Setting up Fiber Structure Parameters and Diffraction Information: The Fiber_refin Statement

FIBEr_refin { $<$fiber_refin-statement$>$ } END

This statement has to be invoked from the main level of X-PLOR.

$<$fiber_refin-statement$>$:==

RESEt

Erases the current fiber_refin data base, that is, the atomic form factors, fiber structure parameters and fiber diffraction data.

AXIAl_repeat_constant=$<$real$>$

defines the length of the axial repeat unit ($c$).

TURNs or T=$<$integer$>$

sets number of helix turns in an axial repeat unit.

UNITs or U=$<$integer$>$

sets number of subunits in an axial repeat unit.

HELIcal_symmetry=($<$integer$>$, $<$integer$>$, ..., $<$integer$>$)

defines the helical symmetry of the structure. The integer number specifies the multiplicity number of the screw rotation. The symmetry relations may only be used in the potential energy calculation for inter-subunit interactions.

GENErate

yield a full set of fiber diffraction data within the resolution range. Fobs, Fcalc, Fpart are set to 0; weight and sigma are set to 1; FOM is set to -1. Action is taken as soon as this statment is issued.

BLMAX=$<$integer$>$

sets maximum number of Bessel terms on a layer line (default=5).

SAMPling_unit=$<$real$>$

sets sampling unit of reciprocal space radius $R$ (default=0.001Å$^{-1}$).

OPTImize

OVERall { $<$xrefin-optimize-overall-statement$>$ } END Optimizes an overall isotropic B-Factor (see X-PLOR Section 14.2).

OPTImize

GROUp { $<$xrefin-optimize-group-statement$>$ } END optimizes group B-factors (see X-PLOR Section 14.3).

OPTImize

BFACtor { $<$xrefin-optimize-bfactor-statement$>$ } END optimizes individual (restrained) isotropic B-factors (see X-PLOR Section 14.4).

DO

$<$xrefin-do-statement$>$ Manipulates structure factors (see X-PLOR Section 13.5).

MAP

{ $<$fiber_refin-map-statement$>$ } END Computes electron density map (see Section 15.0.4).

NDIFfraction_data=$<$integer$>$

defines maximum number of diffraction data (default: 200).

DIFFraction_data_set

{ $<$fiber_refin-diffraction_data-statement$>$ } END Initiates input of diffraction data. It is important to specify the maximum expected allocation for diffraction data (NDIFfraction_data statement) before starting to read the diffraction data.

LOOKup=$<$logical$>$

Flag indicating whether to use lookup tables for the direct summation method (default: true). If LOOKup=T, Lookup tables of $\cos$, $\sin$ and Bessel functions will be generated.

TGRid

sets grid size for Bessel lookup tables (default=0.05, minimum=0.01).

GRADient

Computes norm of gradient of $E_{EMPIRICAL}$ and $E_{FIBER}$, then compares the two norms and computes “ideal" weights $S_f$. Action is taken as soon as this statement is issued.

PRINt R-FActor

Prints R-factor of selected reflections as a function of resolution and stores overall R-factor of selected reflections

PRINt Bessel-Orders

Prints Orders of Bessel functions for each layer line. The number of layer lines is determined by the resolution range and the order of the Bessel functions are determined by the selection rule.

SCATter

$<$selection$>$ $<$real$>$ $<$real$>$ $<$real$>$ $<$real$>$ $<$real$>$ $<$real$>$ $<$real$>$ $<$real$>$ $<$real$>$ Adds an atomic form factor specification to the fiber-refin data base. The statement specifies the coefficients $a_1, b_1, a_2, b_2, a_3, b_3, a_4, b_4, c$ for the selected atoms (default: none). An atom will only contribute to the structure factors if it has been selected in one SCATter statement and if it has been selected in the SELEction statement. Care should be taken not to produce an overlapping definition of atom selections, e.g., if there is a CA ion, one should exclude the CA ion in the atomic form factor definition for carbon atoms.

SELEction=

$<$atom-selection$>$ Selects atoms that will be used in the next structure factor calculation (default: all). An atom will only contribute to the structure factor if it has been selected in one SCATter statement and if it has been selected in the SELEction statement. The selection remains active until a new SELEction statement is issued.

RESOLution

$<$real$>$ $<$real$>$ Sets resolution limits in Å for the selection of diffraction data. One of the $<$real$>$ values is the high resolution limit and the other one is the low resolution limit; it does not matter whether the high or the low resolution limit comes first (default: 10-3 Å).

FWINdow

$<$real$>$ $<$real$>$ Sets $F_{obs}$ amplitude limits for the selection of fiber diffraction data. One of the $<$real$>$ values is the upper value the other one is the lower value; it does not matter whether the upper or the lower limit comes first. (default: 0-100000).

TOLErance=$<$real$>$

Specifies the maximum value $\Delta_{F}$ (in Å) by which any atomic position can deviate from the positions at which ${\cal G}_{calc}$ was last computed during molecular dynamics, energy minimization, or energy calculation. If TOLErance is exceeded, ${\cal G}_{calc}$ and derivatives are recomputed (default: 0.5Å).

WEIGht=$<$real$>$

Specifies the overall weight factor $S_f$ for $E_{fiber}$ (default=1).

UPDAte

Computes ${\cal G}_{calc}$ for selected fiber diffraction data.

$<$fiber_refin-diffraction_data-statement$>$:==

TITLe $<$title information$>$

gives a short description of the fiber diffraction data set.

LAYER LINE $<$integer$>$ HIGHest $<$integer$>$ LOWEst $<$integer$>$

defines a layer line title. The first $<$integer$>$ is the layer line number. The second $<$integer$>$ is the maximum reciprocal space index ($R_s$). The third $<$integer$>$ is the minimum reciprocal space index ($R_s$).

$<$real$>$ $<$real$>$ ...

$<$real$>$ are the diffraction data ${\cal G}_{obs}$.