matchmaps command-line interface

matchmaps is built to be used from the command-line. See the following utilities below. You can also print these messages in the command-line via the --help option.

matchmaps

Compute a real-space difference map. You will need two MTZ files, which will be referred to throughout as ‘on’ and ‘off’, though they could also be light/dark, bound/apo, mutant/WT, hot/cold, etc. Each mtz will need to contain structure factor amplitudes and uncertainties; you will not need any phases. You will, however, need an input model (assumed to correspond with the ‘off’ state) which will be used to determine phases. The input file may be in .pdb or .cif format. Please note that both ccp4 and phenix must be installed and active in your environment for this function to run. More information can be found online at https://rs-station.github.io/matchmaps/index.html

usage: matchmaps [-h] --mtzoff mtzfileoff Foff SigFoff --mtzon mtzfileon Fon
                 SigFon --pdboff PDBOFF [--on-as-stationary] [--alpha ALPHA]
                 [--unmasked-radius UNMASKED_RADIUS]
                 [--rbr-selections [RBR_SELECTIONS ...]]
                 [--ligands [LIGANDS ...]] [--input-dir INPUT_DIR]
                 [--output-dir OUTPUT_DIR] [--spacing SPACING] [--dmin DMIN]
                 [--no-bss] [--verbose] [--eff EFF]
                 [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]
                 [--phenix-version PHENIX_VERSION]

-h, --help

show this help message and exit

--mtzoff <mtzfileoff> <foff> <sigfoff>, -f <mtzfileoff> <foff> <sigfoff>

MTZ or sfCIF containing off/apo/ground/dark state data. Specified as [filename F SigF]

--mtzon <mtzfileon> <fon> <sigfon>, -n <mtzfileon> <fon> <sigfon>

MTZ or sfCIF containing on/bound/excited/bright state data. Specified as [filename F SigF]

--pdboff <pdboff>, -p <pdboff>

Reference PDB or mmCIF corresponding to the off/apo/ground/dark state. Used for rigid-body refinement of both input MTZs to generate phases.

--on-as-stationary

Include this flag to align ‘off’ data onto ‘on’ data. By default, ‘off’ data is stationary and ‘on’ data is moved.

--alpha <alpha>

Alpha to use for error weighting of F-obs prior to Fourier Transform. Weights are computed as: 1 / ((1+(alpha*(SigF^2)) / <SigF>^2). Default value is alpha=0, e.g., no weighting is performed.

--unmasked-radius <unmasked_radius>

Maximum distance (in Anstroms) away from protein model to include voxels. Only applies to the ‘unmasked’ difference map output. Defaults to 5. Note that the regular difference map (e.g. the ‘masked’ version) is not affected by this parameter and maintains a solvent mask radius of 2 Angstroms.

--rbr-selections <rbr_selections>, -r <rbr_selections>

Specification of multiple rigid-body groups for refinement. By default, everything is refined as one rigid-body group.

--ligands <ligands>, -l <ligands>

Any .cif restraint files needed for refinement

--input-dir <input_dir>, -i <input_dir>

Path to input files. Optional, defaults to ‘./’ (current directory)

--output-dir <output_dir>, -o <output_dir>

Path to which output files should be written. Optional, defaults to ‘./’ (current directory)

--spacing <spacing>, -s <spacing>

Approximate voxel size in Angstroms for real-space maps. Defaults to 0.5 A. Value is approximate because there must be an integer number of voxels along each unit cell dimension

--dmin <dmin>

Highest-resolution (in Angstroms) reflections to include in Fourier transform for FloatGrid creation. By default, cutoff is the resolution limit of the lower-resolution input MTZ.

--no-bss

Include this flag to skip bulk solvent scaling in phenix.refine. By default, BSS is included.

--verbose, -v

Include this flag to print out scaleit and phenix.refine outputs to the terminal. Useful for troubleshooting, but annoying; defaults to False.

--eff <eff>

Custom .eff template for running phenix.refine.

--keep-temp-files <keep_temp_files>, -k <keep_temp_files>

Do not delete intermediate matchmaps files, but rather place them in the supplied directory. This directory is created as a subdirectory of the supplied output-dir.

