Servalcat commands¶
SPA¶
refine_spa_norefmac¶
Refinement pipeline for SPA. The weighted and sharpened Fo-Fc map is calculated after the refinement. For details please see the reference.
$ servalcat refine_spa_norefmac -h
usage: servalcat refine_spa_norefmac [-h] (--halfmaps HALFMAPS HALFMAPS | --map MAP | --hklin HKLIN)
[--pixel_size PIXEL_SIZE] [--labin LABIN] --model MODEL -d
RESOLUTION [-r MASK_RADIUS] [--padding PADDING] [--no_mask]
[--no_trim] [--mask_soft_edge MASK_SOFT_EDGE]
[--no_sharpen_before_mask] [--b_before_mask B_BEFORE_MASK]
[--blur BLUR] [--monlib MONLIB] [--ligand [LIGAND ...]]
[--newligand_continue] [--hydrogen {all,yes,no}] [--hout]
[--jellybody] [--jellybody_params sigma dmax] [--jellyonly]
[--pg PG] [--twist TWIST] [--rise RISE]
[--center CENTER CENTER CENTER] [--axis1 AXIS1 AXIS1 AXIS1]
[--axis2 AXIS2 AXIS2 AXIS2] [--contacting_only]
[--ignore_symmetry IGNORE_SYMMETRY] [--find_links]
[--no_check_ncs_overlaps] [--no_check_ncs_map]
[--no_check_mask_with_model] [--keywords KEYWORDS [KEYWORDS ...]]
[--keyword_file KEYWORD_FILE [KEYWORD_FILE ...]]
[--randomize RANDOMIZE] [--ncycle NCYCLE] [--weight WEIGHT]
[--no_weight_adjust]
[--target_bond_rmsz_range TARGET_BOND_RMSZ_RANGE TARGET_BOND_RMSZ_RANGE]
[--adpr_weight ADPR_WEIGHT] [--ncsr] [--bfactor BFACTOR]
[--fix_xyz] [--adp {fix,iso,aniso}] [--refine_all_occ]
[--max_dist_for_adp_restraint MAX_DIST_FOR_ADP_RESTRAINT]
[--adp_restraint_power ADP_RESTRAINT_POWER]
[--adp_restraint_exp_fac ADP_RESTRAINT_EXP_FAC]
[--adp_restraint_no_long_range]
[--adp_restraint_mode {diff,kldiv}] [--refine_h]
[--source {electron,xray,neutron}] [-o OUTPUT_PREFIX]
[--cross_validation]
[--mask_for_fofc MASK_FOR_FOFC | --mask_radius_for_fofc MASK_RADIUS_FOR_FOFC]
[--fsc_resolution FSC_RESOLUTION] [--keep_charges]
[--keep_entities] [--write_trajectory]
EXPERIMENTAL program to refine cryo-EM SPA structures
options:
-h, --help show this help message and exit
--halfmaps HALFMAPS HALFMAPS
Input half map files
--map MAP Use this only if you really do not have half maps.
--hklin HKLIN Use mtz file. With limited functionality.
--pixel_size PIXEL_SIZE
Override pixel size (A)
--labin LABIN F,PHI for hklin
--model MODEL Input atomic model file
-d RESOLUTION, --resolution RESOLUTION
-r MASK_RADIUS, --mask_radius MASK_RADIUS
mask radius
--padding PADDING Default: 2*mask_radius
--no_mask
--no_trim Keep original box (not recommended)
--mask_soft_edge MASK_SOFT_EDGE
Add soft edge to model mask. Should use with --no_sharpen_before_mask?
--no_sharpen_before_mask
By default half maps are sharpened before masking by std of signal and
unsharpened after masking. This option disables it.
--b_before_mask B_BEFORE_MASK
sharpening B value for sharpen-mask-unsharpen procedure. By default it is
determined automatically.
--blur BLUR Sharpening or blurring B
--monlib MONLIB Monomer library path. Default: $CLIBD_MON
--ligand [LIGAND ...]
restraint dictionary cif file(s)
--newligand_continue Make ad-hoc restraints for unknown ligands (not recommended)
--hydrogen {all,yes,no}
all: (re)generate hydrogen atoms, yes: use hydrogen atoms if present, no:
remove hydrogen atoms in input. Default: all
--hout write hydrogen atoms in the output model
--jellybody Use jelly body restraints
--jellybody_params sigma dmax
Jelly body sigma and dmax (default: [0.01, 4.2])
--jellyonly Jelly body only (experimental, may not be useful)
--pg PG Point group symbol
--twist TWIST Helical twist (degree)
--rise RISE Helical rise (Angstrom)
--center CENTER CENTER CENTER
Origin of symmetry. Default: center of the box
--axis1 AXIS1 AXIS1 AXIS1
Axis1 (if I: 5-fold, O: 4-fold, T: 3-fold)
--axis2 AXIS2 AXIS2 AXIS2
Axis2 (if I: 5-fold, O: 4-fold, T: 3-fold, Dn: 2-fold)
--contacting_only Filter out non-contacting strict NCS copies
--ignore_symmetry IGNORE_SYMMETRY
Ignore symmetry information (MTRIX/_struct_ncs_oper) in the model file
--find_links Automatically add links
--no_check_ncs_overlaps
Disable model overlap test due to strict NCS
--no_check_ncs_map Disable map symmetry test due to strict NCS
--no_check_mask_with_model
Disable mask test using model
--keywords KEYWORDS [KEYWORDS ...]
