https://sphire.mpg.de/wiki/ 2026-05-02T23:21:21+00:00 https://sphire.mpg.de/wiki/ https://sphire.mpg.de/wiki/lib/tpl/dokuwiki/images/favicon.ico text/html 2019-04-02T09:20:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:e2bdb&rev=1554189643&do=diff e2bdb Berkeley Data Base Utilities: Examine and interact with a EMAN2DB directory. Usage Usage in command line e2bdb.py --cleanup --force --delete --all --long --short --filt='SUBSTRING' --filtexclude='SUBSTRING' --match='REGULAR_EXPRESSION' --exclude='bdb_NAME' --dump --smalldump --extractplots --check --merge --makevstack='bdb:/Home/user/project#output' --appendvstack='bdb:output' --list='abc.txt' --exlist='xyz.txt' --restore='bdb:vstack' --ppid=PPID --checkctf --… text/html 2019-04-02T09:15:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:e2display&rev=1554189357&do=diff e2display Display Data: Displays images, volumes, or 1D plots. Usage Usage in command line e2display.py input_data_list --classmx=CLASSMX --classes=CLASSES --pdb=PDB --singleimage --plot --plot3 --fullrange --newwidget --ppid=PPID --verbose=n text/html 2019-04-02T10:17:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:e2proc3d&rev=1554193044&do=diff e2proc3d Generic 3D image processing program: The main tasks are: (1) Convert volumes from one format to another, (2) Perform basic image processing operations such as filters, masks, normalization, and etc., (3) Resize/rescale volumes, and (4) Compute FSC curves, structure factors, etc. text/html 2019-04-02T11:24:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sp_batch&rev=1554197062&do=diff sp_batch Batch Pipeline Execution: Run jobs that wait with the execution on each other. Usage Usage in command line sp_batch.py submission_command input_run_dir --hold_flag=HOLD_FLAG --first_hold_number=FIRST_HOLD_NUMBER Typical usage sp_batch exists only in non-MPI version. text/html 2022-03-01T15:13:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sp_center_2d3d&rev=1646144002&do=diff sp_center_2d3d Centering : Utility for centering in 2D or 3D. Usage Usage in command line: sp_center_2d3d.py input_stack_or_volume output_directory --mode=centering_mode --verbosity=verbosity_level --debug --threshsigma=threshold_sigma --applyshift stack_or_volume_to_be_centered --ndilation=number_of_dilations --nerosion=number_of_erosions --volradius=volume_radius --dimensions=number_of_dimensions --stem=output_volume_prefix --threshint=intermediate_threshold --pad=padding_factor text/html 2019-04-02T11:29:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sp_ctf_refine&rev=1554197385&do=diff sp_ctf_refine meridien CTF refine (Meridien): Refine the defocus per particle Usage Usage in command line sp_ctf_refine.py meridien path_to_input_stack output_directory refinement_dir --mask=path_to_mask --range=defocus_range --delta=defocus_delta --resolution=nominal_resolution --pixelsize=pixelsize --number_part=NUMBER_PARTICLES text/html 2019-04-02T11:31:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sp_ctf_refine_stack&rev=1554197481&do=diff sp_ctf_refine manual CTF refine (Stack): Refine the defocus per particle Usage Usage in command line sp_ctf_refine.py manual path_to_input_stack output_directory volume_path params_file --mask=path_to_mask --range=defocus_range --delta=defocus_delta --resolution=nominal_resolution --pixelsize=pixelsize --number_part=NUMBER_PARTICLES --chunk=PATH_TO_CHUNK_FILE --volume2=PATH_TO_VOLUME text/html 2020-10-21T10:17:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sp_eval_isac&rev=1603268223&do=diff sp_eval_isac Separate Into Classes : Separates stacks of particle images into stacks for each class and evaluates results. Usage Usage in command line (beta version): sp_eval_isac.py input_class_avgs output_directory --particles=input_image_stack --align_isac_dir=isac_or_beautifier_dir --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor --ctf=ctf_mode --nvec=number_of_eigenimages --pca_radius=radius --chains_radius=radius --chains_exe=spchains_executable --applyparams=centerin… text/html 2020-01-31T11:38:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sp_separate_class&rev=1580467121&do=diff sp_separate_class Separate Into Classes : Separates stacks of particle images into stacks for each class. Usage Usage in command line: sp_separate_class.py input_class_avgs input_image_stack output_directory --align_isac_dir=isac_dir --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor --nvec=number_of_eigenimages --ctf --verbose text/html 2019-04-02T12:34:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sp_sphire2relion&rev=1554201264&do=diff sp_sphire2relion SPHIRE to RELION Conversion : Convert SPHIRE parameters to RELION. Usage Usage in command line sp_sphire2relion.py output_dir --output_name=OUTPUT_NAME --particle_stack=PARTICLE_STACK --params_2d_file=PARAMS_2D_FILE --params_3d_file=PARAMS_3D_FILE -params_3d_index_file=PARAMS_3D_INDEX_FILE --params_3d_chunk_file_0=CHUNKFILE0 --params_3d_chunk_file_1=CHUNKFILE1 --list=INCLUDE_LIST --exlist=EXCLUDE_LIST --force text/html 2019-04-02T12:49:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:start&rev=1554202162&do=diff Utilities Batch Pipeline Execution Run jobs that wait with the execution on each other Display Data Displays images, volumes, or 1D plots. PDB File Conversion Converts an PDB atomic model into a simulated density map. RELION to SPHIRE Conversion Convert parameters