===============================================================================

		MANUAL FOR RUNNING THE ACCESSIBILITY PROGRAM OR PREPARING
		          AN INPUT FILE FOR THE VOLUME PROGRAM

	   The program is written in VAX-11 FORTRAN which is based on American
	National Standard FORTRAN-77 (ANSI X3.9-1978). 

	   It was modified for compilation on UNIX by P.J. Fleming in 1995

	   Original and earlier versions produced by: B. Lee, F.M. Richards, 
	T.J. Richmond and J.B. Matthew.

	Copywrite (c) Yale University, March 1983 
		(Please note full copywrite statement in header to the 
		ACCESS source code. )

	Present Version:  1995

	Authors: Mark D. Handschumacher and F.M. Richards

	References: For a general introduction to molecular areas and volumes
 		    and the principles used in calculating these properties
 		    see:

		1)  LEE, B. and RICHARDS, F.M., J. Mol. Biol. 55: 379-400 (1971)
			The Interpretation of Protein Structures: Estimation of
			Static Accessibility

		2)  RICHARDS, F.M. Ann. Rev. Biophys. Bioeng. 6:151-176 (1977)
			Areas, Volumes, Packing and Protein Structure

		3)  RICHARDS, F.M. Methods in Enzymology 115: 440-464 (1985)
			Calculation of Molecular Volumes and Areas for 
			Structures of known Geometry

	   For each atom in a list the program ACCESS is designed to 
	find the surface area in square Angstroms that is accessible to a
	probe sphere of a radius specified by the user. The program requires 
	atom identification data and crystallographic coordinates from an 
	input file. The present version will accept: 1) the output file from 
	the Konnert-Hendrickson refinement program, 2) a file from the 
	Brookhaven Protein Data Bank, or 3) a file prodiced internally during 
	operation of this program. (The program can be easily modified to 
	accept other formats). Atom types are identified through residue and 
	atom names. Van der Waals radii are assigned to each atom on the basis 
	of atom type. The values are listed in the subroutine RADASN. The data 
	statements in that program can easily be changed by the user if a 
	different set of standard values are wanted. Any atoms that cannot be 
	identified by this subroutine are assigned a default radius of 1.80 
	angstroms. The radius of the spherical probe may be assigned any value 
	in the range 0.0 to 9.9. Adjustments to the source program must be 
	made to accomodate values outside of this range. A water molecule is 
	commonly assumed to have a radius of 1.40 Angstroms.

	   The output of the program is a file containing all of the input data
	for each atom, the assigned Van der Waals radii, certain internal flags
	indicating the atoms included in the calculation, the accessible area 
	and the contact area. The accessible area is the area in square 
	Angstroms units of the locus of the center of the probe. The contact 
	area is the area in square angstroms on the Van der Waals surface of 
	an atom that can be contacted by the probe.

	   A companion program, ACCFMT.FOR can be used to create area summaries
	by residue type and sequence, including various totals and averages.
	(This is not yet modified for UNIX).

       [NOTE: The initial part of this program may be used to prepare an output
	file to be used as input for the VOLUME program which is a separate
	unit. Instructions for this purpose appear at the appropriate place.]

	OPERATION:
	----------
	   The user must first have access to a an appropriate input file of 
	atom and coordinate data. The accessibility program is then initiated
	by the command:

	access

	A series of prompts for input data will then appear as follows:
		(You may respond in either upper or lower case).

	1) The program will ask you for the NAME of the OUTPUT
	FILE. This file will contain information identifying the type of atom
	in the list, the coordinates if the atom, the Van der Waals radii used
	in the program during the accessibility calculations, and the contact
	surface area and accessible surface area. Coordinates and Van der Waals
	radii are in angstroms and the surface areas are in square angstroms.

	Prompt:

	PROGRAM: ACCESS
	AUTHORS: MARK HANDSCHUMACHER AND F. M. RICHARDS
	VERSION: MARCH 4, 1983

	PURPOSE: CALCULATION OF THE ACCESSIBILITY OF THE VAN DER WAALS SURFACE
		 OF ATOMS TO A PROBE SPHERE OF THE GIVEN RADIUS SPECIFIED BY 
		 THE USER. FOR FURTHER INFORMATION SEE THE MANUAL.

	-----------------------------------------------------------------------

		WHAT IS THE NAME OF THE OUTPUT FILE;===>--->
	Enter:     (X)n.XXX  

	2) You will be asked for the NUMBER of INPUT FILES. You may have
	different coordinate files that you prefer to keep separate 
	except for the running this program. Currently you can specify a 
	maximum of two input files.

	Prompt:
		HOW MANY COORDINATE FILES DO YOU WANT TO READ :--->--->
	Enter:      1 or 2

	3) You will be asked for the NAME(S) of the INPUT FILE(S). 

	Prompt:
		NAME OF COORDINATE FILE (1(or)2):===>--->
	Enter:     (Y)n.YYY

	4) The absolute minimal data neccessary for the program to 
	function would be a list of three dimensional coordinates x, y, and z.
	In this case the default radius would be assigned to all atoms and you 
	would need some means outside of this program for identifying a given 
	atom by the record number of the input list. The maximimum amount of 
	information potentially used in the current version of the program is:
		a) chain number
		b) sequence number
		c) residue name
		d) atom name
		e) x, y, and z coordinates
		f) preassigned Van der Waals radii
		g) a flag value of 1, 0, or -1
		h) the number of the input file - only useful when more than
						  one input file is declared.

