sf_convert - Workstation Version Manual

Converting structure factors from one format to another

(Created Nov. 12, 2007; last modified Mar. 23, 2012) | (Latest version 1.2.00)
Table of Contents
Introduction     TOP

The sf_convert program helps 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. For example, the users can easily convert the deposited mmCIF files to various other formats.

Changes from previous release     TOP
The following changes have been made to the previous version of sf_convert:

  • Added new options:

    -reformat : This option is to revise the header part of the structure factor files and make it a standard mmCIF format (adding neccessary keys for the mmCIF dictionary, removing non-useable tables and changing reflns to diffrn_reflns, moving any text comments to _diffrn.details). The input file for this option is the mmCIF format

    -audit : This option allows you to update _audit records automatically. It is only related to SF annotation/remediation.

  • Improved to function for mmCIF to mmCIF conversion. All the mmCIF items will strickly follow the pdbx dictionary.

  • Added more error detections.

    • What does sf_convert do?     TOP

  • Convert various formats (mmCIF, CIF, MTZ, CNS, Xplor, HKL2000, Scalepack, Dtrek, TNT, SHELX, SAINT, EPMR, XSCALE, XPREP, XTALVIEW, X-GEN, XENGEN, MULTAN, MAIN, OTHER) to the mmCIF format.

  • Utilize the mmCIF file . It can convert from the mmCIF format to other formats (MTZ, CNS, TNT, SHELX, EPMR, XTALVIEW, HKL2000, Dtrek, XSCALE, MULTAN, MAIN, OTHER).

  • Direct conversion from one format to another without losing information.

  • Allow adding the test flag to the SF for the free R calculation.

  • Allow multiple data set conversion. Multiple data sets can be merged into one mmCIF file.

  • Allow manual labeling of data items for CNS and MTZ format for a safer conversion, if the automatic conversion failed.

  • For details, please read the 'Run the program (Xray data)' below.
    • 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/Unix.

    Installations     TOP

    System Requirements:

  • platforms Intel-Linux/Unix
  • 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/Unix.

    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.
    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. 

    
===================================================================
                      sf_convert v1.20                             
===================================================================
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)
-reformat  reformat header part of sf file (sf_convert -reformat ciffile)
-audit   update the audit record (ADD: -audit date :reason@ )
    If only given '-audit date', add auto-corrected info. (yyyy-mm-dd)
    If given '-audit  date :reason@', add reason (start ':' & end '@')
-valid   (sf_convert -valid sffile) show various SF errors, and correct!
-cif_check  Add this option to check pdbx dictionary. (local use only)
-add_map   get map coefficients (FoFc & 2FoFc) adding this option.

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_FWT                       F    
_refln.pdbx_PHWT                      P    
_refln.pdbx_DELFWT                    F    
_refln.pdbx_DELPHWT                   P    
 
 _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