Some useful Python scripts to manipulate Relion tomo STAR files and much more.....
$ git clone https://github.com/fuzikt/tomostarpy.git
$ cd tomostarpy
$ ./INSTALL.sh
Before usage don't forget to source the venv environment if it is not yet activated:
$ source <path_to_tomostarpy>/venv/bin/activate
Get particle parameters (cc, coordinates, Euler angles) from a convmap file at positions defined by a mod file. Output is written in emClarity csv format.
--convmap Input _convmap.mrc file.
--mod Input mod file (Default: empty).
--o Output emClarity csv file (Default: empty).
Generates order_list.csv for RELION from *.tlt file according to dose-symmetric tilting scheme. (Default 2 pos, 2 neg generates: 0,1,-1,-2,2,3,-3,4...).
--i Input *.tlt file.
--o Output csv file.
--nr_pos Number of consecutive positive tilts in output (Default: 2).
--nr_neg Number of consecutive negative tilts in output (Default: 2).
--pacetomo Pace-tomo style dose symmetric (0, ++, --, ++, --.....) (Default: False).
Performs constrained CTF fit on separate tilts using Ctffind4 or Gctf. First, the middle tilt ctf is estimated then the following tilts in each direction are constrained by the --defocus_window of the previous tilt. The max resolution of the fitting is limited by 1/cos(tilt_angle) to avoid overfitting.
--i Input tilt-series MRC file.
--o Output directory of results.
--tlt *.tlt or *.rawtlt file of the tilt series.
--defocus_window Defocus window in Angstroms used for the restrained ctf search of the subsequent tilts (Default: 10000).
--apix Pixel-size in Angstroms (Default: 1.0).
--voltage Acceleration voltage of the microscope in kV (Default: 300.0).
--cs_val Cs value of the microscope (Default: 2.7).
--amp_cont Amplitude contrast used for CTF fitting (Default: 0.07).
--spectr_size Size of the Fourier spectrum used for CTF fitting (Default: 512).
--min_res Minimum resolution in Angstroms used for zero-tilt CTF fitting (Default: 30.0).
--max_res Maximum resolution in Angstroms used for zero-tilt CTF fitting (Default: 8.0).
--min_defoc Minimum defocus in Angstroms used for zero-tilt CTF fitting (Default: 5000.0).
--max_defoc Maximum defocus in Angstroms used for zero-tilt CTF fitting (Default: 75000.0).
--step_defoc Defocus step in Angstroms used for CTF fitting (Default: 100.0).
--threads Number of parallel threads used for calculation by Ctffind4 (Default: 10).
--gctf Use gCTF instead of CtfFind4 (Default: False).
--gpu GPU card ID to be used by gCTF (Default: 0).
--tmpDir Temp directory for storage of the intermediate files (Default: ctffind_tmp).
--ctffind_cmd Name of the Ctffind4 command (Default: ctffind).
--gctf_cmd Name of the gCTF command (Default: gctf).
--path Path to be included in env PATH for Ctffind4 or Gctf (Default: empty).
--verb Verbosity level (0,1) (Default: 0).
Replace dose in warp .tomostar by value from .tltdose file.
--i Input tomostar file.
--itlt Input dosetlt file.
--o Output tomostar file.
Performs conversion from emClarity template matching csv file to Relion star file. It also recalculates the particle coordinates from emClarity partial tomogram to full tomogram.
--i Input emClarity csv file.
--o Output prefix. Prefix of the files generated by the script.
--reconsh emClarity *_recon.sh file of the input csv file. (located in emc_project/recon/)
--tiltcom tilt.com file (generated by IMOD) of the original non-splitted tomogram used by Relion
--mod Modfile used for filtering particles from the input csv. Note: Set the "--modbin" binning factor used for template matching.
--modbin Binning factor used for template matching. Needed only if modfile filtering is enabled. (Default 1)
--outbin Binning factor used for output coordinates and mod files. NOT used for star file (always unbinned)! (Default 1)
--cs Cs value of the microscope. Used in opticsgroup in the output star file. (Default 2.7)
--kv Acceleration voltage of the microscope. Used in opticsgroup in the output star file. (Default 300.0)
--apix Apix of the unbinned tomogram. Used in opticsgroup in the output star file.