	You will be asked for the FORMAT of the INPUT FILE(S).
	The current formats accepted by this program are Konnert - Hendrikson, 
	BNL PROTEIN DATA BANK, and our own 'Accessibility' format.
	The later is a file that contains locations for all the data mentioned
	in the above list. You do not need to have the complete
	set of data expected by the particular format. It is absolutely 
	neccessary, however, to match all data that you will use to the 
	locations designated by the format chosen. An example would be that
	you have a list of atoms, with the atom name, residue type, sequence
	number and coordinates for each atom. You could write a small program 
	to place the information in the same columns used in Brookhaven format.
	Since you don't have a chain number and you have no need for 
	temperature factors in any calculation, you can leave the columns that
	are designated for that information blank. These two pieces of 
	information are part of the standard Brookhaven format. The temperature
	factor is ignored by this program and while it is possible to 
	use the chain number to flag certain atoms, it is not required 
	information 


	Prompt:
		WHAT IS THE FORMAT OF FILE - 1 ( or 2 )
		AVAILABLE OPTIONS ARE:
					1) "WAH"
					2) "BNL"
					3) "RAD"
	Enter:   selected option below
	------
	WAH
	------

	5) You will be presented with a sample of the expected format 
	based on the type you just entered. If all the data fits in the
	appropriate columns you are ready to continue and should type "NEXT"
	If not, you can type "CHANGE". This will send you back to the begining
	at step 1). If it appears that none of the formats you have tried line
	up with the sample formats you will have to write your own program to
	perform this function. It should be mentioned that the decimal points
	of your file do not have to line up with those of the sample.

	Prompt:
		EXPECTED FORMAT FOR FILE - 1 - IS "WAH"
		EXPECTED FORMAT ON TOP    LINE
		READ     FORMAT ON BOTTOM LINE
-------------------------------------------------------------------------------
1 ARG R143NEH1 23456.890 23456.890 23456.890 2345.7890 234.67890 1
1 THR T  1N     69.45647  49.84090   0.79071  29.31636   0.00000
-------------------------------------------------------------------------------

		TYPE "CHANGE" IF YOU WANT TO CHANGE FORMAT ASSIGNMENTS
		TYPE "NEXT"   IF FORMAT IS OK
		TYPE "STOP"   IF YOU WANT TO EXIT FROM PROGRAM

	Enter:   command selection below
	------
	NEXT
	------

	6) After "NEXT" has been entered at step (5) the program reads
	the input file(s), stores all the data into arrays and assigns the
	Van der Waals radii. The number of atoms that have been read into the 
	arrays will be presented. If any atoms have not been found in the 
	radius assignment subroutine the data associated with that atom will be
	displayed with an annotation as to whether the RESIDUE NAME or ATOM
	NAME was not found. If you are concerned because atoms have been 
	assigned default radii you should determine why the atom names or the 
	residue names were not found and try to correct the problem. This may
	mean editing the subroutine responsible for assigning radii to include
	a new RESIDUE TYPE or ATOM NAME. It may also mean that the format of
	your input file was not aligned with the expected format. Once again,
	if everything is satisfactory, you should enter"NEXT" and this will 
	send you on to step (7).

	Prompt:  

		THE NUMBER OF ATOMS FROM FILE - 1 -    =  6612

		NUMBER OF ATOMS READ INTO ARRAYS       =  6612
  
		NUMBER OF ATOMS ASSIGNED DEFAULT RADII =     0

		TYPE "NEXT" IF YOU WANT TO MOVE TO NEXT BLOCK
		TYPE "STOP" IF YOU WANT TO EXIT FROM THE PROGRAM

	Enter: command selection
	------
	NEXT
	------

	7) You will be presented with three options that deal with
	which atoms are to be included in the accessibility calculation.
	The options "ALLATM" and "PRESET" are explained well enough in the
	prompts. The "SUBSET" option is described in a separate section titled
	"CREATION OF SUBSETS" (see below).
	   To allow flexibility and to reduce and eliminate unneccessary 
	repetition of calcuations a flag system is utilized. Every atom is 
	assigned an integer FLAG VALUE of -1, 0, or 1. When the flag has a 
	value of:
	  # -1, the atom is completely ignored during the accessibility 
		calculation. This would be the same as omitting the 
		particular atom from the input coordinate file.
	  #  0,	the area is to be calculated for this atom. The surrounding 
		consists of all other atoms flagged either "0" or "+1".
	  #  1, the atom is considered part of the protein environment but no
		area calculations will be performed on this atom.
		The program will loop through the atoms until an atom has a
		flag value  0. 
	   The program then finds all those atoms with a value of  0  or 1 that
	fall within the 'touching' distance of the atom whose calculation is 
	being performed. This distance will vary with the Van der Waals radii 
	and probe radius chosen.
	   FLAGS can be used for finding changes in the accessibility of the
 	protein upon the removal of SUBSTRATE(S) or upon deletion of a section
	of the protein. They may also be used if you only have an interest in
	the accessibility of certain RESIDUE types or ATOM types and do not
	wish to waste time doing the calculation for all atoms in the 
	coordinate list. 
	   The option "SUBSET" is designed to handle a few of the most logical
	flag assignments. If you have something that cannot be handled by the
	"SUBSET" flag setting subroutine you can then create your own file
	and set the flags as you wish. The file should then be in the
	"RAD" format and you should then enter "PRESET" in this step. 
	The output of this program is acceptable input for the "RAD" format 
	Van der Waals radii are asssigned and there is a column for the 
	FLAG VALUES described in this section in addition to the FLAG VALUES
	used for the "SUBSET" option.

	Prompt:

		THERE ARE THREE BASIC OPERATIONS THAT CAN BE PERFORMED
  	
       		1) ENTERING "ALLATM" WILL CALCULATE THE ACCESSIBLE
                        	     SURFACE OF ALL ATOMS READ INTO
                 	             THE DATA ARRAYS.
  
       		2) ENTERING "SUBSET" WILL ALLOW YOU TO DEFINE A SUBSET
                            	     OF ATOMS. IF YOU HAVE AN INTEREST
                            	     IN A PARTICULAR GROUP OF ATOMS
                           	     THEY CAN BE SPECIFIED RATHER THAN
                           	     PRODUCING LENGTHY OUTPUT FILES AND
                           	     TAKING UP UNNECCESSARY PROGRAM RUN
                           	     TIME. FURTHER INFORMATION WILL BE
                           	     PROVIDED IF THIS OPTION IS ENTERED.
  
      		3) ENTERING "PRESET" THIS OPTION IS AVAILABLE ONLY IF
         			     THE INPUT FILE(S) WERE OF "RAD"
                       		     FORMAT. THIS WILL TAKE THE FLAG
                       		     VALUES FROM THIS FILE AND CREATE
                       		     THE INDICATED SUBSETS BASED ON THE
                       		     STANDARD FLAG VALUES.

