Uppsala Software News @ 2001-12-21
              **********************************

                  http://xray.bmc.uu.se/usf/
                  **************************

               ftp://xray.bmc.uu.se/pub/gerard/
               ********************************


* LSQMAN Version 9.0.2
********
- http://xray.bmc.uu.se/usf/dejavu.html
- Added two more buffers (size controlled by the user through GKBUFFER)
  so that the following commands can be given enough scratch memory:
  LO, GL, DP, SO, NW, QD. The default value of the buffer size was
  changed to 1000000
- BRute_force now ignores residues with negative or zero residue number
  (rather than simply failing)
- OMacro APpend now also writes the Crippen RHO and relative RMSD
  statistics to the lsq_stats_* datablocks
- The SOap_film command now has an optional 'verbose' parameter
  (default value is 'no' to reduce output)
- The DP_improve command has an extra 'max_cycles' parameter to enable
  iterative use until convergence of the superposition
- Improved the recipe in the quick'n'dirty getting-started part of
  the manual
- Implemented my favourite ab initio superposition recipe as an
  LSQMAN macro called "align.lsqmac" (part of OMAC, quod vide). This
  will give you a robust superposition, superimposed PDB files,
  an O macro to display the result (including a soap-film surface),
  a VRML file with the result, a structure-based sequence alignment
  in cut-and-paste-ready format for reports and papers, as well as
  Levitt-Gerstein statistics to assess the significance of the
  structural similarity


* MAPMAN Version 7.4
********
- http://xray.bmc.uu.se/usf/rave.html
- Implemented RS_fit command. See the manual for details.
- WRite for mask now has an extra parameter, namely the comparator
  (<, LT, >, GT, <=, LE, >=, or GE; default >) to define which points
  should be set when writing a map as a mask file


* OOPS2 Version 1.2
*******
- http://xray.bmc.uu.se/usf/xutil.html
- Support for reading RS-fit and RS R-factor values from a list file
  produced by MAPMAN's RS_fit option
- Better handling of HETATMs
- Better handling of nucleic acids


* MKSPAZ Version 2.3
********
- http://xray.bmc.uu.se/usf/spasm.html
- Proper trapping of READ errors
- Can now handle the absence of COMPND records (crashed on Alphas)


* MOLEMAN Version 7.3.3
*********
- http://xray.bmc.uu.se/usf/xutil.html
- Fixed writing of SCALEx cards (unpredictable translations were
  produced by the Linux version ... thanks to Brian Mark for pointing
  this out)


* REST
******
- Minor changes and/or bug fixes for the following programs:
    - SPASM Version 3.7.2
    - MAMA Version 6.0.3
    - MOLEMAN2 Version 2.9.2
    - DEJAVU Version 5.8.3
    - DEJANA Version 1.6
    - ODBMAN Version 2.2.1
    - XPLO2D Version 2.9.5
    - DATAMAN Version 6.1.1


* HIC-Up
********
- http://xray.bmc.uu.se/hicup
- As announced previously, HIC-Up release 5.3 (2001-12-01) is
  now available. It contains information about 3,416 hetero
  entities taken from the PDB.


* OMAC
******
- http://xray.bmc.uu.se/usf/omac_index.html
- align.lsqmac - LSQMAN macro implementing Gerard's favourite
      structure superposition recipe (see under LSQMAN above)
- hetero.pdb - a new version of this file (used to generate
      HIC-Up) is available, now containing 3416 hetero compounds


* FTP
*****
- http://xray.bmc.uu.se/usf/ftp.html
- Just a reminder - if you are looking for a particular file or
  program that you expect to find on the Uppsala ftp-server, fetch
  this file:         ftp://xray.bmc.uu.se/lspub
  It is a text file containing a complete list of all directories
  and files under ftp://xray.bmc.uu.se/pub/alwyn and /pub/gerard.
  It is updated once a day.


Wishing you all a Merry Next-week (whatever the occasion), and
a Happy Week-after-that (whatever the occasion) !


--DVD (The Crystallographer Formerly Known As "CD")