note and knew that it wasn't running through the data any faster than frealign_v8_fftw would. However, it has now finished the per particle search and seems to be burning all the CPU of two processors but accomplishing nothing. It has been sitting in the state for 5 or 10 minutes by now. I also probably should have mentioned that I am using the pre-compiled versions that came in the download...

I'm playing around with the v8 release of frealign. I have been bench-marking the various versions ("vanilla," fftw, mp, mpfftw) using the test data set you include (pdh). Perhaps I'm doing something wrong, but for the search example, I see absolutely no difference when I try to add more processors to the mp and mpfftw versions. I know that the program thinks it has access to more processors since I get things like

Parallel processing: NCPUS = 4

I am putting together a table of differences between 2-D alignment operations for different EM processing packages. Would you please inform me of the following conventions used in the Frealign projection-matching based refinement algorithm:

1) In which direction does inplane rotation proceed? (e.g. positive = counterclockwise) ???
2) in which direction do shifts proceed? (e.g. +x = right, +y=up) ???
3) when performing a particle alignment to a projection, what is the order of operations? (e.g. rotate, shift, mirror) ???

I am learning to use Frealign to refine the structure of a single particle. Do you have an available script file that I can start with?

I read your 2007 JSB paper (FREALIGN: High-resolution refinement of single particle structures) and learned that the frealign can deal with multiple data sets taken at different microscope with different magnification and merge them together? How do I use this feature?

I am reading your Frealign paper. I got several questions:

1) The parameter ASYM could be I, I1, I2, what is the difference? Is it related to the input initial model?

2) In 4.4. "Particle parameters" of your paper, there are two sentences as (in quotes):

I have been trying to do RCT of my receptor with Michael Radermacher and at this point I want to try FREALIGN v7. I have made a couple of attempts, however, there appears to be a problem with the file format of my images, as FREALIGN gives an error when reading the file. I used EMAN to create stacks for refinement with EMAN and then used em2em to convert them into SPIDER stacks. The original images are stored as single SPIDER files, as that is the format Michael is most comfortable with.

I was looking through the code for frealign_v8.f in version 8.08 to learn more about the OpenMP support and found that either OMP_NUM_THREADS or NCPUS can be used to set the number of OpenMP threads desired.

I just had a couple of rather simple questions about this...

First - Is there any difference in performance between the MP version with NCPUS set to 1 and the non-MP version?

I have a problem to convert the imagic stack file of boxed particle into mrc stack file using em2em due to the large file size (~8 GB). Is it possible to have the normalized imagic stack image file as the input image file for running frealign? Is so, how about the format of initial model and the parameter file?

Also, do you have or know any program other than em2em that can convert large data set from imagic stack to mrc stack?

A few questions about frealign v8.07:

- what does FPART in card1 refer to?
- what does DFSTD in card7 refer to and what kind of values should it get?