	Enter: command selection below
	------
	ALLATM
	------

	8) After all flags have been set in step (7) the total number
	of flagged atoms will be broken down into the number of atoms with each
	flag. You will also be presented with the current values for the
	PROBE RADIUS and the STEP THICKNESS.

	Prompt:  

 		ALL ATOM FLAGS HAVE BEEN SET FOR THE ACCESSIBILITY RUN
		------------------------------------------------------
     		THE NUMBER OF ATOMS TO BE OMMITED ENTIRELY =      0
     		THE NUMBER OF ATOMS TO BE INCLUDED         =      0
     		THE NUMBER OF ATOMS TO BE CALCULATED       =   6612
      		THE TOTAL NUMBER OF ATOMS                  =   6612


		ENTER "NEXT  " IF THIS IS ACCEPTABLE
		ENTER "RESET " IF YOU WANT TO REDEFINE THE THE FLAGS

	Enter: command selection below
	------
	NEXT
	------

	9) The PROBE RADIUS is the radius of the sphere for which the
	Van der Waals surface of each atom flagged  0 will be tested. It is
	ordinarily assumed that you will be testing for accessibility to water.
	We use a standard radius of 1.40 Angstroms for water so this is the 
	default value. If you want to change the probe radius because you are
	testing accessibility to something other than water or have a different
	value for water this is where to make the change.
	   The ZSTEP value will determine the accuracy of the accessibility
	calculation. The program finds a given atom whose accessibility is to
	be calcuated. Then it finds all the neighboring atoms (rejecting or
	including according to FLAG value), and sequentially slices through
	the effective spheres of the set of atoms along the z axis. The circle 
	of intersection of the atom whose accessibility is being calculated is
	analyzed to see what arc length of this circle is overlaped by the
	intersecting circles of neighboring atoms. The arc distance that 
	remains is then considered to be accessible to the PROBE. The total 
	accessibility is calculated by simply summing the arc
	distance for all the slices through the particular atom of interest
	and multiplying by the distance between the slices. This distance is
	designated by the variable ZSTEP. The smaller the ZSTEP the more slices
	and the greater the accuracy (also the more computer time). Since
	the smallest Van der Waals radii are on the order of 1.10 Angstroms
	and the probe will usually be 1.40 Angstroms the diameter of the 
	smallest effective sphere = 2.0 x (1.40 + 1.10) = 5.0 Angstroms.
	With a ZSTEP of 0.25 this would give 20 slices through the sphere.
	This is acceptable for most of the conditions for which this program 
	will be utilized. We recommend that the ZSTEP value be no less than 
	0.10 and no greater than 0.50 for the reasons of program time and 
	diminished accuracy respectively.

	=======================================================================

	   If the program "VOLUME" is to be entered, the area calculation need
	not be carried out and can be skipped. The output file will have the 
	same format with or without the area calculation, but in one case it
	will contain actual area data and in the other only dummy entries will
	occur in the columns for area. 

	   The output file for the normal area calculation contains data only
	on those atoms whose area was calculated. When the area calculation is 
	skipped, the output file contains all of the atoms read from the input
 	file(s). The flags indicating OMIT, INCLUDE or CALCULATE remain intact.
 	Thus you may specify subsets of atoms to be used in the VOLUME 
	calculation just as you do for the AREA calculation.

	=======================================================================

	Prompt:
		-------------  ------- -------------------------------------
		PROBE   =         1.40 RADIUS OF PROBE SPHERE IN ANGSTROMS.
		ZSTEP   =         0.25 THICKNESS OF CROSSECTIONS THROUGH   
	        	               ATOMS IN ANGSTROMS.      
		SKIP    =          NO  = DO THE AREA CALCULATION
				  YES  = DO NOT CALCULATE AREA, EXIT FOR
					 VOLUME CALCULATION.
				(NOTE: use capital letters for YES and NO)
		-------------  ------- -------------------------------------
  
		ENTER "PROBE " IF YOU WANT TO CHANGE THE PROBE RADIUS
		ENTER "ZTEP  " IF YOU WANT TO CHANGE THE STEP INCREMENT
		ENTER "SKIP  " IF YOU WANT TO CHANGE THE STATUS OF THE 
			       SKIP VARIABLE.
		ENTER "NEXT  " WHEN YOU ARE DONE.


	Enter: command selection below
	------
	NEXT
	------
	NOTE:  The output file from the area calculation may also be used for 
	       program VOLUME.

	10) The area calculations are now being performed. During the
	interim a few interesting bits of information may flash onto 
	the screen. This is to make you feel as though something is
	actually happening. After every 100 atoms are processed a 
	message will appear indicating how many atoms have been 
	calculated. When this run on the SET or SUBSET you have
	defined is finished, this will be indicated and you will then 
	be asked if you want to try another run. This option was implimented 
	to allow the user to calculate the accessibility of a number 
	of different SUBSET assignments within a given MAINSET coordinate
	list.
  
		XMIN =   24.07699     XMAX =   101.2750    DELTAX =   77.19798
		YMIN =  -9.452740     YMAX =   72.36063    DELTAY =   81.81337
		ZMIN =  -5.940830     ZMAX =   62.11293    DELTAZ =   68.05376

		THE MAXIMUM RADIUS ASSIGNED TO AN ATOM =   3.400000    

		COMPLETED  100  ATOMS
		COMPLETED 6600  ATOMS
		TOTAL NUMBER OF ATOMS WHOSE AREA WAS CALCULATED = 6612
  
		FINISHED WITH ACCESS SUBROUTINE

		DO YOU WANT TO TRY ANOTHER CYCLE:("YES" OR "NO")--->

	Enter: command selection below 
	------
	NO
	------
	If you type "YES" you will be returned to STEP (7) otherwise
	its been a pleasure, aurevoir, ciao, and I hope its been worth
	while.
	   This program is the first version of an exportable package and
	while considerable care has been taken to make running as 'user
	friendly' as possible, there may be some problems that haven't
	been debugged.

		   If you have any questions or problems you can contact 
	F. M. RICHARDS at YALE UNIVERSITY Dept of MOLECULAR BIOPHYSICS & 
	BIOCHEMISTRY.   Try (203)-432-5620.

