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This version (2018/02/26 11:17) is a draft.
Approvals: 0/1


3D Refinement: OLD VERSION!!! Perform 3D structure refinement. This command is planed to removed in near future. It is kept here for the comparison evaluation of performances between continuation refinement from sorting results of this version and local refinement of new version.


Usage in command line  stack  output_directory  initial_volume  --radius=particle_radius  --mask3D=MASK3D  --symmetry=SYMMETRY  --inires=INIRES  --delta=DELTA  --do_final=DO_FINAL  --memory_per_node=MEMORY_PER_NODE  --ctref  --ctref_subset=selection_file_path  --ctref_oldrefdir=refine_dir_path  --ctref_iter=restarting_iteration  --ctref_initvol=restarting_initial_volume  --ctref_orgstack=stack_for_continuation  --ctref_smearing=smear_usage  --ctref_an=angular_neighborhood_for_continuation  --xr=XR  --ts=TS  --skip_prealignment  --initialshifts  --center_method=CENTER_METHOD  --target_radius=TARGET_RADIUS  --shake=SHAKE  --small_memory  --ref_a=REF_A  --ccfpercentage=CCFPERCENTAGE  --nonorm  --function=user_function

Typical usage

sxmeridien_20171120 exists only in MPI version.

1. Fresh run:

mpirun  -np  88  bdb:data  meridien_outdir  ref3d.hdf  --mask3D=mask3d.hdf  --radius=145  --symmetry=c5

2. Continue run/simple restart:

mpirun  -np  88  meridien_outdir

3. Continue run/restart with altered parameters:

mpirun  -np  88  meridien_outdir  โ€”-raduis=140

4. Do only final reconstruction at a specific iteration:

mpirun  -np  88  meridien_outdir  โ€”-do_final=23

5. Do only final reconstruction using the iteration which achieved the best resolution:

mpirun  -np  88  meridien_outdir  โ€”-do_final=0

6. Continuation refinement from sorting results:
Please use --ctref option, then specify the directory where you wish to continue the refinement to --ctref_oldrefdir option and a subset of data to --ctref_subset option. The command will load the refinement information from the directory and continue refinement. Optionally, you can specify the iteration number for continuing refinement using --ctref_iter option, which is not necessarily be the same iteration where you used for the 3D sorting. Also, one can modify refinement parameters of the selected iteration through the other options.

mpirun  -np  88 refine_subset3 --ctref  --ctref_oldrefdir=meridien_outdir  --ctref_iter=20  --ctref_subset=Clusters3.txt


Main Parameters

Input image stack: (default none)
Output directory: The results will be written here. This directory will be created automatically if it does not exist. (default none)
Initial 3D reference: (default none)
Particle radius [Pixels]: Outer radius [in pixels] of particles < int(nx/2)-1 (default -1)
3D mask: Soft mask for the volume. If not given, a hard sphere of radius boxsize/2-1 will be used. (default none)
Point-group symmetry: Symmetry of the refined structure. Acceptable values are: cn, dn, where n is multiplicity. (default c1)
Starting resolution [A]: Resolution used to start the refinement. (default 25.0)
Initial angular sampling step [Degrees]: Initial angular sampling step. (default 7.5)
Do only final reconstruction: Specify the iteration where you wish to perform only final reconstruction using the alignment parameters. By setting to 0, program searches the iteration which achieved the best resolution, then performs only final reconstruction using the alignment parameters. By default, the program performs the final reconstruction using the best iteration after the convergence. (default -1)
Memory per node [GB]: User provided information about memory per node in GB (NOT per CPU). By default, it uses 2GB * (number of CPUs per node) (default -1.0)
Continuation refinement: Continue refinement from a local/exhaustive state using the full dataset or selected subset.(default False)
Selection text file: Selection text file that contains indexes of the data subset. Typically, Cluster#.txt created by sxrsort3d_new (e.g. Cluster1.txt). (default none)
3D refinement directory: The master output directory of 3D refinement run which you wish to continue. (default none)
Restarting iteration: The iteration from which 3D refinement should be continued. (default -1)
Initial 3D reference for continuation: User-provided 3D reference for continuation run. Effective only for continuation refinement. (default none)
BDB stack for continuation
BDB stack for continuation with xform.projection parameters written in the headers. If this option is set, the program ignores the ctref_oldrefdir option. Effective only for continuation refinement. (default none)
Smear usage of initial 3D reconstruction: -1: Use optimal xform.projection parameters only and norm = 1.0; 0: Use all smears; >1: Use option specified number of smears. Effective only for continuation refinement. (default -1)
Initial angular neighborhood [Degrees]: Angular neighborhood for local search during initial 3D reconstruction of continuation refinement. Effective only for continuation refinement. (default -1.0)

Advanced Parameters

Search range [Pixels]: Range for translation search in both directions. Search is +/-xr. It can be fractional (default 5.0)
Search step size [Pixels]: Step size of translation search in both directions. Search is within a circle of radius xr on a grid with steps ts. It can be fractional. (default 1.0)
Do 2D pre-alignment: Indicate if pre-alignment should be used or not. Do not use 2D pre-alignment if images are already centered. By default, do 2D pre-alignment. (default False question reversed in GUI)
Read shifts from header: Start with the shift parameters stored in the image headers. Useful to jumpstart the procedure. (default False)
Centering method: Method for centering averages during initial 2D prealignment of data (0: no centering; -1: average shift method; For 1-7, see center_2D in (default -1)
Target particle radius [Pixels]: For 2D prealignment, images will be shrank/enlarged to this radius. (default 29)
Shake: Shake (default 0.5)
Keep data in memory: Indicate if data should be kept in memory or not. By default, data will be kept in memory. (default False question reversed in GUI)
Projection generation method: Method for generating the quasi-uniformly distributed projection directions. S- Saff algorithm, or P - Penczek 1994 algorithm. (default S)
Correlation peaks to be included [%]: Percentage of correlation peaks to be included. 0.0 corresponds to hard matching. (default 99.9)
Apply image norm correction: Indicate if image norm correction should be applied or not. By default, apply image norm correction. (default False question reversed in GUI)
Reference preparation function: Function used to prepare the reference volume after each iteration. (default do_volume_mask)





Developer Notes

Author / Maintainer

Pawel A. Penczek





See also

References to relevant other routines.


Beta:: Under evaluation and testing. Please let us know if there are any bugs.


There are no known bugs so far.

pipeline/meridien/sxmeridien_20171120.txt ยท Last modified: 2018/06/20 13:12 (external edit)