--script <script>

Name for a file {script}.sh which can be run to repeat this command. By default, this file is called run_matchmaps.sh. Note that this file is written out in the current working directory, NOT the input or output directories

--phenix-version <phenix_version>

Specify phenix version as a string, e.g. ‘1.20’. If omitted, matchmaps will attempt to automatically detect the version in use by analyzing the output of phenix.version

matchmaps.mr

Compute a real-space difference map between inputs in different space groups / crystal packings. You will need two MTZ files, which will be referred to throughout as ‘on’ and ‘off’, though they could also be light/dark, bound/apo, mutant/WT, hot/cold, etc. Each mtz will need to contain structure factor amplitudes and uncertainties; you will not need any phases. You will, however, need an input model (assumed to correspond with the ‘off’ state) which will be used to determine phases. The input file may be in .pdb or .cif format. Please note that phenix must be installed and active in your environment for this function to run. If your mtzoff and mtzon are in the same spacegroup and crystal packing, see the basic matchmaps utility. More information can be found online at https://rs-station.github.io/matchmaps/index.html

usage: matchmaps.mr [-h] --mtzoff mtzfileoff Foff SigFoff --mtzon mtzfileon
                    Fon SigFon --pdboff PDBOFF [--on-as-stationary]
                    [--alpha ALPHA] [--unmasked-radius UNMASKED_RADIUS]
                    [--rbr-selections [RBR_SELECTIONS ...]]
                    [--ligands [LIGANDS ...]] [--input-dir INPUT_DIR]
                    [--output-dir OUTPUT_DIR] [--spacing SPACING]
                    [--dmin DMIN] [--no-bss] [--verbose] [--eff EFF]
                    [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]
                    [--phenix-version PHENIX_VERSION]

-h, --help

show this help message and exit

--mtzoff <mtzfileoff> <foff> <sigfoff>, -f <mtzfileoff> <foff> <sigfoff>

MTZ or sfCIF containing off/apo/ground/dark state data. Specified as [filename F SigF]

--mtzon <mtzfileon> <fon> <sigfon>, -n <mtzfileon> <fon> <sigfon>

MTZ or sfCIF containing on/bound/excited/bright state data. Specified as [filename F SigF]

--pdboff <pdboff>, -p <pdboff>

Reference PDB or mmCIF corresponding to the off/apo/ground/dark state. Used for rigid-body refinement of both input MTZs to generate phases.

--on-as-stationary

Include this flag to align ‘off’ data onto ‘on’ data. By default, ‘off’ data is stationary and ‘on’ data is moved.

--alpha <alpha>

Alpha to use for error weighting of F-obs prior to Fourier Transform. Weights are computed as: 1 / ((1+(alpha*(SigF^2)) / <SigF>^2). Default value is alpha=0, e.g., no weighting is performed.

--unmasked-radius <unmasked_radius>

Maximum distance (in Anstroms) away from protein model to include voxels. Only applies to the ‘unmasked’ difference map output. Defaults to 5. Note that the regular difference map (e.g. the ‘masked’ version) is not affected by this parameter and maintains a solvent mask radius of 2 Angstroms.

--rbr-selections <rbr_selections>, -r <rbr_selections>

Specification of multiple rigid-body groups for refinement. By default, everything is refined as one rigid-body group.

--ligands <ligands>, -l <ligands>

Any .cif restraint files needed for refinement

--input-dir <input_dir>, -i <input_dir>

Path to input files. Optional, defaults to ‘./’ (current directory)

--output-dir <output_dir>, -o <output_dir>

Path to which output files should be written. Optional, defaults to ‘./’ (current directory)

--spacing <spacing>, -s <spacing>

Approximate voxel size in Angstroms for real-space maps. Defaults to 0.5 A. Value is approximate because there must be an integer number of voxels along each unit cell dimension

--dmin <dmin>

Highest-resolution (in Angstroms) reflections to include in Fourier transform for FloatGrid creation. By default, cutoff is the resolution limit of the lower-resolution input MTZ.

--no-bss

Include this flag to skip bulk solvent scaling in phenix.refine. By default, BSS is included.