==============================================================================
	ADDITIONAL NOTES:

	1)WAH FORMATTED FILES - The format is the same as the standard output 
	file from KONNERT - HENDRICKSON REFINEMENT. It is assummed that no 
	header information or remarks are included in these files.

	2)BNL FORMATTED FILES - These files usually have a number of lines of 
	header information dealing with references to papers, crystallographic
	parameters, sequence information and other information realted to the
	structure. This information is typed on the screen record by record
	until a line begining with the word "ATOM  " or "HETATM" is found.
	The "ATOM" or "HETATM" line should match the sample BROOKHAVEN format.
	When the program assigns Van der Waals radii to the atoms an 
	intermediate file is first created. This file contains only those lines
	that have the "ATOM  " or "HETATM" keyword in the first six columns
	of that line. The program will then read the intermediate file line
	by line assigning Van der Waals radii according to atom name and 
	residue type.

	3)RAD FORMATTED FILES - These files are the standard output files of 
	this program. It is generally recommended that when you work on a given
	molecular structure that the accessibility calculation first be 
	performed on the entire structure. This way you will have an output 
	file that can be used for a reference file when different subsets are
	calculated. You can also use this standard output file as the input 
	file for future accessibility calculations on any SUBSET specified by
	the flags. Since the Van der Waals radii have already been assigned and
	are included in the file time can be save by skipping over the radius
	assignment section. Also no intermediate file is needed as in the case
	of BROOKHAVEN files. The time expended creating and reading from this
	file is then eliminated. It is also useful as a reference when subsets
	are calculated. You can then compare subset accessibility to the 
	reference (entire molecule) accessibility. A further advantage is that
	if you want to assign special values to atoms or define a subset that
	can not be created easily within the program you can edit this 
	reference file. An example might be that you want to change the Van der
	Waals radii of a few individual atoms of a given atom name and residue
	type while leaving all the rest at the value assigned in the program.
	This would have to be done by editing or creating a file of the "RAD"
	format with all the particular values you desire. When this file in 
	"RAD" FORMAT is read the Van der Waals radius indicated for each atom 
	is accepted without regard to atom name or residue type.  This is 
	particularly useful when only a few atoms have been assigned default 
	radii because the radius asignment program wasn't prepared for the 
	particular residue type or atom name.

	3)CREATION OF SUBSETS - There are many different ways for selecting
	atoms for input into the accessibility calculation routine. A general
	description of the different ways that an atom can be treated by this
	routine is described in the FLAG assignment step. The creation of
	subsets is done in two basic steps:
	1) Defining the flag value to be assigned to the atoms to be 
	indicated in the second step. To do this you chose among four keywords

	1)"OMIT" - assign flag of -1
	2)"INCL" - assign flag of  1
	3)"CALC" - assign flag of  0
	4)"DONE" - no more flag assignments, proceed to next step in program.

	If one of the first three options is entered you will be presented 
	with five different ways to specify what atoms are to be assigned 
	the particular flag.

	1)"FILE" - assign flag if atom came from one of two input files.
		   This is not available if only one input file was read.

	2)"CHAI(N)" - assign flag to an atom if it has the chain number 
		   specified. Many times a molecule will consist of two 
		   separate chains that are identified in the coordinate list.
		   Two monomers in an asymmetric unit or two subunits in a
		   dimer are usually identified separately.

	3)"ZONE" - assign flag based on a range of the sequence number. 
		   Any atom that has a sequence number greater than or 
		   equal to the starting value entered or less than or equal to
		   the ending value specified will be assigned the designated
		   flag. Repeat this operation for as many sequence
		   pairs as required. Entering the same number twice will 
		   result in the flag assignment to the single residue 
		   specified.

	4)"RESI(DUE)" - assign flag to an atom if the residue name is the same 
		   as the one specified. For instance in a protein you may only
		   be interested in calculating the accessibility of histidine
		   residues. If you enter the standard three letter notation 
		   "HIS" all histidines will be assigned the flag value

	5)"ATOM" - assign flag to an atom if the atom name is the same as the
		   one specified. This is the same as the "RESI" 
		   option, except that atom types are identified.

	6)"SERI(AL) - Assign flag based on a range of serial numbers of atoms
		   in the coordinate list. An atom of serial number equal to
		   or greater than the starting value entered or less than or
		   equal to the ending value entered will be assigned the
		   designated flag. Repeat through as many serial number pairs
		   as required. Entering the same number twice will result in
		   the flag assignment to the single atom specified.

 	   If you have more than one input file you will be asked for the file
	number for which flags are to be set.
	   The ORDER OF OPERATION in setting FLAGS is very important. Any 
	operation that is performed will overwrite the previouse flag value
	assigned to an atom. For example if a zone from 1 to 20 is 
	assigned a FLAG of -1 by using the "OMIT" flag and the "ZONE" 
	operation, and then the "CALC" flag is set to a ZONE from 5 to 10.
	The end result would be that the ZONE from 1 to 4 is OMITTED, the ZONE 
	from 5 to 10 is CALCULATED and the ZONE from 11 to 20 is OMITTED. 
	If CALC was first called for the ZONE from 5 to 10 and the "OMIT" was 
	called for ZONE 1 to 10  all the atoms associated with residues 1 to 
	10 would be OMITTED.









===============================================================================
	
	APPENDICES

	A) SHORT FORM INTRODUCTION
	--------------------------

	Summary of Program Startup and Input/Output

	1) NAME OF OUTPUT FILE:		(X)n.XXX
	2) NUMBER OF COORDINATE FILES	1 or 2	
	3) NAME OF COORDINATE FILE(S)	(Y)n.YYY
	4) FORMAT OF INPUT FILE:	"WAH"		Konnert - Hendrickson
					"BNL"		Brookhaven Data Bank
					"RAD"		output of this program
	5) INPUT FILE FORMAT CHECK:	"CHANGE"	go to step (2)
					"NEXT  "	continue to next block
					"STOP  "	exit from program
	6) PROGRAM READS INPUT FILE(S)
	   LOADS INTERNAL ARRAYS AND
	   ASSIGNS VAN DER WAALS RADII
	   SUMMARY OF OPERATION GIVEN:
					"NEXT  "	continue to next block
					"STOP  "	exit from program
	7) PREPARATION OF KEY ARRAY
	   FLAG ASSIGNMENTS TO ATOMS:
					"ALLATM"	calculate all atoms
					"PRESET"	keep existing flags
					"SUBSET"	define subset of atoms
						"OMIT"		omit atom
						"INCL(UDE)"	include atom
						"CALC(ULATE"	calculate atom
						"DONE"		enter when done
							"FILE"
							   file #
							"CHAIN"
							   chain #
							"ZONE"
							   begining sequence #
							   ending sequence #
							"RESI(DUE)"
							   residue name
							   .
							   .
							   enter "END " 
							"ATOM"
							   atom name
							   .
							   .
							   enter "END "
							"SERI(AL)
							   begining serial #
							   ending serial #

