The PDB_EXTRACT extracts mmCIF data from structure determination applications.  
It eases the tedious process of PDB submission by:

    * Extracting information from ScalePack log files for your PDB deposition.  
    * Extracting information from CCP4 log files such as dm and mlphare.
    * Extracting information from CNS log files.

PDB_EXTRACT runs on Linux machines; There are four executables:

pdb_extract     http://deposit.pdb.org/mmcif/PDB_EXTRACT/pdb-extract.html
pdb_extract_sf  http://deposit.pdb.org/mmcif/PDB_EXTRACT/pdb-extract-sf.html
validation-v8  gives validation letter similar to the one you get from the 
               PDB validation server, ADIT  http://pdb.rutgers.edu/adit/ 
maxit-v8.01-O  just rearranges mmcif file. no documentation


The best way to run the program is to:
1) Make a directory called "extract"
2) Make 3 subdirectores called 
              input_data 
              validation_result
              deposit
3) In the input_data directory put:
              your scalepack file 
              your pdb file 
              your log files form phasing, dm, refinement
4) In the input_data dirctory fill out:
              the  input script .

5) In the "extract" directory copy the following command script and execute it:

#!/bin/sh
# get a mmcif file.
extract -ext input_data/example_1.inp
# use validation-v8 to validate the mmcif file.
validation-v8 -f script_example_1.cif -o 2 -public -exchange
# use maxit-v8.01-O to reorder the mmcif format
maxit-v8.01-O -i script_example_1.cif -o 8 -exchange_in -exchange_out
# move the files to some directory and delete some log files.
mv script_example_1.cif.cif script_example_1_deposit.cif
mv script_example_1.cif deposit/
mv script_example_1_deposit.cif deposit/
mv script_example_1_sf.cif deposit/
mv *.html  *.ps  *.letter  *.wrl  validation_result/
rm -f *log *err procheck* SEQUENCE.DAT *ERR validation.alignment

6) The output mmcif files will be in the "deposit" subdirectory.
7) The validation letter will be in the "validation" subdirectory.
8) For examples see /joule2/programs/pdb-extract/pdb-extract-v1.2/examples