PLAN npeaks [20] d1 [#] d2 [#]If npeaks is positive a Fourier peak list is printed and written to the .res file; if it is negative molecule assembly and line printer plots are also performed. For negative npeaks, distances involving peaks which are less than r1+r2+d1 (the covalent radii r are defined via SFAC; 1 and 2 refer to the two atoms concerned) are printed and used to define 'molecules' for the line printer plots. Distances involving atoms and/or peaks which are less than r1+r2+|d2| are considered to be 'non-bonded interactions'; however distances in which both atoms are hydrogen or at least one is carbon (recognised by SFAC label 'C') are ignored. The default values of d1 and d2 (for negative npeaks) are 0.5 and 2.0 resp. These non-bonded interactions are ignored when defining molecules, but the corresponding atoms and distances are included in the line printer output. Thus an atom or peak may appear in more than one map, or more than once on the same map. A table of the appropriate coordinates and symmetry transformations appears at the end of each molecule.
Negative d2 includes hydrogen atoms in the line printer plots, otherwise they are left out (but included in the distance tables). For the purposes of the PLAN instruction, a hydrogen atom is one with a radius of less than 0.4 Angstrom. Peaks are assigned the radius of SFAC type 1, which is usually set to carbon. Peaks appear on the printout as numbers, but in the .res file they are given names beginning with 'Q' and followed by the same numbers. Since only three digits are available for the number, the absolute value of npeaks may not exceed 999. Peak heights are also written to the .res file (after the sof and dummy U values) in electrons per cubic Angstrom. See also MOLE for forcing molecules (and their environments) to be printed separately.
A default npeaks of +20 is set by FMAP; to obtain line printer plots, an explicit PLAN instruction with negative npeaks is required. If npeaks is positive the nearest unique atoms to each peak are tabulated, together with the corresponding distances. A table of shortest distances between peaks is also produced. If npeaks is positive d1 and d2 have a different meaning. The default of d1 is then -1 and causes the full peaklist to appear in the .res file. If it is positive (say 2.3) then the full peaklist is still printed in the .lst file, but only suitable candidates for (full occupancy) water molecules appear in the .res file (with SFAC 4 and U set to 0.75). The water molecules must be less than 4 Angstroms from an atom which begins with 'O', 'N' or 'W', and may not be less than d2 (default 3.0) from any atom which does not begin with 'O', 'N', 'W' or 'H', and may not be nearer than d1 to any 'O', 'N' or 'W' atom or potential waters which have larger peak heights. This facility is intended for extending the water structure of proteins in connection with BUMP and SWAT. To include the waters in the next refinement job, their names need to be changed and they need to be moved to before the HKLF instruction at the end of the atom list in the new .ins file. It is recommended that the last water is called 'LAST' on the ISOR and CONF instructions so that this name does not need to be updated each job.
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