	8) SUMMARY OF ATOM FLAGS:
				"RESET "	go back to step (7)
				"NEXT  "	go to next block
	9) REDEFINE PARAMETERS: "PROBE "	change the probe radius
				"ZSTEP "	change the step increment
				"SKIP  "	
					"NO "	do area calculation
					"YES"   skip area calculation and
						make VOLUME output file.
				"NEXT  "	do calculations and create
						output files
	10) MAKE ANOTHER RUN	"YES"		go back to step (7)
				"NO "		stop program and close output
						file.
===============================================================================
	SAMPLE FORMATS OF INPUT FILE(S) AND OUTPUT FILE(S)


	1)KONNERT - HENDRIKSON FORMAT
------------------------------------------------------------------------------
 1 ASN N 24CA   -32.94390  -9.02940  -2.14060  20.00000   0.00000
 1 ASN N 24N    -32.80980  -7.59900  -2.82170  30.00000   0.00000
 1 ASN N 24C    -32.40750  -8.76120  -0.77840  22.00000   0.00000
 1 ASN N 24O    -31.37940  -7.46490  -0.29190  20.00000   0.00000
 1 ASN N 24CB   -32.22870  -9.78930  -3.11360  10.00000   0.00000
 1 ASN N 24CG   -30.53010  -8.94000  -3.21090   6.00000   0.00000
 1 ASN N 24OD1  -29.94900  -8.31420  -4.37850  16.00000   0.00000
 1 ASN N 24ND2  -29.63610  -8.35890  -2.14060  14.00000   0.00000
 1 TYR Y 25CA   -32.31810 -10.05750   1.26490  12.00000   0.00000
 1 TYR Y 25N    -32.85450 -10.01280  -0.09730  16.00000   0.00000
 1 TYR Y 25C    -30.61950  -9.02940   1.45950  18.00000   0.00000
 1 TYR Y 25O    -30.08310  -8.04600   2.33520  14.00000   0.00000
 1 TYR Y 25CB   -32.98860 -11.75610   1.45950  26.00000   0.00000
 1 TYR Y 25CG   -32.13930 -12.02430   2.52980  22.00000   0.00000
 1 TYR Y 25CD1  -32.58630 -11.97960   3.79470  22.00000   0.00000
 1 TYR Y 25CD2  -30.97710 -12.29250   2.23790  30.00000   0.00000
 1 TYR Y 25CE1  -31.87110 -12.38190   4.86500  30.00000   0.00000
 1 TYR Y 25CE2  -29.99370 -12.15840   3.21090  30.00000   0.00000
 1 TYR Y 25CZ   -30.57480 -12.42660   4.57310  30.00000   0.00000
 1 TYR Y 25OH   -29.63610 -12.42660   5.64340  30.00000   0.00000
 1 CYS C 26CA   -28.02690  -8.09070   0.48650   6.00000   0.00000
-------------------------------------------------------------------------------

