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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. | |
The following changes have been made to the previous version (1.200) of sf_convert:
-rescut : add '-rescut value', cut high resolution to the given value in the SF file SF_4_validate.cif -sigcut : add '-sigcut value', cut I/SigI to the given value in the SF file SF_4_validate.cif -sigcut : add '-diags diagfile', export diagfile for warning/error message.
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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.
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System Requirements: | |
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. | |
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. | |
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 (version: 1.204 : 2014-07-08 ) =================================================================== 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. -rescut (add '-rescut value', cut high resolution to value in SF_4_validate.cif -sigcut (add '-sigcut value', cut I/SigI to value in SF_4_validate.cif -diags (if add '-diags diagfile', export diagfile for warning/error message. 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: If input SF file name is rxxxxsf.org, the xxxx is used as pdbid. ============================================================================== 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 ':'. Default freeR set (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 (with free set as 1) 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 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 |