Parameters#

rootdir

Path to the working directory.
Type: string
Example: /path/to/working/dir/ or ./working_dir/ or working_dir/

outputdir

Path to the directory where the outputs should be stored. If the specified directory does not exist, it will be created.
Type: string
Optional parameter - default value is outputs/

vol_ext

Type of the format in which the resuls will be written out. The supported formats are EM and MRC.
Type: string
Allowed values: “.em” or “.mrc”
Optional parameter - default is “.em”

tomo_name

Tomogram name (including the path in case the file is not in the rootdir).
Type: string
Example: tomo_126.rec or /path/to/tomo/tomo_126.rec

tomo_num

Identification number of a tomogram. This number will be used to search for the correct tomogram information in the provided wedge list.
Type: integer
Example: 126

tomo_mask_name

Path to the file with tomogram mask. The binary mask has to have the same dimensions as the tomogram. It is used in two ways. First, the bounding box is computed to contain all values equal to 1. This can reduce computation time since the bounding box can be way smaller than the tomogram. The second time, the binary mask is used, is by outputing scores map where the mask is used to multiply the scores map so only values corresponding to the mask regions with value 1 are kept. For the latter, same effect can be achieved by multiplying the scores map after the TM run.
Type: string
Example: tomo_mask_126.rec or /path/to/tomo/mask/tomo_mask_126.rec
Optional parameter

wedgelist_name

Name of the wedge list file (including the path in case the file is not in the rootdir).
Type: string
Example: wedge_list.star or /path/to/wedge/list/wedge_list.rec

tmpl_name

Name of the template file. It can be in MRC or EM format. The constrast of the template has to correspond to the tomogram. For more information see Required inputs.
Type: string
Example: template.em or template.mrc or /path/to/the/template.mrc

mask_name

Name of the mask. It can be in MRC or EM format. For more information see Required inputs.
Type: string
Example: template.em or template.mrc or /path/to/the/template.mrc

symmetry

Symmetry to be applied on the template prior the TM. Currently only cyclic symmetry is supported.
Type: string
Examples: C1 or C6 (the parameter is not case sensitive so c6 would work as well)
Optional parameter - default value is C1 (no symmetry)

anglist_name

Name of the file with Euler angles specifying the rotations. For more information see Required inputs.
Type: string
Examples: angles_5.txt or /path/to/the/angles_5.txt
Optional parameter - if not specified at least angincr has to be set in the parameter file (see below).

angincr

Out-of-plane angular increment in degrees. Defines how dense the cone will be sampled. In “zxz” Euler convention influences the theta (x) and psi (z2) angles.
Type: float
Examples: 10 (for 10 degrees sampling) or 20.5 (for 20.5 degrees sampling)
Optional parameter - if not specified the anglist_name has to be set in the parameter file (see above).

angiter

Out-of-plane angular iterations in degrees. Defines the total cone angle to be sampled as angincr*angiter (the maximum should be 180 degrees for the full sphere). In “zxz” Euler convention influences the theta (x) and psi (z2) angles.
Type: integer
Examples: 5 (with angincr of 10 it will sample the cone angle of 100 degrees)
Optional - if not specified, it will be set so the full sphere is sampled.
Used only if anglist_name is not specified.

phi_angincr

In-plane angular increments in degrees. Defines how densely the in-plane rotation will be sampled. In “zxz” Euler convention influences the phi (z1) angle.
Type: float
Examples: 10 (for 10 degrees sampling) or 20.5 (for 20.5 degrees sampling)
Optional parameter - if not specified it will be set to the same value as angincr parameter.
Used only if anglist_name is not specified.

phi_angiter

In-plane angular iterations. Defines the total in-plane angle to be sampled as phi_angincr*phi_angiter (the maximum should be 180 degrees for the full circle). In “zxz” Euler convention influences the phi (z1) angle.
Type: integer
Examples: 5 (with phi_angincr of 10 it will sample the in-plane angle of 100 degrees)
Optional - if not specified, it will be set so the circle is sampled.
Used only if anglist_name is not specified.