2)	BROOKHAVEN DATA BANK FORMAT
-------------------------------------------------------------------------------

HEADER    ELECTRON TRANSPORT (HEME PROTEIN)       01-JUL-80   4CYT      4CYT   3
COMPND    CYTOCHROME $C (REDUCED)                                       4CYT   4
SOURCE    ALBACORE TUNA (THUNNUS ALALUNGA) HEART                        4CYT   5
AUTHOR    T.TAKANO                                                      4CYT   6
JRNL        AUTH   T.TAKANO,R.E.DICKERSON                               4CYT   7
JRNL        TITL   REDOX CONFORMATION CHANGES IN REFINED TUNA           4CYT   8
JRNL        TITL 2 CYTOCHROME $C                                        4CYT   9
JRNL        REF    TO BE PUBLISHED                                      4CYT  10
JRNL        REFN                                                   353  4CYT  11
REMARK   1                                                              4CYT  12
REMARK   1 REFERENCE 1                                                  4CYT  13
REMARK   1  AUTH   T.TAKANO,R.E.DICKERSON                               4CYT  14
REMARK   1  TITL   CONFORMATIONAL DIFFERENCES BETWEEN FERRI- AND        4CYT  15
REMARK   1  TITL 2 FERROCYTOCHROME $C                                   4CYT  16
REMARK   1  REF    TO BE PUBLISHED                                      4CYT  17
.
.
.
REMARK   2                                                              4CYT  57
REMARK   2 RESOLUTION. 1.5 ANGSTROMS.                                   4CYT  58
REMARK   3                                                              4CYT  59
REMARK   3 REFINEMENT. SIMULTANEOUS MINIMIZATION OF ENERGY AND          4CYT  60
REMARK   3  R-FACTOR (SEE A.JACK,M.LEVITT, ACTA CRYST., V. A34,         4CYT  61
REMARK   3  P. 931, 1978).                                              4CYT  62
REMARK   4                                                              4CYT  63
REMARK   4 STANDARD PROTEIN DATA BANK PROCEDURE IS TO USE A NULL        4CYT  64
REMARK   4 (BLANK) CHARACTER FOR THE CHAIN INDICATOR IN STRUCTURES      4CYT  65
REMARK   4 COMPRISING ONLY ONE CHAIN.  IN THIS CASE THE CHARACTER R     4CYT  66
REMARK   4 (FOR REDUCED) WAS USED TO CONFORM TO THE DEPOSITOR*S         4CYT  67
REMARK   4 PUBLICATIONS AND TO EMPHASIZE THE RELATIONSHIP BETWEEN THIS  4CYT  68
REMARK   4 STRUCTURE AND THE OXIDIZED FORM WHICH IS AVAILABLE FROM THE  4CYT  69
REMARK   4 PROTEIN DATA BANK AS ENTRY 3CYT.                             4CYT  70
REMARK   5                                                              4CYT  71
REMARK   5 STRUCTURE FACTOR DATA FROM THIS ANALYSIS ARE AVAILABLE FROM  4CYT  72
REMARK   5 THE PROTEIN DATA BANK AS A SEPARATE ENTRY (R4CYTSF).         4CYT  73
REMARK   6                                                              4CYT  74
REMARK   6 THE TRANSFORMATION WHICH WILL PLACE THE COORDINATES OF       4CYT  75
REMARK   6 THIS (REDUCED) MOLECULE INTO BEST ALIGNMENT WITH THOSE OF    4CYT  76
REMARK   6 THE OXIDIZED INNER MOLECULE IN THE SPACE OF THE LATTER IS    4CYT  77
REMARK   6 GIVEN BELOW                                                  4CYT  78
REMARK   6    .2868     .8127    -.5072         47.2662                 4CYT  79
REMARK   6    .5553    -.5724    -.6033         17.5577                 4CYT  80
REMARK   6   -.7806    -.1086    -.6155         16.3160                 4CYT  81
REMARK   7                                                              4CYTA 12
REMARK   7 CORRECTION. INSERT NEW PUBLICATION AS REFERENCE 3 AND        4CYTA 13
REMARK   7  RENUMBER SUCCESSIVE REFERENCES.  04-DEC-80.                 4CYTA 14
SEQRES   1 R  104  ACE GLY ASP VAL ALA LYS GLY LYS LYS THR PHE VAL GLN  4CYT  82
SEQRES   2 R  104  LYS CYS ALA GLN CYS HIS THR VAL GLU ASN GLY GLY LYS  4CYT  83
SEQRES   3 R  104  HIS LYS VAL GLY PRO ASN LEU TRP GLY LEU PHE GLY ARG  4CYT  84
SEQRES   4 R  104  LYS THR GLY GLN ALA GLU GLY TYR SER TYR THR ASP ALA  4CYT  85
SEQRES   5 R  104  ASN LYS SER LYS GLY ILE VAL TRP ASN ASN ASP THR LEU  4CYT  86
SEQRES   6 R  104  MET GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY  4CYT  87
SEQRES   7 R  104  THR LYS MET ILE PHE ALA GLY ILE LYS LYS LYS GLY GLU  4CYT  88
SEQRES   8 R  104  ARG GLN ASP LEU VAL ALA TYR LEU LYS SER ALA THR SER  4CYT  89
HET    HEM  R   1      43     PROTOPORPHYRIN IX CONTAINS FE(II)         4CYT  90
FORMUL   2  HEM    C34 H34 N4 O4 FE1 ++                                 4CYT  91
FORMUL   3  HOH   *54(H2 O1)                                            4CYT  92
HELIX    1  NR ASP R    2  CYS R   14  1                                4CYT  93
HELIX    2 50R THR R   49  LYS R   55  1                                4CYT  94
HELIX    3 60R ASN R   60  GLU R   69  1                                4CYT  95
HELIX    4 70R GLU R   69  ILE R   75  1 INCOMPLETE DUE TO PRO 76       4CYT  96
HELIX    5  CR LYS R   87  THR R  102  1                                4CYT  97
TURN     1 T1R GLU R  21  GLY R  24     TYPE II 3(10)                   4CYT  98
TURN     2 T2R LEU R  32  LEU R  35     TYPE II 3(10)                   4CYT  99
TURN     3 T3R LEU R  35  ARG R  38     TYPE II 3(10)                   4CYT 100
TURN     4 T4R ALA R  43  TYR R  46     TYPE II 3(10)                   4CYT 101
TURN     5 T5R ILE R  75  THR R  78     TYPE II 3(10)                   4CYT 102
CRYST1   37.330   87.100   34.440  90.00  90.00  90.00 P 21 21 2     4  4CYT 103
ORIGX1      1.000000  0.000000  0.000000        0.00000                 4CYT 104
ORIGX2      0.000000  1.000000  0.000000        0.00000                 4CYT 105
ORIGX3      0.000000  0.000000  1.000000        0.00000                 4CYT 106
SCALE1       .026788  0.000000  0.000000        0.00000                 4CYT 107
SCALE2      0.000000   .011481  0.000000        0.00000                 4CYT 108
SCALE3      0.000000  0.000000   .029036        0.00000                 4CYT 109
ATOM      1  C   ACE R   0      -4.908  -1.959  10.948  1.00 26.26      4CYT 110
ATOM      2  O   ACE R   0      -5.892  -2.598  10.550  1.00 23.47      4CYT 111
ATOM      3  CH3 ACE R   0      -4.713   -.521  10.460  1.00 18.24      4CYT 112
.
.
.
ATOM    800  O   SER R 103       1.518  -5.558  28.026  1.00 29.45      4CYT 909
ATOM    801  CB  SER R 103       4.397  -3.919  27.306  1.00 32.25      4CYT 910
ATOM    802  OG  SER R 103       3.511  -3.293  26.400  1.00 24.64      4CYT 911
ATOM    803  OXT SER R 103       2.573  -4.368  29.502  1.00 40.45      4CYT 912
TER     804      SER R 103                                              4CYT 913
HETATM  805 FE   HEM R   1      10.847 -15.938  15.534  1.00  7.22      4CYT 914
HETATM  806  CHA HEM R   1      13.726 -14.615  16.758  1.00 11.33      4CYT 915
HETATM  807  CHB HEM R   1       9.227 -12.941  15.857  1.00 15.40      4CYT 916
.
.
.
CONECT  624  623  625  805                                              4CYT1014
CONECT  805  137  624  810  821                                         4CYT1015
.
.
.
CONECT  846  845                                                        4CYT1057
CONECT  847  845                                                        4CYT1058
MASTER       79    0    1    5    0    5    0    6  900    1   48    8  4CYTA 15
END                                                                     4CYT1060
-------------------------------------------------------------------------------

