Initial 3D Model - VIPER: ab initio 3D structure determination using Validation of Individual Parameter Reproducibility (VIPER). Designed to determine a validated initial model using a small set of class averages produced by ISAC2.

Usage in command line

sxviper.py stack  directory  --radius=outer_radius  --sym=sym  --ir=inner_radius  --rs=ring_step  --xr=x_range  --yr=y_range  --ts=translational_search_step  --delta=angular_step  --center=center_type  --maxit1=max_iter1  --maxit2=max_iter2  --mask3D=mask3D  --moon_elimination=moon_elimination  --L2threshold=L2threshold  --ref_a=ref_a  --nruns=nruns  --doga=doga  --fl=fl  --aa=aa  --pwreference=pwreference  --debug

sxrviper exists only in MPI version.

mpirun --npernode 16 -np 24 --host node1,node2 sxviper.py  stack output_directory --fl=0.25 --radius=30 --xr=2 --moon_elimination=750,4.84

A fast track option, that can be used to choose parameters in the appropriate ranges (for example, obtaining adequate spatial frequency filtering --fl) is provided below. Since it employs extreme values for some parameters this command can be used only for parameter tuning for the VIPER algorithm.

mpirun --npernode 16 -np 16 --host node1 sxviper.py  stack output_directory --fl=0.25 --radius=30 --xr=1 --nruns=2   --L2threshold=1.0e300  --doga=-1

The VIPER program needs MPI environment to work properly. Number of used MPI processes must be a multiple of --nruns (default = 6).

Since VIPER makes use of group of processors working together, it is important from a time efficiency point of view to have processors within a group being allocated on the same node. This way any data exchange within the group does not use network traffic. The --npernode option of mpirun is useful in accomplishing this goal. As shown in the example below when --npernode is used mpi allocates the ranks of the processors sequentially, not moving to the next node until the current one is filled. If --npernode is not used then processors are allocated in a round robin fashion (i.e. jumping to the next node with each allocation). Since in VIPER, groups contain consecutively ranked processors, it is important to provide “--npernode XX”, where XX is the number of processors per node.

stack

Input images stack: A small set of class averages produced by ISAC2. (default required string)

directory

Output directory: The directory will be automatically created and the results will be written here. If the directory already exists, results will be written there, possibly overwriting previous runs. (default required string)

--radius

Target particle radius [Pixels]: Use the same value as in ISAC2. It has to be less than half the box size. (default 29)

--sym

Point-group symmetry: Point-group symmetry of the target particle. (default c1)

--moon_elimination

Eliminate disconnected regions: Used to removed disconnected pieces from the model. It requires as argument a comma separated string with the mass in KDa and the pixel size. (default none)

--ir

Inner rotational search radius [Pixels]: Inner rotational search radius [Pixels]. (default 1)

--rs

Ring step size [Pixels]: Step between rings used for the rotational search. (default 1)

--xr

X search range [Pixels]: The translational search range in the x direction will take place in a +/xr range. (default '0')

--yr

Y search range [Pixels]: The translational search range in the y direction. If omitted it will be xr. (default '0')

--ts

Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default '1.0')

--delta

Projection angular step [Degrees]: Projection angular step. (default '2.0')

--center

Center 3D template: 0: no centering; 1: center of gravity (default -1.0)

--maxit1

Maximum iterations - GA step: Maximum iterations for GA step. (default 400)

--maxit2

Maximum iterations - Finish step: Maximum iterations for Finish step. (default 50)

--mask3D

3D mask: Path to 3D mask file. (default sphere)

--L2threshold

GA stop threshold: Defines the maximum relative dispersion of volumes' L2 norms. (default 0.03)

--ref_a

Projection generation method: Method for generating the quasi-uniformly distributed projection directions. S - Saff algorithm, or P - Penczek 1994 algorithm. (default S)

--nruns

GA population size: This defines the number of quasi-independent volumes generated. (default 6)

--doga

Threshold to start GA: Do GA when the fraction of orientation that changes less than 1.0 degrees is at least this fraction. (default 0.1)

--fl

Low-pass filter frequency [1/Pixels]: Using a hyperbolic tangent low-pass filter. Specify with absolute frequency. (default 0.25)

--aa

Low-pass filter fall-off [1/Pixels]: Fall-off of for the hyperbolic tangent low-pass filter. Specify with absolute frequency. (default 0.1)

--pwreference

Power spectrum reference: Text file containing a 1D reference power spectrum. (default none)

--debug

Verbose: Print debug info. (default False)

• This program uses a user-defined projection angle and translation shift to perform 3D reconstruction. The translation shifts, and step are not limited to integer number. For a given delta, the program will perform maxit round refinement. So the final refinement iteration is maxit*(number of delta values).
• For the program to work, attributes xform.projection (Transform object containing three Euler angles and two in-plane shifts) have to be set in the header of each file. If their values are not known, all should be set to zero.
• The program will start alignment from the current alignment parameters xform.projection stored in file headers.
• The program only change the alignment parameters in their header. The images in stack keep untouched. (Neither rotated nor shifted.)

Pawel A. Penczek

Category 1:: APPLICATIONS

sparx/bin/sxviper.py

sxisac2 and sxrviper

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

There are no known bugs so far.