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SPLIce [NBXMod int] { segid resid resid repeat(res resid) }
{ RESEquence segid resid resid repeat(res) }
The SPLICE command replaces one set of residues with another set of residues. The coordinate set is shuffled to preserve backbone positions to the extent possible. Insertions of residues can be performed by splicing multiple residues in place of one residue. The COMPARE command, see Comparisons, in the analysis facility, see Analysis, can be used to generate the necessary SPLICE commands for a homologous transformation of one sequence into another.
When the SPLICE command is used, the residue topology file used to construct the PSF must be present when this command is used because this command regenerates the PSF. A corollary of this is that the SPLICE command can only be used when the entire PSF was generated from a single RTF. Also, any editing on the PSF, (see Edit Command), will be lost. More details on the implementation are given below.
The residues to be replaced are specified by a segment identifier followed by two residue identifiers which start and end the changed segment. If only one residue is to be changed, then both residue identifiers will be the same.
The specification of replacement residues depends on the presence of the RESEQUENCE option. If RESEQUENCE is not specified, then you must specify both the residue names and the residue identifiers for all replaced residues. The advantage of this approach is that residue identifiers outside of the changes are consistent. If RESEQUENCE is specified, then you must specify only the new residue names. All residues within the segment will be renumbered from the first residue.
The shuffling of coordinates is an important feature of this command. During the resequencing operation, all backbone positions (atoms not constructed by the sidechain degree of freedom operator) are conserved for residues that are in the same position relative to the N-terminal side of the splice. Thus, for an equal length change, the backbone will be preserved. For insertions or deletions, then the C-terminal side of the splice will be wrong; although the anchor for a CONGEN search (atoms CA, C, and O) will be preserved. If a splice results in no change in the residue name, then all the sidechain atoms are copied. In addition, when a glycine is changed to any other residue, the position of CB is constructed assuming perfect geometry for a amino-acid as specified in the parameter set.
The actual implementation of the command is to use the equivalent of the GENERATE command (see Generate Command) after modification of the sequence. The NBXMOD option controls the automatic generation of non-bonded exclusions when the GENERATE command is simulated. See Nbxmod, for more details. The first operation performed after the SPLICE command has been successfully parsed is to shuffle coordinates, and to record the position of all disulphides. Then, the PSF is erased and completely regenerated using the new sequence. Disulphides are now added back, and the coordinates for the backbone and endpoints are corrected. The internal coordinates are then cleared, so that a new set of construction rules can be generated, see Internal Coordinates. Finally, the hydrogen bond list, non-bonded list, fixed constraints, harmonic atom constraints, and dihedral angle constraints are all cleared. Any automatic generation options, see Generate Command, are also applied.