--xtilt Tomo X axis tilt in degrees. (Default: 0)
--ytilt Tomo Y axis tilt in degrees. (Default: 0)
Converts emClarity *_aliX_ctf.tlt from tomoCPR to IMOD format *.xf + *.tlt file and Ctffind4 format diag. output *.txt file.
--i Input emClarity *_aliX_ctf.tlt file.
--o Output prefix for IMOD style xf/tlt file and Ctffind4 style diag. output file.
Calculates ZYZ convention Euler angles from a 3x3 rotation matrix.
--i Rotation matrix members in format: m[1,1],m[1,2],m[1,3],m[2,1],m[2,2]
Removes lines defined in --exclude_file from input text file.
--i Input file to exclude lines from.
--o Output file.
--exclude_file Textfile with comma separated list of excluded views (or range of views as in newstack).
Removes tilts defined in --exclude_file from tilt series mrc-stack and corresponding *.rawtlt, *.mdoc.
--i Input prefix mrc-stack.
--o Output prefix.
--exclude_file Textfile with comma separated list of excluded views (or range of views as in newstack).
Select only particles that have a certain amount of neighbors in a particular distance. Useful for filtering out surface features.
--i Input STAR file name with particles.
--o Output STAR file name.
--dist Distance in Angstroms that consider particles as neighbors. (Default 1.0)
--min_neigh Minimum number of neighbors at --dist particle has to be kept in selection! (Default 1)
--min_corr Minimum cross-correlation value of the neighbour to be considered as a true neighbour! (Default 0)
--max_tilt_diff Maximum amount of tilt angle difference in degrees between neighbors to be considered as a true neighbour! (Default 360)
Analyze the Ctffind4 output txt file and write out text file with tilt-numbers that have CTF rings fitted over the threshold. Tilts are numbered from 1.
--i Input Ctffind4 diagnostic txt file.
--o Output text file with tilt numbers under the threshold.
--threshold Threshold (in Angstroms) value for the resolution up to which CTF rings were fit successfully. (Default: 100)
Analyze the input tilt-series mrc stack and write out text file with tilt-numbers that have average signal under the threshold. Tilts are numbered from 1. Useful to remove dark tilts.
--i Input tilt-series mrc-stack.
--o Output text file with tilt numbers under the threshold.
--threshold Threshold value for the average value of the tilt. (Default: 0.5)
Performs merging of separate tilt files from PACE-tomo or dose symmetric SerialEM script into tilt-series files.
--i Input tilts directory.
--o Output directory of merged tilt series.
--start_tilt Angle of the "zero-tilt" - at which the tilt-series begin. Useful for pretilted tilt-series. (Default: 0)
--start_series_nr The sequential number of the start nr. of tilt series (used for continuing the process). (Default: 1)
--prefix Prefix of the output tilt series file. (Default: tomo)
--mdoc_dir Directory where *.mdoc files are located. If empty, no *.rawtlt and merged *.mdoc are generated (Default: empty)
--mdoc_suffix Suffix of the *.mdoc files after the mic name. (Default: .tif.mdoc)
--pre_dose Dose applied before acquiring the first tilt. [e-/A^2]. (Default: 0.0)
--dose Dose applied per tilt. [e-/A^2]. (Default: 0.0)
--apix Pixel size of the merged tilt-series. [A/px]. (Default: 1.0)
--newstack_cmd Name of the IMOD newstack command. (Default newstack)
--alterheader_cmd Name of the IMOD alterheader command. (Default alterheader)
--path Path to be included in env PATH for IMOD! (Default: empty)
--watch_int Time interval in seconds for the watchdog. If set to -1 the watchdog is deactivated and runs a single-batch. (Default: 1)
--verb Verbosity level (0,1,2). (Default: 1)
Performs placeback of oriented arrows (*.bild format) according to the coordinates and euler angles defined in a star file.