	3) "RAD" FORMAT INPUT FILE (EQUIVALENT TO FORMAT OF OUPUT FILE)
-------------------------------------------------------------------------------

       ACCESSIBILITY PROGRAM BY MARK HANDSCHUMACHER AND F.M. RICHARDS - 5/4/83

       OUTPUT                 FILE NAME: SAMPLE.ACC                    
       INPUT FILE NUMBER:  1  FILE NAME: SAMPLE.WH                     
         
       ATMTYP = NAME ASSOCIATED WITH PARTICULAR ATOM TYPE
       RCOV   = COVALENT RADIUS OF ATOM TYPE   
       RVDW   = VAN DER WAALS RADIUS OF ATOM TYPE 
         
        ATMTYP           DESCRIPTION         RCOV   RVDW
        ------      ----------------------  ------ ------
        C4          C - TETRAHEDRAL -  0 H    0.77   0.00
        C4H         C - TETRAHEDRAL -  1 H    0.77   2.00
        C4HH        C - TETRAHEDRAL -  2 H    0.77   2.00
        C4HHH       C - TETRAHEDRAL -  3 H    0.77   2.00
        C3          C - TRIGONAL    -  0 H    0.77   1.70
        C3H         C - TRIGONAL    -  1 H    0.77   1.85
        C3HH        C - TRIGONAL    -  2 H    0.77   1.85
        O1          O - CARBONYL    -  0 H    0.66   1.40
        O2H         O - HYDROXYL    -  1 H    0.66   1.60
        O1O2H       O - CARBOXYL    -1/2 H    0.66   1.50
        N4          N - TETRAHEDRAL -  0 H    0.70   0.00
        N4H         N - TETRAHEDRAL -  1 H    0.70   2.00
        N4HH        N - TETRAHEDRAL -  2 H    0.70   2.00
        N4HHH       N - TETRAHEDRAL -  3 H    0.70   2.00
        N3          N - TRIGONAL    -  0 H    0.70   1.50
        N3H         N - TRIGONAL    -  1 H    0.70   1.70
        N3HH        N - TRIGONAL    -  2 H    0.70   1.80
        S2          S - DIVALENT    -  0 H    1.04   1.85
        S2H         S - SULFHYDRYL  -  1 H    1.04   2.00
        P4          P - PENTAVALENT -  0 H    1.10   0.00
        O1N3HH      A - (O OR N)    -         0.68   1.60
        Z2ION       ZN- PLUS 2 ION  -         0.74   0.74
        FE          FE- HEME IRON   -         0.70   1.70
        ------      ----------------------  ------ ------
       NUMBER OF ATOMS READ FROM INPUT FILE(S) =     21
       NUMBER OF ATOMS ASSIGNED DEFAULT RADII  =      0

       SETTYP ALLATM



       X MIN = -32.989 X MAX = -28.027 DELTA X =    4.962
       Y MIN = -12.427 Y MAX =  -7.465 DELTA Y =    4.962
       Z MIN =  -4.378 Z MAX =   5.643 DELTA Z =   10.022


       NUMBER OF ATOMS CALCULATED =    21
       NUMBER OF ATOMS INCLUDED   =     0
       NUMBER OF ATOMS OMMITED    =     0

       MINIMUM EFFECTIVE RADIUS   =     2.80
       MAXIMUM EFFECTIVE RADIUS   =     3.40
       PROBE RADIUS  =    1.400
       STEP INTERVAL =    0.250

       KEY   = PROGRAM FLAG: "OMIT", "INCLUDE", "CALCULATE"
       INDEX = SERIAL NUMBER OF ATOM
       IC    = CHAIN NUMBER
       IF    = FILE NUMBER
       ATM   = ATOM TYPE
       RES   = RESIDUE TYPE
       NUM   = SEQUENCE NUMBER
       X,Y,Z = ATOM COORDINATES
       VDW   = VAN WAALS RADIUS OF ATOM
       COV   = COVALENT RADIUS OF ATOM
       AAREA = SURFACE AREA OF CONTACT IN SQUARE ANGSTROMS 
               OF THE PROBE WITH THE EFFECTIVE SURFACE
       CAREA = SURFACE AREA OF CONTACT IN SQUARE ANGSTROMS 
               OF THE PROBE WITH THE VAN DER WAALS SURFACE
       FRCT  = FRACTIONAL ACCESSIBILITY (NOT IN USE)

KEY INDEX IC IF ATM  RES NUM    X       Y       Z    VDW  COV  AAREA CAREA FRCT
 -- ----- -- -- -------- --- ------- ------- ------- ---- ---- ----- ----- ----
BEGIN
  0     1  1  1 CA  ASN   24 -32.944  -9.029  -2.141 2.00 0.77  18.7   6.5 0.00
  0     2  1  1 N   ASN   24 -32.810  -7.599  -2.822 1.70 0.70  38.2  11.5 0.00
  0     3  1  1 C   ASN   24 -32.408  -8.761  -0.778 1.70 0.77   3.4   1.0 0.00
  0     4  1  1 O   ASN   24 -31.379  -7.465  -0.292 1.40 0.66  15.5   3.9 0.00
  0     5  1  1 CB  ASN   24 -32.229  -9.789  -3.114 2.00 0.77  45.5  15.7 0.00
  0     6  1  1 CG  ASN   24 -30.530  -8.940  -3.211 1.70 0.77   5.6   1.7 0.00
  0     7  1  1 OD1 ASN   24 -29.949  -8.314  -4.378 1.40 0.66  38.3   9.6 0.00
  0     8  1  1 ND2 ASN   24 -29.636  -8.359  -2.141 1.80 0.70  22.0   7.0 0.00
  0     9  1  1 CA  TYR   25 -32.318 -10.057   1.265 2.00 0.77  13.7   4.8 0.00
  0    10  1  1 N   TYR   25 -32.854 -10.013  -0.097 1.70 0.70   5.0   1.5 0.00
  0    11  1  1 C   TYR   25 -30.619  -9.029   1.459 1.70 0.77   0.1   0.0 0.00
  0    12  1  1 O   TYR   25 -30.083  -8.046   2.335 1.40 0.66  26.7   6.7 0.00
  0    13  1  1 CB  TYR   25 -32.989 -11.756   1.459 2.00 0.77  39.4  13.6 0.00
  0    14  1  1 CG  TYR   25 -32.139 -12.024   2.530 1.70 0.77   0.2   0.1 0.00
  0    15  1  1 CD1 TYR   25 -32.586 -11.980   3.795 1.85 0.77  24.3   7.9 0.00
  0    16  1  1 CD2 TYR   25 -30.977 -12.292   2.238 1.85 0.77  21.4   6.9 0.00
  0    17  1  1 CE1 TYR   25 -31.871 -12.382   4.865 1.85 0.77  38.0  12.3 0.00
  0    18  1  1 CE2 TYR   25 -29.994 -12.158   3.211 1.85 0.77  24.9   8.1 0.00
  0    19  1  1 CZ  TYR   25 -30.575 -12.427   4.573 1.70 0.77   3.6   1.1 0.00
  0    20  1  1 OH  TYR   25 -29.636 -12.427   5.643 1.60 0.66  53.5  15.2 0.00
  0    21  1  1 CA  CYS   26 -28.027  -8.091   0.486 2.00 0.77  71.9  24.9 0.00