--verbose, -v

Include this flag to print out scaleit and phenix.refine outputs to the terminal. Useful for troubleshooting, but annoying; defaults to False.

--eff <eff>

Custom .eff template for running phenix.refine.

--keep-temp-files <keep_temp_files>, -k <keep_temp_files>

Do not delete intermediate matchmaps files, but rather place them in the supplied directory. This directory is created as a subdirectory of the supplied output-dir.

--script <script>

Name for a file {script}.sh which can be run to repeat this command. By default, this file is called run_matchmaps.sh. Note that this file is written out in the current working directory, NOT the input or output directories

--phenix-version <phenix_version>

Specify phenix version as a string, e.g. ‘1.20’. If omitted, matchmaps will attempt to automatically detect the version in use by analyzing the output of phenix.version

matchmaps.ncs

Compute an ‘internal’ real-space difference map between NCS-related molecules. You will need an MTZ file with structure factor amplitudes and optionally containing phases, and a PDB/CIF file.Please note that phenix must be installed and active in your environment for this function to run. More information can be found online at https://rs-station.github.io/matchmaps/index.html

usage: matchmaps.ncs [-h] --mtz [MTZ ...] [--phases PHASES] --pdb PDB
                     --ncs-chains fixed_chain moving_chain [--mapname MAPNAME]
                     [--ligands [LIGANDS ...]] [--input-dir INPUT_DIR]
                     [--output-dir OUTPUT_DIR] [--spacing SPACING]
                     [--dmin DMIN] [--no-bss] [--verbose] [--eff EFF]
                     [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]
                     [--phenix-version PHENIX_VERSION]

-h, --help

show this help message and exit

--mtz <mtz>, -m <mtz>

MTZ or sfCIF file containing structure factor amplitudes. Specified as [filename F SigF] or [filename F]. SigF is not necessary if phases are also provided

--phases <phases>

Optional. Column in MTZ/sfCIF file containing phases. If phases are not provided, phases will be computed via rigid-body refinement of the provided model and structure factor amplitudes.

--pdb <pdb>, -p <pdb>

Reference PDB or mmCIF. If phases are not provided, used for rigid-body refinement of input MTZ/sfCIF to generate phases.

--ncs-chains <fixed_chain> <moving_chain>, -n <fixed_chain> <moving_chain>

NCS chains to overlay and subtract, specified as [fixed_chain, moving_chain].E.g. to overlay chain C onto chain B, specify: –ncs-chains B C

--mapname <mapname>

Base filename for the output map files.

--ligands <ligands>, -l <ligands>

Any .cif restraint files needed for refinement

--input-dir <input_dir>, -i <input_dir>

Path to input files. Optional, defaults to ‘./’ (current directory)

--output-dir <output_dir>, -o <output_dir>

Path to which output files should be written. Optional, defaults to ‘./’ (current directory)

--spacing <spacing>, -s <spacing>

Approximate voxel size in Angstroms for real-space maps. Defaults to 0.5 A. Value is approximate because there must be an integer number of voxels along each unit cell dimension

--dmin <dmin>

Highest-resolution (in Angstroms) reflections to include in Fourier transform for FloatGrid creation. By default, cutoff is the resolution limit of the lower-resolution input MTZ.

--no-bss

Include this flag to skip bulk solvent scaling in phenix.refine. By default, BSS is included.

--verbose, -v

Include this flag to print out scaleit and phenix.refine outputs to the terminal. Useful for troubleshooting, but annoying; defaults to False.

--eff <eff>

Custom .eff template for running phenix.refine.

--keep-temp-files <keep_temp_files>, -k <keep_temp_files>

Do not delete intermediate matchmaps files, but rather place them in the supplied directory. This directory is created as a subdirectory of the supplied output-dir.

--script <script>

Name for a file {script}.sh which can be run to repeat this command. By default, this file is called run_matchmaps.sh. Note that this file is written out in the current working directory, NOT the input or output directories

--phenix-version <phenix_version>

Specify phenix version as a string, e.g. ‘1.20’. If omitted, matchmaps will attempt to automatically detect the version in use by analyzing the output of phenix.version