--i Input star file file.
--o Output prefix
--length Length of the arrow in Angstroms. (default: 200)
--thickness Radius of the arrow base in Angstroms. (default: 1/20 of the arrow length)
--cmm Generate cmm file as well.
--color_lb Label from the star file that will be used for rainbow coloring of the arrows and cmm markers. (default: empty)
--invert Invert the pointing direction of the arrow.
--tomo_name Use only particles from tomogram equal in rlnTomoName. OPTIONAL: If not set all particles used in place-back
Performs placeback of a PDB structure into full tomogram volume according to the coordinates and euler angles defined in a star file.
--i Input star file file.
--i_pdb Input star file file.
--o Output prefix
--center_offset PDB center offset. (default: 0,0,0)
--backbone Store only backbone atoms in the output.
--tomo_name Use only particles from tomogram equal in rlnTomoName. OPTIONAL: If not set all particles used in place-back
--separate_pdb Write separate PDB file per particle
Performs placeback of polygons (*.bild format) according to the coordinates and euler angles defined in a star file.
--i Input star file file.
--o Output prefix
--n Order of the polygon (3 - triangle; 4 - square; 5 - pentagon etc. (default: 3))
--size Distance between the center and the vertex in Angstroms. (default: 200)
--pre_rot Pre rotation (in degrees) applied to the polygon before placing back. (default: 0)
--cmm Generate cmm file as well.
--color_lb Label from the star file that will be used for rainbow coloring of the arrows and cmm markers. (default: empty)
--tomo_name Use only particles from tomogram equal in rlnTomoName. OPTIONAL: If not set all particles used in place-back
--single Creates a single polygon with applied ---pre_rot and of size --size. Useful to find the --pre_rot parameter. No input star file needed.
Performs placeback of a subvolume into full tomogram volume according to the coordinates and euler angles defined in a star file.
--i Input star file file.
--isub Input file of sub-volume to be placed.
--itomo Input file of the stencil tomogram. Size and origin is taken from this file and applied on the output.
--o Output prefix
--cmm Create Chimera cmm file with the coordinates of the placed sub-volumes.
--tomo_name Use only particles from tomogram equal in rlnTomoName. OPTIONAL: If not set all particles used in place-back
--bin Binning factor of the stencil tomogram. If not provided calculated from MRC header and star file
--no_partial Do not place partial volumes. If the subvolume is partially out of the output volume, it is not placed at all. This avoids "half-cut" sub-volumes in the output.
--recenter Recenter the particles by subtracting rlnOriginX/Y/ZAngst from X/Y/Z coordinates.
--color_lb Label from the star file that will be used for rainbow coloring of the cmm markers.
--color_map Create map with coloring values stored as pixel value.
--radial_color Create map with coloring values storing the value of radial distance form the center of the box. Useful for radial coloring.
--color_map_threshold Threshold value at which the contour of the --isub in the output color map should contain values
--color_map_extend Extend the border around the threshold meeting value by this amount of pixels.
--xtilt Tomo X axis tilt in degrees. (Default: 0)
--ytilt Tomo Y axis tilt in degrees. (Default: 0)
--gpu Use GPU acceleration.
Remove duplicate particles appearing both in --i1 --i2 from --i2 and write result into --o.
--i1 Input1 STAR filename.
--i2 Input2 STAR filename.
--o Output STAR filename.
--tol Tolerance in pixels of considering the coordinates of particles to be the same (Default: 3).
Rotate and shift REMARK 350 BIOMT matrices from PDB file, using a given matrix or ZYZ convention euler angles.
--i Input PDB file.
--o Output file.
--i_mat Input file with rotation and translation matrix in BIOMT format used for the rotation. If defined --rot, --tilt, and --psi are ignored.
--rot Euler angle ROT in degrees. (Default 0.0)
--tilt Euler angle TILT in degrees. (Default 0.0)
--psi Euler angle PSI in degrees. (Default 0.0)
--x X shift in Angstroms. (Default 0.0)
--y Y shift in Angstroms. (Default 0.0)
--z Z shift in Angstroms. (Default 0.0)
Rotate the inplane coordinates X, Y of the subvolume.
