• Introduction
• Changes from previous release
• What does sf_convert do?
• Program access
• Installation
• Installation of binary distribution
• Installation of source code distribution
• Run the program (Xray data)

We have developed the program sf_convert to help depositors easily convert various structure factor data formats to the mmCIF format (macromolecular Crystallographic Information File) for deposition. It also has other functions for the user to utilize the deposited SF data.

System Requirements:

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.

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: Users working on Sun platforms 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.

Type sf_convert or sf_convert -h for help.

Usage: 'sf_convert  -i input_format -o output_format -sf data_file'
   or simply type:  'sf_convert  -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)
-cif   followed by cif file (must contain symmetry and cell parameters)
-man   manually type in cells & symmetry (a,b,c,alpha,beta,gamma,p21)
       (separate each item by a comma ',' without space).
       This option can be replaced by -pdb!
-flag  followed by a number for Rfree test set.
       (e.g. '-flag 8' means 8% of reflection selected for free R test)
-sf_type  followed by I or F. (If not given, guessed by program)
-label   followed by label name for CNS & MTZ (see 'sf_convert -h')
-freer   followed by the free test value in CNS & MTZ (see 'sf_convert -h')
-format  guess the format of the SF file (sf_convert -sf sffile -format)
-valid   (sf_convert -valid sffile) show various SF errors, and correct!

Example: convert any supported formats to mmCIF:  
    sf_convert  -o mmcif -sf sf_file_name

Example: convert any supported formats to mtz:(cell in sf file)
    sf_convert  -o MTZ  -sf sf_file 

Example: convert any supported formats to mtz:(cell NOT in sf file)
    sf_convert  -o MTZ  -sf sf_file -pdb pdbfile
    sf_convert  -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;

==============================================================================
Note:  
 1. If MTZ format is involved, newer version of CCP4 must be installed!
 2. -pdb or -cif or -man must be given for conversion to MTZ file,
    if input SF file does not contain symmetry and cells.
 3. If -man is used, separate each item by a comma ',' without space.
 4. If input format is OTHER, you should provide a ASCII file 
    with H, K, L, F, SigmaF separated by space.
 5. CIF and mmCIF are for small molecule and macro-molecule format.
==============================================================================

For CNS/Xplor/MTZ to mmCIF, if automatic conversion failed,
or there are multiple datasets in the SF file, use option '-label'
Each label be separated by a comma ',' and each data set be separated by a ':'.
The default freeR values =1 for CNS, =0 for mtz. If not, specify by freer=?. 

All the data labels follow those of CCP4 as below. 
THE LABELS ARE CASE SENSITIVE!!. 

If the labels involved in the '(' or ')', they must be quoted by ' '

Examples for manual conversion:
 1. convert CNS to mmcif for one data set
    sf_convert -i cns -o mmcif -sf data_file   
    -label FP=? , SIGFP=?, FREE=? , FREER=1 

 2. convert CNS to mmcif for two data sets
    sf_convert -i cns -o mmcif -sf data_file -label 
          FP=? ,SIGFP=?, I=?, SIGI=? , FREE=? : FP=? , SIGFP=?, I=?, SIGI=? 

 3. convert MTZ to mmcif for one data set
    sf_convert -i mtz -o mmcif -sf data_file -label FP=? ,SIGFP=?, FREE=?

 4. convert MTZ to mmcif for two data set
    sf_convert -i mtz -o mmcif -sf data_file -label FP=? ,SIGFP=?,I=?,SIGI=?
              FREE=? : FP=? , SIGFP=?, I=?, SIGI=? 

 5. convert MTZ to mmcif (one data set with anomalous)
    sf_convert -i mtz -o mmcif -sf data_file -label FP=? ,SIGFP=? , 
              FREE=? , 'F(+)=?' ,'SIGF(+)=?','F(-)=?' ,'SIGF(-)=?'

 6. convert MTZ to mmcif (specify free data set to 2)
    sf_convert -i mtz -o mmcif -sf data_file -freer 2 -label FP=? ,SIGFP=? , 
              FREE=? , 'F(+)=?' ,'SIGF(+)=?','F(-)=?' ,'SIGF(-)=?'

Note: The question marks '?' correspond to the labels in the SF file.

      mmCIF token                    type     data label   

 _refln.F_meas_au                     F           FP 
 _refln.F_meas_sigma_au               Q           SIGFP 
 _refln.intensity_meas                J           I     
 _refln.intensity_sigma               Q           SIGI   

 _refln.F_calc                        F           FC     
 _refln.phase_calc                    P           PHIC   
 _refln.phase_meas                    P           PHIB   
 _refln.fom                           W           FOM    
 
 _refln.pdbx_HL_A_iso                 A           HLA   
 _refln.pdbx_HL_B_iso                 A           HLB   
 _refln.pdbx_HL_C_iso                 A           HLC   
 _refln.pdbx_HL_D_iso                 A           HLD   
 
 _refln.pdbx_F_plus                   G           F(+)   
 _refln.pdbx_F_plus_sigma             L           SIGF(+) 
 _refln.pdbx_F_minus                  G           F(-)   
 _refln.pdbx_F_minus_sigma            L           SIGF(-)
 _refln.pdbx_anom_difference          D           DP   
 _refln.pdbx_anom_difference_sigma    Q           SIGDP
 _refln.pdbx_I_plus                   K           I(+)   
 _refln.pdbx_I_plus_sigma             M           SIGI(+)
 _refln.pdbx_I_minus                  K           I(-)   
 _refln.pdbx_I_minus_sigma            M           SIGI(-) 

_refln.status                         I           FREE