anglist_order

Specifies the order in which the input angles are specified. For more information see Required inputs and Differences to STOPGAP
Note that this parameter influences also the order in which the angle list is written out if it is generated on-the-fly during the TM.
Type: string
Allowed values: “zxz” or “zzx”
Optional parameter - default is “zxz”

smap_name

Prefix of the name used to store scores map. The final name will be created as {prefix}_{template_num}_{tomo_number}.em. For example, if the value is set to “scores” and there is only one line in the parameter file (i.e., one template and one tomogram, which has tomo_num 126) the final scores map will be stored in scores_0_126.em. If there are two lines of parameters, with the same tomo_num but different templates, the final scores maps will be stored in scores_0_126.em and scores_1_126.em.
Type: string
Examples: scores
Optional parameter - default is “scores”

omap_name

Prefix of the name used to store angles map. The final name will be created as {prefix}_{template_num}_{tomo_number}.em. in similar way as for smap_name (see above). Note that the indices in angles maps are numbered from 0, see Differences to STOPGAP for more information.
Type: string
Examples: angles
Optional parameter - default is “angles”

lp_rad

Low-pass filter radius in Fourier pixels/voxels to be applied to the template. To compute this value from the desired resolution, use following formula: round(template_box_size * pixel_size / resolution) where template_box_size is one dimension of the template.
Type: float
Examples: 20 (or 20.0)

lp_sigma

Sigma cut-off for the low-pass filter.
Type: float
Examples: 2.0 or 3.0
Optional parameter - default is 3.0

hp_rad

High-pass filter radius in Fourier pixels/voxels to be applied to the template. To compute this value from the desired resolution, use following formula: round(template_box_size * pixel_size / resolution) where template_box_size is one dimension of the template. Note that for most of the cases the optimal value is 1 (i.e. no high-pass filter).
Type: float
Examples: 2 (or 2.0)

hp_sigma

Sigma cut-off for the high-pass filter.
Type: float
Examples: 2.0 or 3.0
Optional parameter - default is 2.0

binning

Binning of the tomogram. This value is used to adapt the values in the wedge-list (which are unbinned) to the correct binning. Note that binning of 1 corresponds to unbinned data (i.e. without any binning). Value of 2 corresponds to the data that were downsampled by factor 2, value of 3 corresponds to the data that were downsampled by factor 3.
Type: integer
Examples: 1 or 2 or 3 or 4
We have noticed that sometimes better results are achieved by setting this parameter to 1 regardless of actual binning.

calc_exp

Whether to apply exposure-filtering to the wedge mask.
Type: boolean
Optional parameter - default is True

calc_ctf

Whether to apply CTF-filtering to the wedge mask.
Type: boolean
Optional parameter - default is True

apply_laplacian

Whether to apply laplacian transform to the volumes prior TM.
Type: boolean
Optional parameter - default is False

noise_corr

How many rounds of noise randomization should be run. If no randomization is wanted, the parameter should be set to 0.
Type: integer
Optional parameter - default is 1

write_raw

Whether to write out the scores maps also without the noise randomization filtering. This parameter is used only if noise_corr is set to values higher than 0.
Type: boolean
Optional parameter - default is False

tiling

Type of tomogram splitting during parallelization.
Type: string
Allowed values: “legacy” (replicating the original matlab source), “legacy_fix” (fixing a bug in the legacy tiling) or “new” (optimal tiling)
Optional parameter - default is currently “legacy_fix” but will be changed to “new”

IMPORTANT: You have to either use anglist_name or the angles parameters (angincr, angiter, phi_angincr, phi_angiter). If you keep both options in the parameter file the TM will run however it will produce outputs with zero values (“black” volumes).

Path specification#

Each folder or file name can be specified either by a relative or an absolute path. All relative paths are evaluated w.r.t. the rootdir parameter. For example, if rootdir is “/path/to/the/rootdir/” and a template is specified as “inputs/microtubule.em” (or “./inputs/microtubule.em”) then the full path to the template will be “/path/to/the/rootdir/inputs/microtubule.em”. IF the template is “microtubule.em” then the full path will be “/path/to/the/rootdir/microtubule.em”. In case the rootdir is a relative path then the full path will be assembled w.r.t. to the folder from which you run gapstop command or, in case you run it on cluster and specify a working directory there, then the full path will be w.r.t. the working directory. For example, if the rootdir is “./tm_tutorial/” and you run gapstop command from the folder “/path/to/my/current/folder/” the full path will be “/path/to/my/current/folder/tm_tutorial/” for the rootdir and all other relative paths in the parameter list will be assembled w.r.t. this path.