Uppsala Software News @ 960311
                ******************************


* XPLO2D Version 1.4
********
  Finally: documentation for this program has been written !
  Also: for the auto-dictionary option, MASS statements in
topology files are now correct (modulo hydrogens !) for all
elements of the periodic table (up to ~100), provided that
the first two characters of the atom name represent the
element type (i.e., the good old PDB convention).
  In addition, the program now knows the NONBonded (Lennard-
Jones) parameters for 34 elements.
  The OMAC/het_dicts script has been updated so that it works
again with the latest version of XPLO2D.


* MAPMAN (not the XDL-version) Version 4.4
********
  Handling of Mappage "prod" and "plus" improved (they are now
recalculated whenever the dynamic range of the map changes;
more informative error message when Prod is out of range).
  New VAlue_at command to list electron-density values at
a specific grid point or for a range of grid points.
  New CHange_value command to reset the density for all points
whose density lies within a certain range to a new value.  This
can be used, for instance, if you want to contour a map extracted
with (M)AVE at negative levels.  Since the areas outside the mask
will have a density of 0.0, you may want to reset those to a value
which is smaller than the minimum density inside the mask.


* DATAMAN (not the XDL-version) Version 3.7.3
*********
  Some minor bug fixes (reading an empty file generates an error;
no more attempts to calculate statistics for zero observations,
such as in the TWin and GEmini commands).


* XPAND Version 1.1
*******
  Changed Water_scrutiniser command such that the output can be
written to a log file instead of the screen, and (optionally)
the waters which look okay can be written to a new PDB file
(handy if you use XPAND to filter potential new waters picked
from a difference map).


* MAPFIX Version 1.2
********
  The program is now sensitive to the CCP4 environment variable
CLIBD to derive the local name of the symm-op file.
  Bug fixed which limited maximum size of map sections to 60,000.


* MOLEMAN Version 7.1.2
*********
  New DUMP command to quickly write a PDB file with no questions
asked (other than the filename; all other settings will be the
same as the last time you used the WRITe command).
  New definition of core areas in the RAMAchandran plot (only for
PostScript output !):
"Outliers are defined as residues lying outside the core areas in which 98% of
 all non-Gly residues were found to lie in a sample of 403 PDB structures of
 <= 95% homologous structures (Hobohm & Sander list) at 2.0 A resolution or
 better (GJK, October 1995, unpublished results; data for 74,893 residues).
 Outliers are shown as asterisks in the plot; core areas are coloured grey."
Note that this definition is rather merciless for your average low-
resolution model !  But at least it has a well-defined meaning.


* ODBMAN Version 1.2.1
********
  Minor bug fix for the HIstogram command.  Reduced array dimensioning
by 75% so that the program will run on smaller machines.


* FAQ
*****
  Finally processed a lot of old O-info postings.


* OMAC
******
- qalpha.omac and qbeta.omac - at last, two macros to generate "ideal"
  poly-Ala helices and strands on the fly !  Requires MOLEMAN plus a
  set of bones (or atoms) so you can define the start and end points.
- the "makemap.csh" script to produce CCP4 maps from a model plus MTZ file
  has been changed such that:
  (a) you can now select the coefficients of the third map yourself
      (e.g., 3Fo-2Fc, Fo, Fc, 100Fo-99Fc, or whatever)
  (b) it automatically generates an O macro to draw the maps ;-)
- gsp_forms.rtf: now available in RTF format so you can read them into
  your favourite text processor and print them in a format suitable
  for local printers/paper sizes
- combine_ps: a C-shell script from Kay Diederichs which combines N
  PostScript files (e.g., from O2D) into one file (for use with "psnup")
- other files that have been changed/made cleverer in the past couple of
  months: pickwater.csh, rebuild_menu.odb, denzan, newo.omac, het_dicts,
  and auto_amore.com (and, of course, software.faq)


* LIBERTIES
***********
  Those of you who want to use the three models X, Y and Z from the
Liberties paper (GJ Kleywegt & TA Jones, "Where freedom is given,
liberties are taken", Structure 3: 535-540 (1995)), e.g. for teaching
purposes, can download them from rigel.bmc.uu.se (anonymous ftp), in
directory pub/structures.  The models are:
- X = crabp2 traced backwards; refined to 3.0 A; R 0.214, Rfree 0.617
- Y = crabp1 as published (PDB ID: 1CBR); R 0.251, Rfree 0.320
- Z = crabp1 ignoring 8-6 A data, NCS etc.; R 0.169, Rfree 0.323


* HINT
******
  Editing a PostScript file (e.g., to add labels or special characters)
is usually a pain-in-the-derriere, trial-and-error process.  I haven't
found any Macintosh program that will allow you to import PostScript
*and* edit it on an object basis.  However, there is a utility program
called EPStoPICT which will convert (encapsulated or normal) PostScript
into vector or raster PICT files.  This means that you can add text,
remove extraneous bits of the picture (e.g., unwanted density from an
OPLOT file ;-), add labels, arrows etc. with MacDraw, Claris Works
or any other DRAW/PAINT program on your Mac.  Even the text labels
are recognised as such and can be edited.  The only drawback is that
there is no way back (there probably is, but I don't know about it
yet), i.e. you can't convert the PICT back to vector PostScript. 
  To find the site nearest you that carries the program, goto
http://www.shareware.com/, select the Search option, and look for
"epstopict".  This will give you a list of ftp sites ranked
according to the expected reliability of the transfer.  The program costs
US$ 25 per machine, or 40 if you want a disk with the latest version.
  There is a cheaper way to do all this: open your PostScript file
in MacGhostScript (free), and save it as a PICT file.  Import this into
your drawing program, ungroup the picture and start editing.  Drawbacks:
slower, more work and font information does not appear to be preserved
(which means re-doing your labels).  But it's free (important for
Dutchmen & Scotchmen).


* WEBBING
*********
  With all these amazing Web search engines, it is now possible
to look for answers to your O questions in both the FAQ, old
O-info postings plus anything else on the Web on the entire
planet.  Simply use a standard search engine and type your
keyword(s), press Submit and voila.  For example, looking for
"pep_flip" on DECs Alta Vista gives 49 hits (@ 960305) within two
seconds, including questions from the FAQ in Aarhus, the archive
of old O-info messages, some of our pre-prints in Uppsala, program
manuals etc.  Great stuff (and DEC provides the computing power
free of charge) !  Alta Vista can be found at:
     http://altavista.digital.com/
(in my experience this one gives the largest number of hits); they
also have a snippet of HTML code to paste into your own HTML page
so you can do rapid searches from there.


--cd