-------------------------------------------------------------------------------
	TYPICAL OUTPUT OF AN AREA FILE FROM ACCESS (above) PRODUCED
		BY THE PROGRAM ACCFMT

	(This has not been modified for UNIX yet).
-------------------------------------------------------------------------------


 **************************************************

 RUN :     15-JUN-88          14:55:17

 **************************************************

                  PROGRAM ACCFMT
 	FORMATTED OUTPUT BY RESIDUE TYPE
         OF AREA FILE FROM PROGRAM ACCESS

 **************************************************

        INPUT  FILE NAME = 1PCY.DAT                      
        OUTPUT FILE NAME = 1PCY.ARE                      

 **************************************************

 ATOM SEARCH STOPPED AT THE FOLLOWING ENTRY
                U    CU    1
        NO MATCH FOR RESIDUE TYPE 

 **************************************************



 GLY      N    CA     C     O   MAIN  SIDE TOTAL                                  			                             
     6   0.0   0.0   0.0   0.0   0.0   0.0   0.0
    10   1.5  20.1   1.9  13.5  37.0   0.0  37.0
    24   0.0  22.7   0.0  15.6  38.3   0.0  38.3
    34   0.0  16.9   0.0   0.0  16.9   0.0  16.9
    49   1.6  41.2   2.1  27.9  72.8   0.0  72.8
    67   0.0  17.8   2.5  15.0  35.3   0.0  35.3
    78   0.0  23.2   0.0   0.0  23.2   0.0  23.2
    89   4.4  40.6   2.5  25.5  73.0   0.0  73.0
    91   0.0  22.8   0.0   8.1  30.9   0.0  30.9
    94   0.0   5.0   0.9   0.9   6.8   0.0   6.8

  AVE    0.8  21.0   1.0  10.6  33.4   0.0  33.4


 ALA      N    CA     C     O    CB   MAIN  SIDE TOTAL                            			                             
     7   0.0   0.0   0.0   0.0  15.4   0.0  15.4  15.4
    13   0.0   0.0   0.0   0.0  16.7   0.0  16.7  16.7
    33   0.0   0.4   0.0   0.0  12.6   0.4  12.6  13.0
    52   0.0   0.0   0.0   0.0   6.2   0.0   6.2   6.2
    65   0.0   0.0   0.0   0.0  41.0   0.0  41.0  41.0
    73   3.0   0.0   0.0  11.7  24.7  14.7  24.7  39.4
    90   0.6   6.1   0.6   3.1  14.2  10.4  14.2  24.6

  AVE    0.5   0.9   0.1   2.1  18.7   3.6  18.7  22.3

--------------

 PRO      N    CA     C     O    CB    CG    CD   MAIN  SIDE TOTAL                                                
    16   0.0   4.4   0.0   0.0  26.8   5.9   3.5   4.4  36.2  40.6
    23   0.0   0.0   0.4   1.6  14.3   3.2   0.1   2.0  17.6  19.6
    36   0.0   0.0   0.0   0.5   0.6  16.9  36.8   0.5  54.3  54.8
    47   0.0   3.9   0.0   0.0   5.8   0.4   0.0   3.9   6.2  10.1
    86   0.0  14.6   0.5  16.9  32.8   1.0   0.9  32.0  34.7  66.7

  AVE    0.0   4.6   0.2   3.8  16.1   5.5   8.3   8.6  29.8  38.4

---------------

 THR      N    CA     C     O    CB   OG1   CG2   MAIN  SIDE TOTAL                            	                   
    69   2.5   0.0   0.0  16.0   0.4  21.9  20.0  18.5  42.3  60.8
    97   0.0   0.0   0.0   0.0   1.1   5.3  16.1   0.0  22.5  22.5

  AVE    1.3   0.0   0.0   8.0   0.8  13.6  18.1   9.3  32.4  41.7

---------------

 ASP      N    CA     C     O    CB    CG   OD1   OD2   MAIN  SIDE TOTAL                       	                  
     2   0.0   0.0   0.0   0.0   4.7   0.5  29.0  16.6   0.0  50.8  50.8
     8   1.2   3.1   0.4  27.9  28.2   3.7   5.9  22.7  32.6  60.5  93.1
     9   0.8  11.4   2.5  25.7  39.7   2.5   0.0  37.9  40.4  80.1 120.5
    42   0.0   2.5   0.0   0.0   0.0   2.1   4.6  28.7   2.5  35.4  37.9
    44   0.0   5.0   0.0  17.5  14.0   3.8  38.3  33.9  22.5  90.0 112.5
    51   1.8   4.0   0.0   0.0  18.5   3.4  25.6   9.2   5.8  56.7  62.5
    61   0.0   7.1   0.0   0.0  10.0   3.0  28.3  14.8   7.1  56.1  63.2

  AVE    0.5   4.7   0.4  10.2  16.4   2.7  18.8  23.4  15.8  61.4  77.2

----------------

 **************************************************

 GRAND TOTALS:   MAIN CHAIN =   881.9
                 SIDE CHAIN =  3084.0
                        ALL =  3965.9

 **************************************************