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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 ().
**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 (default=0.001Å).
**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 , 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 and , then compares the two norms and computes “ideal" weights . 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 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 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 (in Å) by which any
atomic position can deviate from the positions at which
was last computed during molecular dynamics,
energy minimization, or energy calculation. If
**TOLErance**is exceeded, and derivatives are recomputed (default: 0.5Å). **WEIGht=real**- Specifies the overall weight factor for (default=1).
**UPDAte**- Computes 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 (). The third integer is the minimum reciprocal space index ().
**real real ...**- real are the diffraction data .

*Xplor-NIH 2024-09-13*