2.07 *****************
* GMAP WRITE-UP *
*****************
Gmap (Graphics Map) can be used to create map and skeleton files
for use with external graphics programs. The program is interactive
and prompts for all information. It reads a standard FSFOUR map and
prompts the user to provide range information (fractional coordinate
limits) for the region to be extracted. Any region is valid, including
positive and negative coordinates, and spanning of unit cells. It
prompts for the names of the input and output map files, and the type
of output file desired. Currently one can output one of two map file
types: TOM/O or CHAIN. TOM/O files can be read by the programs TOM
(IRIS version of FRODO) as well as by O. CHAIN files can be read by
the CHAIN program. If a CHAIN file is requested the user will be
asked if CHAIN is to be run on an SGI or ESV workstaion. The standard
deviation for the output map is then given to aid in contour level
selection later in the graphics programs.
The user is then asked if a skeleton should be generated, and if
so, for the base and step level for skeletonisation. Suggested base and
step levels are 1.25*sigma and sigma, respectively. The user is then
prompted for the minimum length to designate main chain skeletons
(typically 10). After skeletonisation, one is prompted for the type
of skeleton output desired. Two types are available: TOM skeleton
files and O skeleton data blocks. In both cases one is prompted for
the output file name. If an O skeleton data block is requested, the
O molecule name (not to exceed 5 characters) is also prompted for.
One can create both TOM and O skeleton output in the same job.
INPUT FILE: Standard FSFOUR map, in the default orientation (NORN=0).
NOTES:
1) Generation of the graphics maps can be highly machine specific.
The current versions of GMAP, if run on an IRIS, SUN, ESV,
IBM R6000, or DEC ALPHA (OSF or OPENVMS) workstation will produce
map files readable by TOM, O or CHAIN on SGI or ESV workstations.
In all cases the map files are directly readable by TOM, O or CHAIN
on the target workstation, but will have to be transferred to
the graphics workstation (by ftp, with type BINARY set) unless the
disks are cross mounted via NFS. At present there is no provision
to create map files for older (non-workstation, eg PS300) graphics
programs.
2) The map files produced are binary, random access "DSN6" like maps,
and should be used directly in the graphics programs without the
need for running "mappage", "vaxmap" or any other formatting
programs.
3) With some versions of TOM, it may be necessary to recompile TOM
on SGI workstations with the f77 flag -old_rl set for the map
files to be used correctly.
4) TOM style skeleton files are binary files which can be used
with the TOM program on an IRIS, even if they are created with
the VAX version of GMAP. If such files are generated on a VAX
they must be transferred to an IRIS (via ftp, with the type
binary flag set) prior to use on the workstation. If GMAP is
run on an IRIS, the TOM style skeleton file can be used directly.
O style skeleton data blocks are ascii files, and can be
created and used interchangeably on all computer systems.
5) Some versions of TOM limit skeleton files to a maximum of 16000
skeleton points. The current program can generate larger files
since O can handle them, but it may be necessary to reduce the
region and/or increase the base until the number of points is
below 16000 if TOM is to be used.
6) The skeletonisation routine is essentially that which originated
in Uppsala, and is simply incorporated in GMAP for convenience.