++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
		      	THE LOG_SCRIPT.INP FILE FOR X-RAY
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

			 NOTES AND REMINDER 
This script file is used to enter the names of the crystallographic 
software used for structure determination and the log, PDB, mmCIF or 
text files generated by them.

PLEASE COMPLETE the ENTRY FIELDS (If applicable) according to the type of 
your experiment and use the command 'extract -ext log_script.inp' to obtain 
the completed structure data ready for validation and deposition.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
			GUIDELINES FOR USING THIS FILE
  1. Only strings included between the 'lesser than' and 'greater than' 
     signs (<.....>) will be parsed for evaluation by the program. Therefore, 
     DO NOT write either on the left or right of the 'less than' and 'greater 
     than' signs respectively.

  2. All alphanumeric values or strings that you include in the different 
     categories should be within double-quotes. Blank spaces or carriage 
     returns within a pair of double quotes are ignored by the program. 
     DO NOT use double quotes (") within strings that you enter.
   
  3. Log files used for generating the deposition should be generated from 
     the best (usually the last) trial for each crystallographic software.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

~~~~~~~~~~~~~~~~~~~~~~~~~~~~START INPUT DATA BELOW~~~~~~~~~~~~~~~~~~~~~~~

===============PART 1: Structure Factor for Final Refinement==============
NOTE:
     * 	If the reflection data format is not one of those listed below, 
	please use OTHER for the data format, and provide an ASCII file 
	that has at least five values [H, K, L, I (or F), sigmaI (or sigmaF)] 
	for each reflection and seperate each item by one or more spaces.   
	Include the test flags as the sixth column in the file (if available).

     Reflection data format:
  	CNS|XPLOR|SHELX|TNT|MTZ|HKL|SCALEPACK|DTREK|SAINT|3DSCALE|
        XDS|XSCALE|mmCIF|OTHER

<reflection_data_type = "F" >      [enter I (intensity) or F (amplitude)]
<reflection_data_format = "CNS" >    
<reflection_data_file_name = "input_data/gere-nat.cv " >


==============PART 2: Structure Factors for Protein Phasing================
NOTE:
     *  Enter this category, if you have more than one complete reflection 
	file (e.g. in the case of MAD,SIRAS, MIR). If you want to get 
        statistical information for the data set, please enter the LOG file
        which was generated from the data scaling.

     Reflection data format:
  	HKL|SCALEPACK|DTREK|SAINT|3DSCALE|XDS|XSCALE|

<scale_data_type = "I" >          [enter I (intensity) or F (amplitude)]
<scale_program_name = "HKL" >

For data set 1:
<crystal_number  = "1" >         Crystal ID
<diffract_number = "1" >         Diffraction ID
<scale_data_file_name  = "input_data/w1.sca " >
<scale_log_file_name   = " " >

For data set 2:
<crystal_number  = "1" >
<diffract_number = "2" >
<scale_data_file_name  = "input_data/w2.sca " >
<scale_log_file_name   = " " >

For data set 3:
<crystal_number  = "1" >
<diffract_number = "3" >
<scale_data_file_name  = " input_data/w3.sca" >
<scale_log_file_name   = " " >

--- add more if need ---

==================PART 3: Statistics for Indexing =====================
NOTE: 
     * 	This is only for the reflection data of final structure refinment.

     Software for indexing is one of the following: 
	(HKL|DENZO|DTREK|MOSFLM|XDS)

<data_indexing_software = "HKL" >
<data_indexing_LOG_file_name = " " >
<data_indexing_CIF_file_name = " " >  (if mmCIF format)

==================PART 4: Statistics for Data Scaling=====================
NOTE: 
     * 	The log file included here should have scaling statistics of 
	the file used for the final structure refinement. If multiple data 
	sets were scaled and merged for refinement (as described in Part 1
	above) use the log file generated during merging of the data sets. 

     Software for scaling is one of the following: 
	(HKL|SCALEPACK|DTREK|SAINT|3DSCALE|SCALA|XDS|XSCALE|XENGEN|PROSCALE)

<data_scaling_software = "HKL" >
<data_scaling_LOG_file_name = "input_data/sclepack1.log " >
<data_scaling_CIF_file_name = " " >  (if  mmCIF format)

==============PART 5: Statistics for Molecular Replacement================
NOTE: 
     *	The log files should be from the best trial of MR. If the
        translation and rotation log file are generated seperately, please 
        give both file.
 
     Software is one of the following:
	(CNS|AMORE|MOLREP|EPMR|PHASER)

<mr_software = "PHASER " >
<mr_log_file_LOG_1 = " " >
<mr_log_file_LOG_2 = " " >

=================PART 6: Statistics for Protein Phasing===================
NOTE: 
     *  The phasing method should be one of (SAD|MAD|SIR|SIRAS|MIR|MIRAS).
	The log file should be from the best trial of phasing.
	
     Software is one of the following:
	(CNS|MLPHARE|SOLVE|SHELXS|SHELXD|SNB|BNP|SHARP|PHASES)

<phasing_method = "MAD" >        
<phasing_software = "CNS" >

<phasing_log_file_LOG_1 = "input_data/mad_sdb.dat " >    
<phasing_log_file_PDB_1 = " " >    (if PDB format (heavy atom coordinates))
<phasing_log_file_CIF_1 = " " >    (if mmCIF format)

<phasing_log_file_LOG_2 = "input_data/mad_summary.dat " >
<phasing_log_file_PDB_2 = " " >
<phasing_log_file_CIF_2 = " " >

<phasing_log_file_LOG_2 = "input_data/mad_fp.dat " >
<phasing_log_file_PDB_2 = " " >
<phasing_log_file_CIF_2 = " " >

... add more if needed ...

===============PART 7: Statistics for Density Modification================
NOTE: 
     *  The log file should be from the best trial of density modification.
	
     Software is one of the following:
	(CNS|DM|RESOLVE|SOLOMON|SHELXE)

<dm_software = "CNS " >
<dm_log_file_LOG_1 = "input_data/density_modify.dat " >
<dm_log_file_CIF_1 = " " >         (if mmCIF format)

===============PART 8: Statistics for Structure Refinement================
NOTE: 
     *  The log file should be from the final trial of structure refinement.
        
     Software is one of the following:
	(CNS|REFMAC5|PHENIX|SHELXL|TNT|PROLSQ|NUCLSQ|RESTRAIN)

<refine_software = "CNS" >

<refine_log_file_PDB_1 = " " >  (coordinate file in PDB format)
<refine_log_file_CIF_1 = "input_data/deposit_cns.mmcif  " >  (mmCIF file containing refinement statistics)
<refine_log_file_LOG_1 = " " >



=======================PART 9: Data Template File=========================
NOTE: 
	This file 'data_template.text' was generated by using the
	command 'extract -pdb pdb_file' or 'extract -cif cif_file'. It 
	contains the sequences of all unique polymers (protein or nucleic 
	acid) present in the structure. It also contains other 
	non-electronically captured information. Please complete the 
	data template file before running pdb_extract.

<data_template_file = "input_data/data_template.text" >


==========================PART 10: Output Files============================
NOTE: 
        If you do not give the output file names, the default names
        pdb_extract_sf.mmcif containing structure factors and 
        pdb_extract.mmcif containing coordinates will be assigned 
        by the program


<sf_output= "script_example_1_sf.cif " >            (for structure factors)
<statistics_output= "script_example_1.cif " >    (for coordinates and statistics)

=====================================END==================================