from RELION to SPHIRE formats. SPHIRE to RELION Conversion Convert parameters from SPHIRE to RELION formats. text/html 2019-04-02T10:08:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sxheader&rev=1554192480&do=diff sp_header Header Operations: Perform operations on headers of hdf or bdb file. Usage Usage in command line sp_header.py stack --params=PARAMS_NAME_LIST --import=INPUT_PARAMS_PATH --export==OUTPUT_PARAMS_FILE --delete --zero --one --set --consecutive --randomize --rand_alpha --print --backup --restore --suffix=PARAMS_FILE_SUFFIX text/html 2019-04-02T09:33:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sxpdb2em&rev=1554190434&do=diff sp_pdb2em PDB File Conversion: Converts an atomic model stored in a PDB file into a simulated electron density map. The coordinates (0,0,0) in PDB space will map to the center of the volume. Usage Usage in command line sp_pdb2em.py input_pdb output_hdf --apix=PIXEL_SIZE --box=BOX_SIZE --het --chains=CHAIN_STRING --center=CENTERING_METHOD --O --tr0=MATRIX_FILE_PATH --set_apix_value=PIXEL_SIZE_STRING --quiet text/html 2019-04-02T10:54:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sxpipe_angular_distribution&rev=1554195261&do=diff sp_pipe angular_distribution Angular Distribution: Generate a chimera .bild file for the visual representation of the resulting projection parameters. Usage Usage in command line sp_pipe.py angular_distribution params_file output_folder --prefix=None --method=S --pixel_size=1.0 --delta=3.75 --symmetry=c1 --box_size=256 --particle_radius=120 --dpi=72 text/html 2019-04-02T10:42:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sxpipe_moon_eliminator&rev=1554194521&do=diff sp_pipe moon_eliminator Volume Adjustment: Eliminate moons or remove dusts from the background of a 3D density map based on the expected molecular mass. Usage Usage in command line sp_pipe.py moon_eliminator input_volume_path input_volume_path_2nd output_directory --pixel_size=PIXEL_SIZE --mol_mass=KILODALTON --use_density_threshold=THRESHOLD --moon_distance=PIXEL_DISTANCE --ndilation=DILATION_PIXEL_WIDTH --edge_width=SIGMA_PIXEL_WIDTH --resample_ratio=RATIO_OR_DIR_PATH --box_s… text/html 2019-04-02T10:24:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sxpipe_organize_micrographs&rev=1554193459&do=diff sp_pipe organize_micrographs Organize Micrographs/Movies: Organize micrographs/movies by moving micrographs/movies listed in a selecting file from a source directory (specified by source micrographs/movies pattern) to a destination directory. Usage text/html 2019-04-02T10:29:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sxpipe_resample_micrographs&rev=1554193764&do=diff sp_pipe resample_micrographs Resample Micrographs: Resample micrographs in input directory specified by input micrograph pattern with user-specified ratio. This operation changes the image dimensitions and the pixel size. Mainly, it is designed to reduce the demensions and pixel size of micrographs taken with the super resolution mode of the K2 direct electron detector. text/html 2019-04-02T10:59:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sxpipe_restacking&rev=1554195590&do=diff sp_pipe restacking Restacking: Generate all necessary information to restack the input stack (i.e., particle image ID list, CTF parameters list, projection parameters list) while appling micrograph selection list. Optionally, the command can directly output the virtual stack. In addition, this command can be used to generate all parameters files for reboxing (i.e. original/centered particle coordinates list files, CTF parameters list, original/centered projection parameters list as well as mic… text/html 2019-04-08T16:15:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sxprocess&rev=1554732943&do=diff sp_process Miscellaneous Commands: Carry out various SPARX commands on image series, and generate data and initialize database for demo script. Usage Usage in command line sp_process.py inputfile outputfile micrograph_prefix --order --order_lookup --order_metropolis --order_pca --initial=INITIAL --circular --radius=RADIUS --changesize --ratio=RATIO --pw --wn=WN --phase_flip --makedb=param1=value1:param2=value2 --generate_projections=param1=value1:param2=value2 --isacgroup… text/html 2019-04-02T10:57:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sxrelion2sphire&rev=1554195444&do=diff sp_relion2sphire RELION to SPHIRE Conversion: Create several types of parameter text files and per-micrograph virtual stacks of particle images in bdb format from parameters stored in a RELION STAR file Usage Usage in command line sp_relion2sphire.py input_star_file output_directory --relion_project_dir=DIR_PATH --star_section=SECTION_STRING --outputs_root=ROOT_NAME_STRING --box_size=BOX_SIZE --do_not_create_stack text/html 2018-06-20T13:12:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://sphire.mpg.de/wiki/doku.php?id=pipeline:utilities:sxsummovie&rev=1529493130&do=diff sxgui_unblur Micrograph Movie Summation: Sum micrograph movies with Summovie. Usage Usage in command line sxsummovie.py summovie_path input_micrograph_pattern input_shift_pattern output_directory --selection_list=SELECTION_LIST --nr_frames=NUM_OF_FRAMES --first=FIRST_FRAME --last=LAST_FRAME --pixel_size=PIXEL_SIZE --nr_threads=NUM_OF_THREADS --apply_dose_filter --voltage=VOLTAGE --exposure_per_frame=EXPOSURE --pre_exposure=EXPOSURE --dont_restore_noise