sf_convert - Workstation Version Manual

Converting structure factors from one format to another

(Created Nov. 12, 2007; last modified Dec. 20, 2007) | (Latest version 1.000)
Table of Contents
Introduction     TOP
Structure factors (SF) are used to validate the solution of crystal structures. In addition to the amplitude and intensity, it is also recommended that the data related to each reflection (such as the phases, FOM, status ...) are deposited to the PDB.

The program sf_convert can easily convert various SF formats to the mmCIF SF format for use in validation and deposition. sf_convert also offers ways to utilize the structure factors and related information deposited in the PDB.

What does sf_convert do?     TOP

sf_convert is used to convert structure factors from one format to another with the simple Unix command option: 

 sf_convert  -i input_format -o output_format -sf data_file

-i     input format: 
       mmCIF, CIF, MTZ, CNS, Xplor, HKL2000, Scalepack, Dtrek, TNT, 
       SHELX, SAINT, EPMR, XSCALE, XPREP, XTALVIEW, X-GEN, XENGEN, 
       MULTAN, MAIN, OTHER.

-o     output format:
       mmCIF, MTZ, CNS, TNT, SHELX, EPMR, XTALVIEW, HKL2000, Dtrek,
       XSCALE, MULTAN, MAIN, OTHER.

-sf    input structure factor file name.
 

type 'sf_convert  -h ' for details!
  • Any one of the input formats can be converted to various other formats.

  • When converting to the mmCIF formats, all the mmCIF data items (as listed below), if they exist, are written to the mmCIF file. 
    mmCIF Data Items 
_refln.crystal_id 
_refln.F_calc  
_refln.F_meas  
_refln.F_meas_au  
_refln.F_meas_sigma  
_refln.F_meas_sigma_au  
_refln.F_squared_calc  
_refln.F_squared_meas  
_refln.F_squared_sigma  
_refln.fom  
_refln.index_h  
_refln.index_k  
_refln.index_l  
_refln.intensity_calc  
_refln.intensity_meas  
_refln.intensity_sigma  
_refln.pdbx_F_minus  
_refln.pdbx_F_minus_sigma  
_refln.pdbx_F_plus  
_refln.pdbx_F_plus_sigma  
_refln.pdbx_HL_A_iso  
_refln.pdbx_HL_B_iso  
_refln.pdbx_HL_C_iso  
_refln.pdbx_HL_D_iso  
_refln.pdbx_I_minus  
_refln.pdbx_I_minus_sigma  
_refln.pdbx_I_plus  
_refln.pdbx_I_plus_sigma  
_refln.phase_calc  
_refln.phase_meas  
_refln.scale_group_code  
_refln.status  
_refln.wavelength_id

  • When converting to various other formats from the mmCIF format, all mmCIF data items are parsed and applied to other formats (like CNS/XPLOR, MTZ ...).

  • The program also generates a testing data (random number) set by giving an option '-flag number'.

    • Program access     TOP
    The source and binary versions of sf_convert can be downloaded from the address http://deposit.pdb.org/software . The source is available under an Open Source license. The binary distributions are available for Intel-Linux, SGI-IRIX, DEC-Alpha, and Sun-Solaris.

    Installations     TOP

    System Requirements:

  • platforms Intel-Linux, SGI-IRIX, DEC-Alpha, and Sun-Solaris
  • C/C++ compilers
    • Installation of binary distribution     TOP
    It is recommended to install the binary distribution, since it is very fast to install. The binary distributions are available for Intel-Linux, SGI-IRIX, DEC-Alpha, and Sun-Solaris.

    Step 1. Uncompress and unbundle the distribution using the following command:

    zcat sf-convert-vX.XXX-XXX.tar.gz | tar -xf -

    The executable file sf_convert is in the directory sf-convert-vX.XXX-XXX/bin.

    Installation of source code distribution     TOP
    		 
    1.  Installation   
 
    Uncompress and unbundle the distribution using the following command:

        zcat sf-convert-vX.XXX-XXX.tar.gz | tar -xf - 

2.  Building the Application

    Position in the sf-convert-vX.XXX-XXX directory and run "make" command:

        cd sf-convert-vX.XXX-XXX 
        make

    The executable file sf_convert is in the sf-convert-vX.XXX-XXX/bin.
    subdirectory.

    NOTE: The users who are working on Sun platform are advised to
    check the compiler flags in etc/make.platform.sunos5 file. Depending on
    the compiler version, users may be required to make modifications to those
    compiler flags.
    Run the program     TOP
    There is a test example included in this distribution. To run the example, from the directory sf-convert-vX.XXX-XXX directory run the "make test" command. The output files are in the sf-convert-vX.XXX-XXX/sf-convert-vX.X/test.

    Type sf_convert or sf_convert -h for help. 

    
Usage: sf_convert  -i input_format -o output_format -sf data_file

-i     input format: 
       mmCIF, CIF, MTZ, CNS, Xplor, HKL2000, Scalepack, Dtrek, TNT, 
       SHELX, SAINT, EPMR, XSCALE, XPREP, XTALVIEW, X-GEN, XENGEN, 
       MULTAN, MAIN, OTHER.

-o     output format:
       mmCIF, MTZ, CNS, TNT, SHELX, EPMR, XTALVIEW, HKL2000, Dtrek,
       XSCALE, MULTAN, MAIN, OTHER.

-sf    input structure factor file name.


Optional options:
-out   followed by output file name (If not given, default by program)
-pdb   followed by PDB file (must contain symmetry and cell parameters)
-man   manually typing in cells & symmetry (a,b,c,alpha,beta,gamma,p21)
-flag  followed by number (e.g. 8 percent of reflection for free R)
-sf_type  followed by I or F. 
-format  guess the format of the SF file 

Note:  
    -pdb or -man is ONLY for conversion to MTZ file (CCP4 must be installed).
    If -pdb is used, PDB file must have symmetry and cells
    If -man is used, separate each item by a comma ',' without space.
    CIF and mmCIF are for small molecule and macro-molecule format

    If input format is OTHER, you should provide a ASCII file 
    with H, K, L, F, SigmaF separated by space.

Example of CNS to mmCIF conversion:  
    sf_convert  -i cns -o mmcif -sf sf_file_name

Example of Scalepack to MTZ conversion:  
    sf_convert  -i Scalepack -o MTZ  -sf sf_file 
    or  
    sf_convert  -i Scalepack -o MTZ  -sf sf_file -man  a,b,c,alpha,beta,gamma,P21

Default data type: F for EPMR, TNT, OTHER, MULTAN, MAIN,XTALVIEW;
                   I for SHELX,HKL2000,DTREK,XSCALE,XPREP,SAINT;