• Introduction
• 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
-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.

Note: If the input option '-i input_format' is ommited, the program will
guess the input format for conversion. The simple command line is 
'sf_convert   -o output_format -sf data_file'. 


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 type in cells & symmetry (a,b,c,alpha,beta,gamma,p21)
       (separate each item by a comma ',' without space).
-flag  followed by a number for Rfree test.
       (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')
-format  guess the format of the SF file (sf_convert -sf sffile -format)

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 HKL -o MTZ  -sf sf_file 
    sf_convert  -i HKL -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, CCP4 must be installed!
 2. -pdb 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 can not be 
performed, or there are multiple datasets in the SF file, the option '-label'
should be provided!
Each label is separated by a comma ',' and each data set is separated by a ':'

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:
 1. convert CNS to mmcif for one data set (if auto conversion failed)
    sf_convert -i cns -o mmcif -sf data_file -label FP=? , SIGFP=?, FREE=?

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

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