Output files
XLENS produce a code.LPT containing the program results that you can see using an ASCII editor or select the editor button on the toolbar of XLENSG program.
The following files can be also created.
File code.PKS
This file contains the atomic peaks found by the peak search subroutine. The internal structure of the file is:
1. line: TITLE
2. line: number of lines with atomic coordinates.
3. line and following ones: Atomic coordinates.
The required information for each atom (one line per atom) is,
atomic-type x y z multiplicity (free format)
A minus sign before the atomic type causes this atom to be ignored. Alternatively, the number of lines (or atoms) to be read can be reduced by changing the number in the second line.
File code.PKS can be included in file code.CDR for Karle-recycling (KARLE=1) or for Fourier refinement (IFOU=1). Notice that the first line must begin with MODEL.
File code.FAS
This file contains the refined phase values. The internal structure is:
1. line: number of refined phases Format: I8
2. line and following ones: h k l En(H) phi(H) Format: 3I4,F10.2,I5
En is the quasi-normalised E-value and phi the refined phase value.
File code.MAP
This file contains the Fourier map of the NMAP solution. This file can be directly processed by two programs for visual inspection:
a) Program FAN of the FROG-PC series of programs for electron-density and model investigations for proteins [Vernoslova,E.A. & Lunin,V.Yu. Inst. of Mathematical Problems of Biology, Pushchino (Russia). J.Appl. Cryst. (1993), 26, 291-294]. The internal structure of the formatted code.MAP file is:
1. line: ‘$$GA’,’X’,’Y’,’Z’,’ A’
2. line: ’ FOURIER-MAP FROM XLENS’
3. line: A1,B1,C1,ALFA,BETA,GAMMA (= unit cell parameters; Format 6G10.4)
4. line: NXMX,NYMX,NZMX,M1,NXMX-1,M2,NYMX-1,M3,NZMX-1
(NXMX, NYMX, NZMX are the number of grid points in the x, y and z directions respectively; M1 = M2= M3 =0; Format 9I5)
Next lines:
DO IZ=0,NZMX-1
((Z(IX,IY),IX=0,NXMX-1),IY=0,NYMX-1)
END DO
wherein Z is the matrix (0:127,0:127) with the function values; Format 9G10.4.
b) The Program GFourier of the FullProf Suite recognises file code.MAP . It is able to represent graphically the Fourier map.
File code.FST
This is the input file for program FStudio, a program in the FullProf Suite for the graphical representation of atoms in the unit cell. The peaks found by XLENS in the Fourier map are ordered in decreasing height and assigned to atomic types according to the order specified in CONTENTS. In difficult cases it is advisable to check that the assigned atomic types are consistent with the peak heights. The two values written behind the peak coordinates are the peak height (normalised to 1000 for the largest peak) and the peak multiplicity, respectively.
Crystal structure of aerinite, a pyroxene-like mineral used as blue pigment in the romanic frescos of the Catalan Pirenees. The structure was solved with XLENS from synchrotron powder diffraction data.
Copyright © 2010, Jordi Rius & FullProf Suite Team