BLOC Command

BLOC  n1  n2  atomnames
If n1 or n2 are positive, the x, y and z parameters of the named atoms are refined in the corresponding cycle. If n1 or n2 are negative, the occupation and displacement parameters are refined in cycle. Not more than two such parameters may be specified on a single BLOC instruction, but the same atoms may be mentioned in any number of BLOC instructions. To refine both x, y and z as well as displacement parameters for an atom in the same block, n1 and n2 should specify the same cycle number, but with opposite signs. A BLOC instruction with no atom names refines all atoms in the specified cycles. The pattern of blocks is repeated after the maximum block number has been reached if the number of L.S. refinement cycles is larger than the maximum BLOC |n1| or |n2|. If a cycle number less than the maximum |n1| or |n2| is not mentioned in any BLOC instruction, it is treated as full-matrix. The overall scale, batch/twin scale factors, extinction coefficient, SWAT g parameter and free variables (if present) are refined in every block. Riding (hydrogen) atoms and atoms in rigid groups are included in the same blocks as the atoms on which they ride.

For example, a polypeptide consisting of 30 residues (residue numbers 1..30 set by RESI instructions) could be refined efficiently as follows (all non-hydrogen atoms assumed anisotropic):

 BLOC 1
 BLOC -2 N_1 > O_16
 BLOC -3 N_14 > O_30
which would ensure 3 roughly equally sized blocks of about 800 parameters each and some overlap between the two anisotropic blocks to avoid problems where they join. The geometric parameters would refine in cycles 1,4,7 .. and the anisotropic displacement parameters in the remaining cycles. An alternative good blocking strategy would be to divide the structure into three overlapping blocks of xyz and Uij parameters, and to add a fourth cycle in which all xyz but no Uij values are refined (these four blocks would then also each contain about 800 parameters), i.e.:

 BLOC 1 -1 N_1 > O_11
 BLOC 2 -2 N_10 > O_21
 BLOC 3 -3 N_20 > O_30
 BLOC 4
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