Uppsala Software News @ 2002-12-23
              **********************************

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

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


* MOLEMAN2 Version 3.1.2
**********
- http://xray.bmc.uu.se/usf/xutil.html
- New PDb SAnity command that checks various aspects of alternate
  locations and occupancies. Since alt. locs. are often generated
  by editing a PDB file, mistakes are easily make and hard to spot.
  This command makes the task of finding oddities a lot simpler
- The program now uses the insert code to delineate different residues
  (in addition to residue number, residue type, chain name, and
  seqment ID)
- Further improved the macro produced by the ONo OOps command
- Various minor changes and bug fixes


* OOPS2 Version 1.2.5
*******
- http://xray.bmc.uu.se/usf/xutil.html
- Minor changes to default cut-off values, etc.
- In the O macros, centre on the CA atom if the residue has one (else
  on its centre-of-mass as before). Also, execute the string of user
  commands directly after centering (i.e., before printing the list
  of remarks about the residue in question)


* LSQMAN Version 9.4
********
- http://xray.bmc.uu.se/usf/dejavu.html
- Fixed a bug that prevented the MR, MD and VM commands from working ...
- Several minor changes to the NW, DP, and LO commands
- All (I hope ...) rotation matrices are now printed out in the "normal"
  (non-O-ish) way (thanks to Pete Dunten for pointing out the previous
  inconsistencies)
- New AA_substitution_matrix command with which you can read in an
  SBIN-style substitution matrix, which will be used by the NWunsch
  command (suggested by Mike Sierk). To download the SBIN-style
  matrices, go to http://xray.bmc.uu.se/usf/libs.html#SBI
- New XAlignment command to read in an external sequence alignment and
  apply it to two structures (suggested by Mike Sierk)
- Added some suggestions to the manual on how to compare the quality of
  two or more alignments (http://xray.bmc.uu.se/usf/lsqman_man.html#H7)


* MAPMAN Version 7.5.4
********
- http://xray.bmc.uu.se/usf/xutil.html
- New output format MPI (for MPI-style EM maps)


* DATAMAN Version 6.2.6
*********
- http://xray.bmc.uu.se/usf/xutil.html
- New SIgmas CEntric_vs_acentric command that calculates <Sigma(Fobs)>
  and <Fobs/Sigma(Fobs)> separately for centric and acentric reflections.
- If reading a reflection fails, the number of reflections that had
  already been read when the error occured is now printed


* HISTORY
*********
- http://xray.bmc.uu.se/usf/macsym.html
- The history facility in MAMA, MAPMAN, DATAMAN, LSQMAN, MOLEMAN2 and
  ODBMAN now also has an option to output the history (list of previous
  commands) without the command numbers. This is handy if you want to
  cut and paste some of your commands into a macro file. To get this
  list, use "# !" (instead of "# ?", which gives the list *including*
  the command numbers)


* DATABASES
***********
- http://xray.bmc.uu.se/usf/libs.html
- The DEJAVU and SPASM databases have been updated (using PDB
  subsets from Roland Dunbrack's PISCES server)
- There are two new DEJAVU databases, generated on 11 November 2002:
  -  25% sequence ID - 2193 PDB entries (~49,000 SSEs)
  - 100% sequence ID - 7951 PDB entries (~188,000 SSEs)
- There are two new SPASM databases, generated on 11 November 2002:
  -  25% sequence ID - 2186 PDB entries (~586,000 residues)
  - 100% sequence ID - 7907 PDB entries (~2,179,000 residues)


* OMAC
******
- http://xray.bmc.uu.se/usf/omac_index.html
- delete.odb (contributed by Andre Ambrosio (ambrosio@if.sc.usp.br)):
  contains a macro called "@Delete" which will do a mutate_delete,
  refi_init, refi_gen and draw an all-atoms object of the mutated
  molecule
- refmac_from_o.txt (also contributed by Andre Ambrosio): contains
  an O macro and REFMAC script that enable you to quickly run some
  cycles of reciprocal-space refinement from within O
- cheap_dejavu.csh: vastly improved version of this script that will
  run the OMAC-macro "align.lsqmac" to align a large number of
  structures to one structure that you provide


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

P.S.: If you want to read some of the hate-mail and other silly
      mailbox fodder USF officials sometimes receive, have a look
      at http://xray.bmc.uu.se/dombo/weirdmails.html

P.P.S.: some people wondered whatever happend to my series of
      useful words. Well, basically, we reached the letter Z ...
      If you want to read them again, they live on the Dombo site:
      http://xray.bmc.uu.se/dombo/useful_idiom.html

P.P.P.S.: A Merry Christmas (modulo personal belief system) and
          a Happy New Year (modulo local convention) !