no subject (file transmission)
public at mrc-lmb.cam.ac.uk
public at mrc-lmb.cam.ac.uk
Mon Dec 4 10:25:39 PST 2000
ANNOUNCEMENT OF NEW RELEASE OF MRC IMAGE PROCESSING SUBROUTINES
---------------------------------------------------------------
imsubs2000 and plot2k
---------------------
In response to concerns expressed by some users, particularly Steve
Fuller and Helen Saibil, we have updated the basic MRC image format
handling routines to make the file headers completely compatible with
the current format and content of the CCP4 x-ray crystallographic system.
The details of changes to the header in the imsubs2000 system are described
below. We have also taken the opportunity to replace the relatively small
amount of embedded line graphics, which on the old system used PLOT82
subroutines, intermediate .plt files and the program laserplot to turn
.plt files into postscript. This has been replaced by a set of subroutines
(plot2k) which generate postscript files directly. The new system will read
image and map files with either old-style (provided they are architecture
compatible with the system on which they are being processed) or new-style
file headers, but will only write new-style headers. Hence, once a user decides to change to the new system, all programs which
access MRC format files must be 2000-compatible. Although old-style
machine-compatible files may still be read by all the programs, those programs
which write into the header (e.g. autocorrlk, backautok) may fail. In this
case, messages will be displayed to help the user to re-format their maps.
Programs are available within the package for converting files between machine
architectures (byte_swap_map) and from old to new style maps (image_convert).
The new header contains a "machine stamp" to identify the machine on which the
file was written and appropriate manipulations, transparent to the user, are
made to unscramble the data when reading a file generated on a foreign machine.
You may also find a few bugs have been removed from some of the programs in
the process of the update.
There is no pressure for users to change but in future only new style programs
(imsubs2000/plot2k) will be maintained and developed here. The old-style
programs will remain available on request for some time but new users
should install the new programs. This release should be regarded as a
"beta test", though most of the programs have been tested fairly extensively
at LMB, so we wish to hear about any problems that might arise (e-mails to
Jude Smith: jms at mrc-lmb.cam.ac.uk).
The new MRC image processing system is available via ftp; please contact
Jude at jms at mrc-lmb.cam.ac.uk who will then mail you the details. Your name
and email address will then be added to the list of outside users in the file
outside_users.doc in /image2000/doc. This may be useful to you if you
ever need to find someone near you who uses the programs.
Tony Crowther, Richard Henderson and Jude Smith 1Dec2000
***********************************************************************
Brief details of changes to header from imsubs to imsubs2000:
Positions 50-52 contain the origin (x,y,z) [the old style origin (x,y) was in
positions 54-55].
Position 53 contains the flag MAP to identify file type
Position 54 contains machine stamp computed by CCP4 subroutine
Position 55 contains the RMS value of density in the map
As a result of these changes, the amount of "extra" space available in the
header has been reduced from locations 25-53 to locations 25-49.
In practice the changes are relatively minor and new-style file headers can
be read by the old programs as long as they do not need to use the phase
origin information, and as long as they were written on the same machine.
However, this is definitely not recommended.
The main change we have made in existing programs using imsubs is to change
calls to IALORG and IRTORG to include 3 not 2 origin parameters. There are
a few new imsubs routines available. Much more extensive changes have been
made to programs which included calls to PLOT82 routines, as the structure
of plot2k is rather different (see plot2k documentation in image2000/doc)
Again, the change as far as users are concerned is minor. Laserplot commands
in old scripts are simply deleted since output postscript files will be sent
directly to be printed.
Full specification of the new file header in imsubs2000:
************************************************************************
* *
* Map/Image Header Format for imsubs2000 *
* *
* Length = 1024 bytes, organized as 56 LONG words followed *
* by space for 10 80 byte text labels. *
* *
* 1 NX number of columns (fastest changing in map) *
* 2 NY number of rows *
* 3 NZ number of sections (slowest changing in map) *
* 4 MODE data type : *
* 0 image : signed 8-bit bytes range -128 *
* to 127 *
* 1 image : 16-bit halfwords *
* 2 image : 32-bit reals *
* 3 transform : complex 16-bit integers *
* 4 transform : complex 32-bit reals *
* 5 NXSTART number of first column in map (Default = 0) *
* 6 NYSTART number of first row in map " *
* 7 NZSTART number of first section in map " *
* 8 MX number of intervals along X *
* 9 MY number of intervals along Y *
* 10 MZ number of intervals along Z *
* 11-13 CELLA cell dimensions in angstroms *
* 14-16 CELLB cell angles in degrees *
* 17 MAPC axis corresp to cols (1,2,3 for X,Y,Z) *
* 18 MAPR axis corresp to rows (1,2,3 for X,Y,Z) *
* 19 MAPS axis corresp to sections (1,2,3 for X,Y,Z) *
* 20 DMIN minimum density value *
* 21 DMAX maximum density value *
* 22 DMEAN mean density value *
* 23 ISPG space group number 0 or 1 (default=0) *
* 24 NSYMBT number of bytes used for symmetry data (0 or 80)*
* 25-49 EXTRA extra space used for anything - 0 by default *
* 50-52 ORIGIN origin in X,Y,Z used for transforms *
* 53 MAP character string 'MAP ' to identify file type *
* 54 MACHST machine stamp *
* 55 RMS rms deviation of map from mean density *
* 56 NLABL number of labels being used *
* 57-256 LABEL(20,10) 10 80-character text labels *
* *
* Symmetry records follow - if any - stored as text as in *
* International Tables, operators separated by * and grouped into *
* 'lines' of 80 characters (ie. symmetry operators do not cross *
* the ends of the 80-character 'lines' and the 'lines' do not *
* terminate in a *). *
* *
* Data records follow. *
* *
* *
************************************************************************
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