Frealign with mask

Submitted by rainfieldcn on Tue, 2015-07-14 19:59

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Frealign

Dear Frealign developers,
I am told that Frealign has the mask option and I want to try it out.
I have just downloaded the latest version V9.10. But when I type frealign_template, I didn't find those masking settings.
I am wondering if I downloaded the wrong file or the template with mask option is not public available yet?
Thanks,
Lei

/t1/lei/soft/frealign_v9.10/bin/frealign_template

# Computer-specific setting
cluster_type none ! Set to "sge", "lsf", "slurm", "pbs" or "condor" when running on an SGE, LSF, SLURM, PBS or CONDOR cluster, otherwise set to "none".
nprocessor_ref 16 ! Number of CPUs to use during refinement.
nprocessor_rec 16 ! Number of CPUs to use during reconstruction.
mem_per_cpu 2048 ! Memory available per CPU (in MB).

# Refinement-specific parameters
MODE 1 ! 1, 2, 3 or 4. Refinement mode, normally 1. Set to 2 for additional search.
start_process 2 ! First cycle to execute. Output files from previous cycle (n-1) required.
end_process 2 ! Last cycle to execute.
res_high_refinement 6.0 ! High-resolution limit for particle alignment.
res_high_class 8.0 ! High-resolution limit to calculate class membership (OCC).
thresh_reconst 0.0 ! Particles with scores below this value will not be included in the reconstruction.
nclasses 1 ! Number of classes to use.

# Search-specific parameters
res_search 30.0 ! High-resolution limit for orientational search.
thresh_refine 50.0 ! Mode 4: Score threshold above which search will not be performed.
DANG 200.0 ! Mode 3 and 4: Angular step for orientational search.
ITMAX 200 ! Mode 2 and 4: Number of repetitions of grid search with random starting angles.
Bsearch 2000.0 ! B-factor filtering (when > 0) applied during search.

# Dataset-specific parameters
data_input particle ! Root name for parameter and map files.
raw_images /path/partice_stack
image_contrast N ! N or P. Set to N if particles are dark on bright background, otherwise set to P.
outer_radius 170.0 ! Outer radius of spehrical particle mask in Angstrom.
inner_radius 0.0 ! Inner radius of spehrical particle mask in Angstrom.
mol_mass 2500.0 ! Molecular mass in kDa of particle or helical segment.
Symmetry C1 ! Symmetry of particle.
pix_size 1.237 ! Pixel size of particle in Angstrom.
dstep 5.0 ! Pixel size of detector in micrometer.
Aberration 2.0 ! Sherical aberration coefficient in millimeter.
Voltage 300.0 ! Beam accelleration voltage in kilovolt.
Amp_contrast 0.07 ! Amplitude contrast.

# Expert parameters (for expert users)
XSTD 0.0 ! Tighter masking of 3D map (XSTD > 0) or particles (XSTD < 0).
PBC 20.0 ! Discriminate particles with different scores during reconstruction. Small values (5 - 10) discriminate more than large values (50 - 100).
refineangleinc 4 ! When larger than 1: Alternate between refinement of OCC and OCC + angles.
refineshiftinc 4 ! When larger than 1: Alternate between refinement of OCC and OCC + angles + shifts.
res_reconstruction 0.0 ! High-resolution limit of reconstruction. Normally set to Nyquist limit.
res_low_refinement 0.0 ! Low-resolution limit for particle alignment. Set to particle dimention or larger.
FMAG F ! T or F. Set to T to refine particle magnification. Not recommended in most cases.
FDEF F ! T or F. Set to T to refine defocus per micrograph. Not recommended in most cases.
FASTIG F ! T or F. Set to T to refine astigmatism. Not recommended in most cases.
FPART F ! T or F. Set to T to refine defocus for each particle. Not recommended in most cases.
FFILT T ! T or F. Set to T to apply optimal filter to reconstruction. Recommended in most cases.
FMATCH F ! T or F. Set to T to output matching projections. Only needed for diagnostics.
FBEAUT F ! T or F. Set to T to apply symmetry also in real space. Not needed in most cases.
FBOOST F ! T or F. Set to T to allow potential overfitting during refinement. Not recommended in most cases.
RBfactor 0.0 ! B-factor sharpening (when < 0) applied during refinement. Not recommended in most cases.
mp_cpus 1 ! Number of CPUs to use for each reconstruction job.
restart_after_crash F ! T or F. Set to T to restart job if it crashes.
delete_scratch T ! Delete intermediate files in scratch directory.
qsub_string_ref "" ! String to add to cluster jobs submitted for refinement (only for SGE and PBS clusters).
qsub_string_rec "" ! String to add to cluster jobs submitted for reconstruction (only for SGE and PBS clusters).
first_particle
last_particle
frealign_bin_dir
scratch_dir

# Janelia-specific parameters
night_queue T ! T or F. Set to T to use night queue.
reschedule_if_qw T ! T or F. Set to T to reschedule jobs on the normal queue if some end up waiting on night queue.

niko Tue, 2015-07-14 20:14

I just checked and the latest version has the masking option:

# Masking parameters (for expert users)
mask_file            
mask_edge             5		! Width of cosine edge in pixels to add around mask. Set to 0 to leave mask unchanged.
mask_outside_weight   0.0	! Factor to downweight density outside of mask (normally 0.0 - 1.0).
mask_filt_res         0.0	! Filter radius (in A) to low-pass filter density outside density. Set to 0.0 to skip filtering.
mask_filt_edge        5		! Width of cosine edge in reciprocal pixels to add to filter function.

Please download the latest version and try again.

rainfieldcn Wed, 2015-07-15 13:02

Hi Niko,
It worked this time. the previous error is probably due to the multiple version existed on our workstation and I messed up with path variables.
This time, when I started from par file, added mask without any reconstruction, I got an error: ERROR: mask and map dimension differ.
Then I run frealign one round without mask, it run and calculated the reconstruction. After that, I add the mask, it seems working.
So, does it mean I should get reconstruction first before I apply mask in the mparameters file?
Thanks,
Lei

niko Wed, 2015-07-15 13:07

Yes, the scripts currently assume that you have a reconstruction from a previous cycle (or from another source) available. If no further errors occur you can assume that it worked.