--i Input star file.
--o Output star file.
--ang Rotation angle in degrees. (Default 0.0)
--xmax X-size of the unbinned tomogram. (Default 4092)
--ymax Y-size of the unbinned tomogram. (Default 5760)
Set the Euler angles (tilt, psi) of the particles along a filament according to the angles of the between the neighboring particle centers.
--i Input STAR filename with particles.
--o Output STAR filename.
Rotate the values in IMOD xf file to change the rotation of the finally aligned stack.
--i Input IMOD xf file.
--o Output IMOD xf file.
--ang Rotation angle in degrees. (Default 0.0)
Select particles from star file according to matching particle coordinates listed in Chimera cmm or IMOD mod file.
--i Input STAR filename with particles.
--o Output STAR filename.
--cmm Chimera CMM file with desired coordinates.
--mod IMOD mod file with desired coordinates.
--bin Binning factor of the IMOD mod file.
Shift particle coordinates in input STAR file, by recalculating the difference between the two reconstructions defined in --tiltcom1 and --tiltcom2.
--i Input STAR file name with particles.
--o Output STAR file name.
--tiltcom1 tilt.com file (generated by IMOD) of the tomogram of the input coordinates
--tiltcom2 tilt.com file (generated by IMOD) of the tomogram for the output coordinates
--xtilt Tomo X axis tilt in degrees. (Default: 0)
--ytilt Tomo Y axis tilt in degrees. (Default: 0)
Sort particles in star file to order based on the minimal distance between consecutive particles. In general, this should form a filament path.
--i Input STAR file name with particles.
--o Output STAR file name.
Split a particle star file into separate files per tomoName containing the corresponding particles.
--i Input star file.
--o Output directory name.
Visual editor to add, remove, combine particles from tomo STAR files.
--i Input star file. Possible to open multiple star files delimited by comma.
--itomo Input mrc file. Possible to open multiple mrc files delimited by comma.
--o Output star file name. Possible to change later in the gui.
--tomo_name Use only particles from tomogram equal in rlnTomoName. OPTIONAL: If not set all particles will be visualized.
--color_lb Label from the star file that will be used for rainbow coloring of the markers.
--bin User provided binning of the --itomo. If not set the apix of the first MRC file in --itomo is taken to calculate the binning.
--point_size Size of the points in pixels.
--angles_mrc emClarity *_angles.mrc from template matching, to be used for newly added particles orientations. Same named *_angles.list must be present in the directory.
Performs conversion from Relion star file to emClarity template matching csv file. It also generates *.recon.coords files for tomogram subareas.
--i Input particle star file.
--o Output prefix. Prefix of the files generated by the script.
--itomo Input tomogram star file.
--splitX Number of subareas to split the tomograms on X axis. Default: 2
--splitY Number of subareas to split the tomograms on X axis. Default: 2
--bin Binning factor used for the output mod files. Default: 1
Creates a star file with sub-subtomo coordinates similar to sub-particle approach in SPA.
--i Input star file.
--o Output star file.
--cmm A CMM file defining the location(s) of the subparticle(s) (use instead of --vector). Coordinates should be in Angstrom.
--vector Vector defining the location of the subparticle. (default: 0,0,1)
--length Alternative length of the vector. Use to adjust the subparticle center (A). (default: length of the given vector)
--sym Symmetry of the particle. (default: C1)
--align_subparticles Align subparticles to the standard orientation.
--randomize Randomize the order of the symmetry matrices. Useful for preventing preferred orientations.
--unique Keep only unique subparticles within angular distance (useful to remove overlapping subparticles on symmetry axis).
--mindist Minimum distance between the subparticles in the image (all overlapping ones will be discarded; pixels).
--side Keep only particles within specified angular distance from side views (all others will be discarded; degrees).
--top Keep only particles within specified angular distance from top views (all others will be discarded; degrees).
--library_path Define LD_LIBRARY_PATH used. Default: empty