4.62. SHELIN: Enter SHELX file
Author: Syd Hall, Crystallography Centre, University of Western Australia, Nedlands 6907, Australia
SHELIN reads a standard Shelx (Sheldrick, 1986) input file and extracts those commands and data required to perform the standard data initialization calculations STARTX, ADDREF and ADDATM. Any other XTAL calculations using the archive bdf generated by these routines may directly follow the SHELIN input. As well as the archive bdf, SHELIN generates a line file for subsequent applications.
4.62.1. Recent Modifications
SHELIN originally worked by including the SHELX.ins instruction file inline within the Xtal .dat input stream. To aid and facilitate data exchange, this behaviour is now activated only by use of the old command line option. The new default behaviour is to read external .ins and .hkl files, although thereafter the behaviour is largely as documented below. Any SHELX dummy Q atom sites are now written as peaks to a compid.pek file. These can then be viewed within the Xtal molecular graphics program PIG.
4.62.2. Shelx Commands And Data
All Shelx commands and data may be input into SHELIN but only the following commands are used to generate XTAL input data. Shelx commands and data not listed below will be ignored.
TITL (optional; the TITL header may be omitted) CELL LATT (optional if lattice is primitive noncentrosymmetric) SYMM (any number; SYMM X,Y,Z is not entered) SFAC (any number; but no Cromer-Mann coefficients allowed) UNIT (any number) |
The lines CELL to UNIT must be entered first, and in this order. They are used to initialize the STARTX calculation.
The HKLF line is used to initialize the ADDREF calculation. If code is blank the format of the reflection data is assumed to be'3I4,2F8.2'. If code is nonblank the format is assumed to be '3I3,F7.2,F6.2'. The reflection data input sequence is terminated by a reflection with h=k=l=0 or h=k=l=99.
The FVAR line is used to initialize the ADDATM calculation. The parameter K is the Frel scale factor. Both formats of the standard atom lines may be entered in any order (either with an isotropic U (one line) or with anisotropic U's(two lines)). If anisotropic U's are entered, it is assumed that U11 and U22 are on the first line followed by an '='. An END line must follow the last atom line, and this END must be the last line in the Shelx sequence.
The use of the END line in a Shelx sequence has a special meaning for SHELIN. It is assumed to close the SHELIN sequence. Be careful to remove any superfluous END lines from the SHELIN file.
4.62.3. Function
SHELIN is a relatively special program within the XTAL System in that it both creates the input data for STARTX (and optionally ADDREF and/or ADDATM), and then directly initiates the execution of these routines.
The first stage of SHELIN is to read the SHELX commands and data from the standard line file and converts these into the equivalent XTAL control and data lines. These are output to the formatted file shx.Only the selected SHELX commands and data lines described above are interpreted.
The second stage of SHELIN is to redirect the line input stream from the file shx. This means that after the END line terminating the SHELIN lines, the nucleus starts to input the generated XTAL lines from shx and these are used to control the XTAL calculations STARTX, ADDREF and ADDATM.
The second last line in the shx file is the command 'reset inp <ioinp:>'. This command causes the line input stream to be returned to normal line input, so that additional XTAL commands may be executed. It should also be noted that the lines in shx may also be used in subsequent XTAL applications without having to use the SHELIN sequence.
4.62.4. File Assignments
A SHELIN run sequence writes and reads archive bdf's
Reads a SHELX ins input file
Optionally reads a SHELX hkl reflection file
Writes XTAL input lines to the line file shx
Optionally writes dummy sites to the Xtal binary pek file
4.62.5. Example
SHELIN TITL IK 9/4 PHOTOREAKTIVES BUTENOLID RG PBCN 8/88 CELL 1.54179 15.180 7.413 22.607 90 90 90 SYMM .5-X,.5 -Y, .5+Z SYMM -X, Y, .5-Z SYMM .5+X, .5-Y, -Z SFAC C H O UNIT 128 128 16 BOND 1 FMAP 2 L.S. 4 HKLF -3 2 0 0 24.99 -7.66 1 4 0 0 20.51 -6.52 1 6 0 0 23.06 3.47 1 8 0 0 19.46 2.48 1 10 0 0 15.21 1.70 1 ....... ....... 6 8 0 -1.95 -0.50 1 8 8 0 2.28 0.45 1 99 99 99 0.00 0.00 0 FVAR 0.81554 O1 3 0.13876 0.08798 0.50278 11.00000 0.04336 0.06483 = 0.04712 -0.00264 0.00342 -0.00309 O2 3 0.13828 0.14520 0.60009 11.00000 0.05341 0.09107 = 0.05675 -0.01351 0.01645 -0.00162 C1 1 0.18085 0.12821 0.55575 11.00000 0.05144 0.04701 = 0.05208 -0.00446 0.00460 -0.00039 ........ ........ H16A 2 0.44180 0.18390 0.52360 11.00000 0.05000 H16B 2 0.45100 0.33370 0.57250 11.00000 0.05000 END PIG |
The output line file SHX for the above example follows:
STARTX CELL 15.18000 7.41300 22.60700 90.00000 90.00000 90.0000 LATICE C P SYMTRY X,Y,Z SYMTRY 1/2-X,1/2-Y,1/2+Z SYMTRY -X,Y,1/2-Z SYMTRY 1/2+X,1/2-Y,-Z CELCON C 128 CELCON H 128 CELCON O 16 DATDEF PARENT EXPER 1 1.54179 ADDREF HKLIN HKL FREL SIGF RCOD HKL 2 0 0 24.990 7.660 2 HKL 4 0 0 20.510 6.520 2 HKL 6 0 0 23.060 3.470 1 HKL 8 0 0 19.460 2.480 1 HKL 10 0 0 15.210 1.700 1 ..... ..... HKL 6 8 0 1.950 .500 2 HKL 8 8 0 2.280 .450 1 ADDATM SCALE 1 .81554 ATOM O1 .13876 .08798 .50278 3.42357 1.00000 UIJ O1 .04336 .06483 .04712 -.00309 .00342 -.00264 ATOM O2 .13828 .14520 .60009 4.21708 1.00000 UIJ O2 .05341 .09107 .05675 -.00162 .01645 -.01351 ATOM C1 .18085 .12821 .55575 4.06154 1.00000 UIJ C1 .05144 .04701 .05208 -.00039 .00460 -.00446 ....... ....... ATOM H16A .44180 .18390 .52360 3.94784 1.00000 ATOM H16B .45100 .33370 .57250 3.94784 1.00000 RESET INP 5 FINISH |