Uppsala Software News @ 2003-03-14
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                  http://xray.bmc.uu.se/usf/
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               ftp://xray.bmc.uu.se/pub/gerard/
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* MOLEMAN2 Version 3.2
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- http://xray.bmc.uu.se/usf/xutil.html
- New BFactor PSeudo command to replace the atomic B-values by various
  other properties. This makes it easy to use external software to
  colour-ramp molecular drawings using these properties (e.g., O or
  Rasmol). The properties include the various coordinates, residue
  and atom indices, distances to the centre-of-gravity (or any point),
  convexity (A Pintar et al, Bioinformatics 18, 980-984 (2002)), as
  well as Halle's method to predict B-factors from packing density
  considerations (B Halle, PNAS 99, 1274-1279 (2002))
- To make working with the BFactor PSeudo command easier, a number of
  other new commands have been implemented as well: BF SAve, BF REstore,
  BF SCale, and BF ODb (the latter writes the atomic B-values to an
  O datablock file)
- New version (3.0) of the library file (moleman2.lib), now with 153
  residue types defined (including many popular hetero compounds):
     ftp://xray.bmc.uu.se/pub/gerard/xutil/xutil_etc/moleman2.lib


* SOD Version 0.9
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- http://xray.bmc.uu.se/usf/xutil.html
- In task MULT, the program now also calculates the entropy for
  every residue in the alignment, and writes this information to
  the O datablock file and uses it to colour-ramp your molecule.
  For an example, go to http://xray.bmc.uu.se/usf/xutil.html#EXA
  and look under SOD. Four differently coloured CA traces of a
  fasciculin are shown, conveying information generated by SOD
  from an alignment of 163 fasciculin sequences.


* DATAMAN Version 6.2.7
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- http://xray.bmc.uu.se/usf/rave.html
- Minor changes


* VOIDOO Version 3.3
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- http://xray.bmc.uu.se/usf/voidoo.html
- Increased dimensioning of some arrays
- Added some residues to the library file (cavity.lib):
    ftp://xray.bmc.uu.se/pub/gerard/voidoo/voidoo_etc/cavity.lib


* OMAC
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- http://xray.bmc.uu.se/usf/omac_index.html
- hetero.pdb - new version of this file, now containing 3941 hetero
  compounds


* HIC-Up hiccup
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- http://xray.bmc.uu.se/hicup
- A new version of HIC-Up was released in January, now containing
  over 3900 compounds. However, as Scott Garman discovered, gremlins
  have eaten ~2200 of these compounds in the lists of entries sorted
  by trivial name, residue name, non-hydrogen atoms and chemical
  formula. However, the search box that uses Google to search HIC-Up
  (at http://xray.bmc.uu.se/hicup/search.html) works properly, and
  the composition-based lists do contain all hetero compounds
  (http://xray.bmc.uu.se/hicup/comp_index.html). Sorry about the
  inconvenience this may cause. It will be fixed with the next
  release of HIC-Up.


* SERVERS
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- http://portray.bmc.uu.se/
- Both the SPASM and the DEJAVU server now use the latest (November 2002)
  databases
- Note that the latest DEJAVU 100% database contains the intact capsid
  structure 1GAV, which contains 510 secondary structure elements and
  breaks DEJAVU. A new version of the database file, in which only one
  copy of the capsid protein has been included, is available from the
  ftp server:
    ftp://xray.bmc.uu.se/pub/gerard/dejavu/dejavu_100_nov02.lib.gz


* DOMBO
*******
- http://xray.bmc.uu.se/dombo
- Volume 12, issue number 1 (14 March, 2003), is now available (in
  PDF format only). Besides the usual rubbish, this issue includes
  two complaints about CCP4 error messages and a selected bibliography
  of "Jones TA [AU]".


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

Note: for a rare glimpse of Alwyn demonstrating the new automatic
      tracing algorithm in O, called Connect_the_Dots, see:
        http://xray.bmc.uu.se/dombo/pics/alwyn_folding.jpg
      Alwyn himself emulates a partially traced protein (note the
      two strands [arms] and the two short helices [legs]).