PART n sofThe following atoms belong to part n of a disordered group. The automatic bond generation ignores bonds between atoms with different PART numbers, unless one of them is zero (the value before the first PART instruction). If a site occupation factor (sof) is specified on the PART instruction, it overrides the value on the following atom instructions (even if set via an AFIX instruction) until a further PART instruction, e.g. 'PART 0', is encountered).
If n is negative, the generation of special position constraints is suppressed and bonds to symmetry generated atoms with the same or a different non-zero PART number are excluded; this is suitable for a solvent molecule disordered on a special position of higher symmetry than the molecule can take (e.g. a toluene molecule on an inversion center). A PART instruction remains in force until a further PART instruction is read; 'PART 0' should be used to continue with the non-disordered part of the structure.
Some care is necessary in generating hydrogen atoms where disordered groups are involved. If the hydrogen atoms are assigned a PART number, then even if the atom to which they are attached has no part number (i.e. PART 0) the above rules may be used by the program to work out the correct connectivity for calculating the hydrogen atom positions. HFIX hydrogens are assigned the PART number of the atom to which they are attached. If the hydrogens and the atom to which they are attached belong to PART zero but the latter atom is bonded to atoms with non-zero PART, the LOWEST of these non-zero PART numbers is assumed to be the major component and is used to calculate the hydrogen positions. As an example, assume that one of the valine residues (Val32) in a small protein is disordered so that one of the methyl groups is common to both components and the other is disordered unequally over the two remaining positions. Hydrogens could be added for the major component only as follows:
HFIX_val 37 CG1 CG2 HFIX_val 13 CB : RESI 32 Val N ..... CA ..... C ..... O ..... CB ..... CG1 ..... PART 1 CG2 1 ... ... ... 21 ... PART 2 CG2' 1 ... ... ... -21 ... PART 0 :where free variable 2 is the occupation factor for PART 1 (say 0.7) and the occupation factor of the second component is tied to 1-fv(2) (i.e. 0.3). The value for this free variable is set on the FVAR instruction and is free to refine. If there were more than two components, a linear free variable restraint (SUMP) could be used to restrain the sum of occupation factors to (e.g.) 1. The hydrogens for the second component could be added in a subsequent job with the help of AFIX instructions:
: CB ..... PART 1 ! This hydrogen for the major component was AFIX 13 ! generated in the previous run (but Part 1 HB 2 ... ... ... 21 -1.2 ! must be added and its sof changed now !). PART 2 !! AFIX 13 !! These four lines are added now; HFIX HB' 2 ... ... ... -21 -1.2 !! would not be a valid alternative. PART 0 !! AFIX 0 CG1 ..... AFIX 37 ! HG1A 2 ... ... ... 11 -1.5 ! Generated from HFIX in previous run. HG1B 2 ... ... ... 11 -1.5 ! HG1C 2 ... ... ... 11 -1.5 ! AFIX 0 ! PART 1 CG2 1 ... ... ... 21 ... AFIX 37 ! HG2A 2 ... ... ... 21 -1.5 ! Generated from HFIX in previous run. HG2B 2 ... ... ... 21 -1.5 ! HG2C 2 ... ... ... 21 -1.5 ! AFIX 0 ! PART 2 CG2' 1 ... ... ... -21 ... AFIX 37 !! HG2D 2 ... ... ... -21 -1.5 !! These five lines are added now - in this HG2E 2 ... ... ... -21 -1.5 !! case HFIX 37 CG2'_32 could also be used. HG2F 2 ... ... ... -21 -1.5 !! AFIX 0 !! PART 0 :
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