U.S. flag

An official website of the United States government
  next up previous contents index  Xplor-NIH home Documentation

Next: Requirements Up: Rotation Search Previous: Rotation Search

Syntax

SEARch Rotation
{ $<$xrefin-search-rotation-statement$>$ } END is an xrefin statement. Action takes place as soon as the END statement is issued.
$<$xrefin-search-rotation-statement$>$
:==
DELTa=$<$real$>$
specifies an angular grid interval. DELTa should be less than ${\rm ArcSin}[ 1 / (3 d_{min} v_{max})]$, where $1/d_{min}$ is the high-resolution limit (see Section 13.3) and $v_{max}$ is the maximum Patterson vector length of the search model (see Section 19.5.3 for an example). This is a conservative estimate. In many cases, it will be sufficient to double this estimate. Note that the CPU time requirement for the rotation function is roughly an inverse cubic function of DELTa. Thus, one should use the largest possible value for DELTa (default: 0.0).
EPSIlon=$<$real$>$
specifies $\epsilon$ for the peak cluster analysis. Multiple entries produce multiple cluster analysis (default: 0.2).
FORMatted=$<$logical$>$
should be set to FALSE if the map files are binary files (default: TRUE).
LIST=$<$filename$>$
specifies the file for the list of rotation function peaks after the cluster analysis (grid points are mapped into an asymmetric unit of the rotation function) (default: OUTPUT).
NLISt=$<$integer$>$
specifies that the analysis of the rotation function will be restricted to the $<$integer$>$ highest grid points.
NPEAks=$<$integer$>$
selects the $<$integer$>$ strongest Patterson vectors of map P1 that satisfy the range and threshold criteria (default: 5000).
OUTPut=$<$filename$>$
specifies the file for the complete rotation function.
P1INput=$<$filename$>$
reads Patterson map P1.
P2INput=$<$filename$>$
reads Patterson map P2.
PSIMIn=$<$real$>$
PSIMAx=$<$real$>$ PHIMIn=$<$real$>$
PHIMAx=$<$real$>$ KAPPAMIn=$<$real$>$ KAPPAMAx=$<$real$>$ is spherical polar angle sampling (as defined in Section 2.4). Specified are the minimum and maximum values for $\psi$, $\phi$, $\kappa$ (default: 0).
RANGe=$<$real$>$=$<$real$>$
selects the Patterson vectors of map P1 based on the distance of the vectors from the origin (default: 3-20 Å).
SELF=$<$logical$>$
is a flag for cluster analysis that determines the symmetry of map P1. If FALSE, map P1 is treated with $P_1$ symmetry, whereas map P2 is treated with crystallographic symmetry, as in the xrefin symmetry statement. If TRUE, both P1 and P2 are treated with crystallographic symmetry.
T1MIn=$<$real$>$
T1MAx=$<$real$>$ T2MIn=$<$real$>$
T2MAx=$<$real$>$ T3MIn=$<$real$>$ T3MAx=$<$real$>$ is equidistant Eulerian angle sampling ($\theta_1$, $\theta_2$, $\theta_3$, as defined in Section 2.4) using DELTa intervals. Specified are the minimum and maximum values for $\theta_1$, $\theta_2$, $\theta_3$ (default: 0 ).
THREshold=$<$real$>$
selects the Patterson vectors of map P1 according to the value of the Patterson map: if this value is larger than the specified threshold, the Patterson vector is selected (default: 500).
TPMIn=$<$real$>$
TPMAx=$<$real$>$ TMMIn=$<$real$>$
TMMAx=$<$real$>$ T2MIn=$<$real$>$ T2MAx=$<$real$>$
is Lattman's (1985) pseudo-orthogonal sampling, using DELTa as the interval for $\theta_2$. Specified are the minimum and maximum values for $\theta_{+}$, $\theta_{2}$, and $\theta_{-}$ (default: 0 and none).

next up previous contents index
Next: Requirements Up: Rotation Search Previous: Rotation Search   Contents   Index
Xplor-NIH 2024-09-13