The Keywords

MODE Must be the first keyword.

update allatoms/waters initialises the update mode. allatoms indicates that both protein and water atoms from the model will be considered for update. waters indicates that only water atoms (residue name HOH or WAT) will be updated. Metals will be treated as non-water atoms. The distance constraints for the addition of new atoms are: the shortest distance between new atom and any of the existing atom is 1.0 Å (allatoms) and any of the O or N of the existing atoms (waters) is 2.3 Å; the longest distance is 3.3 Å in both cases. The distance constraint for removal is 3.5 Å or longer to any of the existing atoms. Partially occupied atoms will not be used for merge, their occupancy is accounted for in removal. These atoms are used anyway as seeds (parent atoms) for the new atom search.

mirbuild initialises the mirbuild mode. The pseudo protein set of atoms will be placed into the input density map. The distance constraints are 1.1 to 1.8 Å  between the atoms.

shakemodel light/allatoms initialises the shaking mode for a shock-like modification of the current model. light indicates that only atoms with atomic number 8 (oxygen) or lower will be treated. allatoms indicates application to any atom in the model regardless of their type.

reflaver initialises the mode of weighted averaging of structure factors obtained from multiple refinements of several slightly different models.

CELL Cell parameters a, b, c, $\alpha$, $\beta$, $\gamma$ in Å and degrees. This keyword is optional for MODE update allatoms/waters and shakemodel light/all atoms and is obligatory for MODE mirbuild.

SYMMetry The crystal symmetry. Can be given either as a space group name or number (e.g. P212121 or 19). Obligatory for MODE update allatoms/waters, mirbuild and shakemodel light/all atoms.

RESOlution Resolution of the X-ray data (R $_{\rm min}$, R $_{\rm max}$). Obligatory for MODE update allatoms/waters, mirbuild and reflaver.

FIND The addition of new sites in MODE update allatoms/waters.

After atoms you should give the number of atoms to add. At the end of refinement (it may take 20 to 50 cycles) the model should contain all atoms. The target number of atoms in the final model can be estimated by multiplying the number of protein atoms by 1.2, the 20% extra corresponds both to ordered water molecules and weaker, slighlty disordered, ones which are important for the pseudo solvent continuum. The number of atoms allowed to be added in each cycle depends on the resolution. A simple empirical guide is that the maximum number to add is $N\times0.08/d^3$, where N is the current number of atoms and d is the highest resolution in Å. Thus at a resolution of 1.8 Å and a coordinate file of 2,000 atoms the maximum number to be added is 27. New atoms will be automatically assigned a temperature factor on the basis of the density height.

The string after chain is the chain identifier for new atoms. All new atoms will have this chain identifier and be numbered sequentially.

The subkeyword after cutsigma can be either the number or auto. The number is a MAPIN2 density cutoff. Atoms will be looked for in density above cutsigma $\times$ r.m.s. density. A value of 3 to 4 is typical. The statistically significant density threshold can be defined automatically if auto is used. This can be used for MODE update waters as it prevents too many extra atoms being added. However it may not work satisfactorily if the resolution is lower than 1.5 Å or the model is too far from being finally refined.

REMOve Removal of atoms in MODE update allatoms/waters. The removal of atoms influences the success of refinement to a much greater extent than addition of new atoms and should certainly be used.

The number after atoms is the maximum number of atoms to reject at each cycle. A value of about 25 to 100% of the number of atoms to be added is recommended.The actual number will be defined by the program.

The number after cutsigma gives the MAPIN1 density cutoff. Atoms will be considered for rejection only if they are located in density below cutsigma $\times$ r.m.s. density. A value around 1 is recommended.

The number following the merge keyword is the shortest distance between two atoms if they are to be merged. Partially occupied atoms are not used for merging. The keyword is optional. Any pair closer than this will be inspected. In a case of a water-water pair the atom with the higher temperature factor will be rejected and the second assigned to the weighted average xyz and 1/B parameters. If any water appears to be at the merging distance to a non-water (protein or metal) atom, it will be removed. A merging distance value of 0.6 Å is default for mode update atoms and the value of 2.2 is recommended for mode update waters where the default is no merging.

keep zeroocc is an optional keyword. Default is to remove atoms with zero occupancy from the PDB file.

REFIne This initialises the sphericity based real space refinement of individual atoms. The keyword is optional in MODE update allatoms/waters.

The subkeyword can be either allatoms (all atoms will be refined - not recommended unless the resolution is about 1.0 Å) or waters (strongly recommended for analyse waters mode, especially if the resolution is higher than 2.0 Å).

MIRBuild Obligatory keyword for MODE mirbuild.

The number after atoms indicates the approximate number of atoms to be placed into the MIR(AS) MAPIN2 map. It should correspond to the total number of atoms expected to be in the model. The number after models specifies how many different models can be output. It may be 1, 2 or 3. These different models are subsequently used for multiple refinement and weighted averaging.

SHAKemodel Obligatory keyword for MODE shakemodel. There are four optional subkeywords.

The number after bexcl is the highest temperature factor cutoff. Atoms with higher temperature factors will be excluded from the PDB file.

The two numbers after breset define the low and high limits for truncation of atomic temperature factors.

The number after randomise defines the r.m.s. uniform random shift in Å to be applied to the coordinate set.

The three numbers after shift define the systematic shift along in Å the crystallographic axes to be applied to the coordinate set.

LABIn Obligatory keyword for MODE reflaver. Input MTZ file labels for structure factors from multiple refinements have to be given, e.g. FP=FP SIGFP=SIGFP FC1=FC1 PHIC1=PHIC1 etc. The maximum number of FCx/PHICx is 8. free is optional.

LABOut Obligatory keyword for MODE reflaver. Output MTZ file labels for weighted average structure factors, phases and figures of merit should be provided.

END Must be the last data card terminating input to ARP/wARP .