Uppsala Software News @ 960712
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* CT2HET Version 0.3
********
You may now use the wildcard "**" (or " *") to mean *any* type of
atom in your searches.
  In addition to atoms and bonds, you may now also define dihedrals
and impropers in order to narrow down the search.  These can be used
to find flat rings/groups, specific cis or trans forms, specific chiral
atoms, etc.  See the manual for examples.


* XPLO2D Version 1.5
********
Several small changes to the AUTO option (generation of X-PLOR
dictionaries):
- fixed dihedrals which are flat (0 or 180 degrees) are really added to
  the topology file (i.e., not commented out);
- the force constants for bond lengths, bond angles, fixed dihedrals and
  impropers are now entered in one go (so that the OMAC/het_dicts doesn't
  crash if there are no dihedrals or impropers);
- separate distance cut-offs to determine if two atoms are bonded, one if
  both atoms are light (H..Ne), the other if either or both are heavy
  (Na..); this produces better topology files if there are heavy atoms
  in your hetero-compound.


* MOLEMAN Version 7.2.3
*********
When generating O dictionary files, the program now prompts for two
separate distance cut-offs to determine if two atoms are bonded, one if
both atoms are light (H..Ne), the other if either or both are heavy (Na..).


* DICTIONARIES
**************
URL http://onyx.bmc.uu.se/~gerard/manuals/gerard_manuals.html now
contains some useful links for those who are looking for O and/or
X-PLOR dictionaries for hetero-compounds.  As mentioned earlier,
the O dictionaries now contain support for the Chemscape Chime
plug-in for Netscape (really cute !).  The O dictionaries have been
updated today using the new version of MOLEMAN, which should have
produced better connectivity entries for compounds containing
heavy atoms (e.g., F3S).


* OMAC
******
New additions:
- test_o_colours_black.ps -> PostScript file showing the pre-defined
  O colours against a black background;
- macsplit.csh -> C-shell script to take an O macro created by SPASM
  and split it into separate macros, one for each "hit" found in the
  PDB.  The enthusiastic C-shell afficionado may want to change this
  script so it works with DEJAVU macros as well;
- daily -> simple C-shell script which backs up all files that have
  changed in the past N days to another disk.  After having experienced
  two disk crashes, I wrote this & use it once a day in between real
  tape backups.
The het_dicts script has been changed to accomodate changes to the
input of MOLEMAN and XPLO2D (see above).


* FAQ
*****
Finally started processing my 10-month back-log.  The current version
contains 448 questions and answers.


* MOLEMAN2 Version 1.0.1
**********
Several bug fixes (previously available via rigel.bmc.uu.se).


* MAPMAN Version 4.6.1
********
Masks are now written in OMASK format.  This is the format that is
written by O, and in the future X-PLOR will also read and write
masks in this format.  You can still read masks in any of the old
format types; to write out masks using an old format type, use
the WRite command in MAMA.
  Note for *PROGRAMMERS* -> there is a new set of Fortran subroutines
on the server (pub/fortran/latest_mask_io.f) for reading and writing
masks in any of the O/MAMA/RAVE formats.  They supercede the routines
in "new_mask_io.f".


* MAMA Version 3.8.1
******
Default mask output format changed to OMASK (see note about MAPMAN
above).  You can still write masks in any of the other MAMA/O formats
by supplying the format type as a parameter.


* DATAMAN Version 4.1.1
*********
Minor bug fixes.


* LSQMAN Version 4.6.1
********
Minor changes.


* COMING SOON
*************
- Pat Fleming (Yale) will compile an R10000 version of the entire
  RAVE package (including ESSENS), which will be made available to
  other users
- ESSENS (as part of RAVE) plus a pre-print of the paper (as soon
  as we get the referees' comments)


* NOT COMING SOON AT ALL
************************
The next "Uppsala Software News".  Until mid-October, I will be
travelling most of the time.  Will read my mails, but won't be able
to do too much in this period.


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