=======================================================================
pdb_extract is a wwPDB program to extract statistical information from the 
output files produced by various programs and assemble this information 
into one mmCIF file for wwPDB deposition.

In the following instruction, text after '>' sign indicates command to run

====================== 0.  Requirements =============================
1.  This python program has been tested on Linux and Mac platforms
2.  Requires Python3 >= 3.6
3.  Python dependency: The program requires python packages 'mmcif'.
	These packages can be installed by pip or pip3. e.g.
    >pip3 install mmcif

    * mmcif package requires cmake, flex, and bison

====================== 1.  Installation =============================
1.	Uncompress the package:
	>tar -zxvf pdb-extract-v4.2-prod-src.tar.gz

2.	Go to the extracted pdb-extract-prod-py/ folder, run install.sh, e.g.
	>/bin/bash install.sh
	This will install the required maxit package.

3.	(Optional) Dictionary update.
    It is not necessary to run this step, unless you have installed the PDB-Extract 
	previously and only want to synchronize with the latest wwPDB mmCIF dictionary, 
	by running the updateDictionary.sh

====================== 2. Test run  =====================
1.	Simply type
	>pdb_extract.py
	You should see the following prompt:
	
usage: pdb_extract.py [-h] [-NMR | -EM | -ED]
                      (-iPDB PDB-input | -iCIF mmCIF-input) [-iENT TEMPLATE]
                      [-o CIF_OUTPUT] [-e PHASING_METHOD]
                      [-r REFINEMENT [REFINEMENT ...]]
                      [-s SCALING [SCALING ...]]
                      [-i INDEXING_INTEGRATION [INDEXING_INTEGRATION ...]]
                      [-p PHASING [PHASING ...]]
                      [-m MOLECULAR_REPLACEMENT [MOLECULAR_REPLACEMENT ...]]
pdb_extract.py: error: one of the arguments -iPDB -iCIF is required
	
2.	Type
	>pdb_extract.py -h
	will provide detailed instruction on the input parameters and files

3. 	Go to pdb-extract-prod-py/data/test_data, run a simplest example
    >cd data/test_data
	>pdb_extract.py -iPDB 3bn6.pdb
	when it's finished, you should see the pdb_extract_out.cif result file in 
	the folder. Congratulations, your installation and setup are good.
	More examples are included in the next section

====================== 3. Use PDB_extract  =====================
EXAMPLES OF USING PDB_EXTRACT:     

# Example 1. Converts pdb into mmcif format only

	pdb_extract  -iPDB refmac_output.pdb -r REFMAC -o output.cif
 
** Note: 
	'refmac_output.pdb' contains coordinates which was generated by REFMAC
	'output.cif' is author-named output mmCIF file

# Example 2: Extract statistical information from SCALEPACK log file 
	(command should in one line, or extended by '\'):

	pdb_extract	-iPDB refmac_output.pdb	\
			-r REFMAC
        	       	-s SCALEPACK  scalepack.log 	\
	                -o output.cif

** Note: 
	'scalepack.log' contains data reduction statistics generated by SCALEPACK

# Example 3: Add author & structural information to make a complete mmcif 
	file for wwPDB deposition.

	pdb_extract 	-iPDB   refmac_output.pdb  	\
			-f REFMAC
        	       	-s SCALEPACK  scalepack.log 	\
                 	-iENT 		data_template.text 	\
	                -o output.cif
** Note: 
	'data_template.text' contains author and structural information. 

# Example 4: Assemble a complete mmcif file from a MR experiment. 

	pdb_extract 	-iPDB  refmac_output.pdb  	\
			-i HKL-2000
			-r REFMAC
                 	-s XSCALE    xscale.log  		\
                 	-m PHASER   	\
                 	-iENT 	data_template.text 		\
	                -o output.cif
	
# Example 5. Assemble a  mmcif file from cif input file. 
	pdb_extract	-iCIF 	refmac_output.cif \
		 	-r REFMAC   \
                 	-s XSCALE    xscale.log  		\
              		-iENT data_template.text 		\
               		-o  output.cif
** Note: 
	'refmac_output.cif' is cif format structure coordinates file.
			
# Example 6. Assemble an NMR struture.
	pdb_extract	-NMR \
			-iPDB  nmr.pdb \
              		-iENT data_template.text 		\
               		-o  output.cif
			
# Example 7. Assemble an EM struture.
	pdb_extract	-EM \
			-iPDB  em.pdb \
              		-iENT data_template.text 		\
               		-o  output.cif
	
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