Programs FANTOM and EXDIS have been written almost exclusively in standard FORTRAN-77. All source files are grouped in the files *.f. Subroutines which call machine dependent system routines, are FMTIME, FMDATE, NAGMIN, NAGRP and DUMPIT. These subroutines are collected in unix.f for SUN and SGI UNIX systems, in aix.f for IBM AIX systems, in cray.f for the CRAY Y-MP, and in nec.f for the NEC SX-3. In addition, an UNIX library routine GETENV(3F) is called from fantom.f to get the value of an environmental variable. All modern FORTRAN compilers should be able to handle this call. For further details about the source code files see the file README.1st in the subdirectory source where source, include and make files are located.

To compile and link FANTOM and EXDIS, edit Makefile and modify compilation options specific for your machine. Save Makefile and execute "make" command in the UNIX shell. This produces two executable files. Move these files to one of the directories in your executable path. Important: after compilation an environmental variable FANTOM_DIR should be set. This variable indicates the main FANTOM directory. For example, if the FANTOM package has been expanded into /usr/local/lib/DIST_FANTOM directory, then before running the program C shell (tcsh and csh) users should type:

and Bourne shell (sh) users, if any, should type the following sequence of commands:

These commands can be for convenience included in the shell initialization files or, alternatively, in a shell script starting FANTOM. The following files are, or may be, used by the program by default:

AMINO ACID LIBRARY FILE $FANTOM_DIR/library/dpec.lib

TORSION ANGLE SYMMETRY NUMBERS $FANTOM_DIR/library/sym.lib

VAN DER WAALS RADII AND ATOMIC SOLVATION PARAMETERS $FANTOM_DIR/library/total.asp

ON-LINE HELP FILE $FANTOM_DIR/library/fantom.hlp

USER’S CPU OVERVIEW FILE ./user.cpu

With the default parameters defined in the INCLUDE files *.incl FANTOM demands a memory of about 21 MB on SGI Indigo² and 45 MB on Cray J90. Single precision on a 32-bit machine may worsen the convergence of minimizations. Therefore two versions of the include file precis.incl are included (precis.single, precis.double). Copy the file of your choice to precis.incl to obtain a single or double precision version of FANTOM.

The most important parameters that limit the size of input or output data are defined in the include files as follows:

size of protein

MAXRES residues 250

MAXANG dihedral angles 2,000

MAXATM atoms 4,500

MAXVEC pairs of interacting atoms 1,000,000

MAXBRA branches in the polypeptide tree 2

MAXLOP number of variable loops 5

MAXLNK number of additional covalent bonds 5

MAXTYP atom types 16

accessible surf.

MOV atoms intersecting any other atom 150

MAXARC accessible arcs on any atom (hydro.f) 40

MAXC number of cells in cubic lattice 8,000

MAXINC number of atoms per cube 200

MAXSURF length of the nonempty ube list 400

size of residues

MRATM atoms per residue 50

MRANG dihedral angles per residue 15

MAXVAL connectivities of each atom 4

constraints

MAXRE upper and lower distance limits 10*MAXATM

MAXCC fixed distance limits for cyclization 20

MAXFX fixed distance limits MAXCC*(MAXLOP+1)

MAXDH dihedral angle constraints 460

protocol

MAXSUM summaries 9

library

MAXLIN lines in amino acid library 3,000

MAXGRP groups in amino acid library 100

comparison

MXCONF conformations checked for identity 6,000

MXSAM identical conformations 1,000

MXSYM amino acids in symmetry library 24

NXRES residues (for comparison only) 220

NRANG angles per residue (for comparison only) 15

Every time a user starts FANTOM, the date and time are written to a user CPU overview file. No user CPU overview file will be created if the logical variable CPULOG in the block data file ecblk.f is set to .FALSE. (default in Version 4.0 and later).