Uppsala Software News @ 2002-10-23
              **********************************

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

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


* MAC OS X VERSIONS AVAILABLE
*****************************
- http://xray.bmc.uu.se/usf/ftp.html
- As announced previously, all programs have now been ported to
  Mac OS X. I haven't received any complaints so far, so either
  everything works fine, or nothing works at all :-)


* FTP AREA FILE COMPRESSION
***************************
- ftp://xray.bmc.uu.se/pub/gerard
- From now on, tar files are gzip-ed instead of compress-ed, so
  if you have any hard-wired links to ".Z" files, please change them
  to ".gz" in your scripts, web-pages, etc.


* MOLEMAN2 Version 3.0.6
**********
- http://xray.bmc.uu.se/usf/xutil.html
- Renamed the VRml LIst_colours command to VRml NAmed_colours (to
  avoid a clash with the VRml LIquorice command ... thanks to Kevin
  Battaile for pointing this out)
- ODL objects produced by some of the ONo commands now have default
  names that begin with an underscore to prevent any clashes with
  POV-Ray terms (such as "plane")
- New ONo INertia_axes_odl command to generate an ODL file to draw
  the axes of inertia for the selected set of atoms (following a
  question from Michael Merckel)
- Improved the macro produced by the ONo OOps command


* SBIN
******
- http://xray.bmc.uu.se/usf/sbin.html
- New versions of STRUPRO (1.6), MSEQPRO (1.4), and STRUPAT (1.2)
- Two new substitution matrices are available, namely the HDSM
  and SDM structure-based matrices of Sippl et al. (Prot. Engng.
  18, 545-550, 2000). Download from the ftp area or through
  http://xray.bmc.uu.se/usf/libs.html#SBI
- Both STRUPRO and MSEQPRO can now read both integer and real
  substitution matrices (the HDSM and SDM matrices are real)
- Both STRUPRO and STRUPAT now skip CA atoms in alternative
  conformations (i.e., with alt. loc. indicator not equal to
  space or "A")


* MAPMAN Version 7.5.3
********
- http://xray.bmc.uu.se/usf/rave.html
- Most changes this time are to the RS_fit command which is used
  in the calculations for the next release of EDS
- RS_fit command now tries to figure out for each residue whether it
  is an Amino acid, Nucleic acid, Water, or Hetero-entity and prints
  this in the list file
- RS_fit command prints more statistics (both to the screen and the
  log file)
- RS_fit command now handles SCALE1/2/3 cards and if the
  fractionalisation matrix calculated from the cell constants (read
  from the CRYST1 card) differs from that provided on the SCALEn
  cards, then all coordinates will be fractionalised (using SCALEn)
  and then re-orthogonalised (using the CRYST1 cell)
- RS_fit command: if a negative radius is supplied, it is assumed to
  be the resolution (*-1) and the radius is calculated according to:
  (1) if resolution < 0.6 A then radius = 0.7 A;
  (2) if resolution > 3.0 A then radius = resolution/2 A;
  (3) else radius = 0.7 + (resolution-0.6)/3 A
- RS_fit command: new parameter to determine how obs_map and cal_map
  are to be scaled: Q = Quick-n-dirty (ratio of sums of absolute
  densities, summed over all grid points in the maps), or M = Masked
  (only sum over grid points within the envelope of the total set of
  atoms; this is slower but better)
- Various minor changes and bug fixes


* DATAMAN Version 6.2.4
*********
- http://xray.bmc.uu.se/usf/rave.html
- Most changes here are also related to the next release of EDS
- The STats command now performs a bunch of sanity checks (esp. useful
  when you are dealing with structure-factor files downloaded from the
  PDB which can be totally screwed up ...)
- New FAke_sigmas command (sets all Sigma = SQRT | Fobs | )
- The STats command will print a warning if it suspects that Sigmas
  are fake (either ~ constant, or ~ constant * Fobs, or ~ constant *
  SQRT(Fobs))
- New SIgmas LImit command to reset very small or large sigmas (e.g.,
  to replace zero or negative values)
- Minor changes


* LSQMAN Version 9.3
********
- http://xray.bmc.uu.se/usf/dejavu.html
- IMprove command: single chain names may now be used and are
  interpreted to mean the entire chains (e.g.: IMprove m1 a m2 c)
- REad command: optional parameters "chain" and "atom" to read just a
  single chain (default * = all) and/or a single type of atom
  (default * = all). For example: read m1 pdb1pmp.ent c " ca "
  will only read the CA atoms of chain C from file pdb1pmp.ent


* XPLO2D Version 3.0.2
********
- http://xray.bmc.uu.se/usf/xutil.html
- Minor changes and bug fixes


* HETZE Version 1.0.1
*******
- http://xray.bmc.uu.se/usf/xutil.html
- Minor changes and bug fixes


* OMAC
******
- http://xray.bmc.uu.se/usf/omac_index.html
- on_jaguar.odb - Alwyn's set of on_* datablocks (but with a
                  safer use of the escape key)


* MISCELLANEOUS
***************
- All programs that use the history facility (e.g., MAPMAN, LSQMAN,
  DATAMAN, MOLEMAN2, MAMA) can now recall up to 500 commands.


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