refmac keyword(s)
--keyword_file KEYWORD_FILE [KEYWORD_FILE ...]
refmac keyword file(s)
--randomize RANDOMIZE
Shake coordinates with the specified rmsd value
--ncycle NCYCLE number of CG cycles (default: 10)
--weight WEIGHT refinement weight. default: automatic
--no_weight_adjust Do not adjust weight during refinement
--target_bond_rmsz_range TARGET_BOND_RMSZ_RANGE TARGET_BOND_RMSZ_RANGE
Bond rmsz range for weight adjustment (default: [0.5, 1.0])
--adpr_weight ADPR_WEIGHT
ADP restraint weight (default: 1.000000)
--ncsr Use local NCS restraints
--bfactor BFACTOR reset all atomic B values to the specified value
--fix_xyz Fix atomic coordinates
--adp {fix,iso,aniso}
ADP parameterization
--refine_all_occ
--max_dist_for_adp_restraint MAX_DIST_FOR_ADP_RESTRAINT
--adp_restraint_power ADP_RESTRAINT_POWER
--adp_restraint_exp_fac ADP_RESTRAINT_EXP_FAC
--adp_restraint_no_long_range
--adp_restraint_mode {diff,kldiv}
--refine_h Refine hydrogen against data (default: only restraints apply)
--source {electron,xray,neutron}
-o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
--cross_validation Run cross validation. Only "throughout" mode is available (no "shake" mode)
--mask_for_fofc MASK_FOR_FOFC
Mask file for Fo-Fc map calculation
--mask_radius_for_fofc MASK_RADIUS_FOR_FOFC
Mask radius for Fo-Fc map calculation
--fsc_resolution FSC_RESOLUTION
High resolution limit for FSC calculation. Default: Nyquist
--keep_charges Use scattering factor for charged atoms. Use it with care.
--keep_entities Do not override entities
--write_trajectory Write all output from cycles
fofc¶
$ servalcat fofc -h
usage: servalcat fofc [-h] [--halfmaps HALFMAPS HALFMAPS | --map MAP]
[--pixel_size PIXEL_SIZE] --model MODEL -d RESOLUTION
[-m MASK] [-r MASK_RADIUS] [--no_check_mask_with_model]
[-B B] [--half1_only] [--normalized_map]
[--no_fsc_weights] [--sharpening_b SHARPENING_B]
[--trim] [--trim_mtz] [--monlib MONLIB] [--omit_proton]
[--omit_h_electron] [--source {electron,xray,neutron}]
[-o OUTPUT_PREFIX] [--keep_charges]
Fo-Fc map calculation based on model and data errors
options:
-h, --help show this help message and exit
--halfmaps HALFMAPS HALFMAPS
--map MAP Use only if you really do not have half maps.
--pixel_size PIXEL_SIZE
Override pixel size (A)
--model MODEL Input atomic model file
-d RESOLUTION, --resolution RESOLUTION
-m MASK, --mask MASK mask file
-r MASK_RADIUS, --mask_radius MASK_RADIUS
mask radius (not used if --mask is given)
--no_check_mask_with_model
Disable mask test using model
-B B Estimated blurring
--half1_only Only use half 1 for map calculation (use half 2 only
for noise estimation)
--normalized_map Write normalized map in the masked region. Now this is
on by default.
--no_fsc_weights Just for debugging purpose: turn off FSC-based
weighting
--sharpening_b SHARPENING_B
Use B value (negative value for sharpening) instead of
standard deviation of the signal
--trim Write trimmed maps
--trim_mtz Write trimmed mtz
--monlib MONLIB Monomer library path. Default: $CLIBD_MON
--omit_proton Omit proton from model in map calculation
--omit_h_electron Omit hydrogen electrons from model in map calculation
--source {electron,xray,neutron}
-o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
output file name prefix (default: diffmap)
--keep_charges Use scattering factor for charged atoms. Use it with
care.
trim¶
$ servalcat trim -h
usage: servalcat trim [-h] [--maps MAPS [MAPS ...]] [--mask MASK]
[--pixel_size PIXEL_SIZE] [--model MODEL [MODEL ...]]
[--no_expand_ncs] [--padding PADDING]
[--mask_cutoff MASK_CUTOFF] [--noncubic] [--noncentered]
[--no_shift] [--no_shift_keep_cell]
[--force_cell FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL]
[--disable_cell_check] [--shifts SHIFTS]
Trim maps and shift models into a small new box.
optional arguments:
-h, --help show this help message and exit
--maps MAPS [MAPS ...]
Input map file(s)
--mask MASK Mask file
--pixel_size PIXEL_SIZE
Override pixel size (A)
--model MODEL [MODEL ...]
Input atomic model file(s)
--no_expand_ncs Do not expand strict NCS in MTRIX or _struct_ncs_oper
--padding PADDING padding in angstrom unit (default: 10.0)
--mask_cutoff MASK_CUTOFF
Mask value cutoff to define boundary (default: 0.5)
--noncubic
--noncentered If specified non-centered trimming is performed. Not
recommended if having some symmetry
--no_shift If specified resultant maps will have shifted origin
and overlap with the input maps.
--no_shift_keep_cell Keep original unit cell when --no_shift is given
--force_cell FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL
Use specified unit cell parameter
--disable_cell_check Turn off unit cell consistency test
--shifts SHIFTS Specify shifts.json to use precalculated parameters
If --mask is provided, a boundary is decided using the mask and --padding.
Otherwise the model is used.
Utilities¶
TBD