Uppsala Software News @ 2001-11-20
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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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* LSQMAN Version 8.9
********
- http://xray.bmc.uu.se/usf/dejavu.html
- The MPlot command has been extended to also produce a "CD plot"
  (grey-scale mapping of pair-wise distances; see Jones, T.A. and
  Kleywegt, G.J. (1999). CASP3 comparative modelling evaluation.
  Proteins: Struct. Funct. Genet. Suppl. 3, 30-46). This is a very
  informative plot for comparing an ensemble of structures of the
  same macromolecule (NMR, NCS, multiple complexes and/or mutants,
  etc.). See the manual for an explanation and an example.
- Increased the maximum number of steps in a MOrph to 999 (someone
  actually requested this ...)
- The buffer array size for 2D plots can now be passed through the
  environment variable or command-line argument GKBUFFER (e.g.:
  run lsqman gkbuffer 1000000); otherwise, the default is 500000
  points; this affects the QD command, for instance
- Removed a terrible bug from the MOrph code (when one uses Internal-
  coordinate morphing with the TRACe quasi-atom type; thanks to
  Jinghua Tang for informing me !)
- Implemented the NMr_model_mode command to decide if all models
  or only the first model of an NMR ensemble should be read
- Changed the default values for some of the SEt commands (e.g., most
  settings now use the Maiorov-Crippen RHO as the optimisation
  criterion for superposition-operator IMprovement)


* MOLEMAN2 Version 2.9.1
**********
- http://xray.bmc.uu.se/usf/xutil.html
- The PRot MC, PRot CA and Nucleic DUarte commands now delete the
  PostScript file they normally produce if it contains no residues
- These three commands now also have an extra (optional) argument
  to decide whether the analysis should be carried out for all chains
  in one go, for one chain in particular, or for each chain in turn
  (in the latter case, you will get one PostScript file for each
  chain, so this makes it easy to inspect Ramachandran plots on
  a chain-by-chain basis, for instance - try it out on 1F83 if
  you want an interesting example)


* XPLO2D Version 2.9.4
********
- http://xray.bmc.uu.se/usf/xutil.html
- AUTO: recognises optional command-line argument "-force" which will
  force the program to try and create dictionaries even if there are
  "silly" bond lengths and angles (these should only be used for map
  calculations, *NOT* for refinement !)
- AUTO: if "-force" is used, print warnings in the X-PLOR, O and TNT
  parameter files for short bond distances (< 0.5 A) and short angles
  (< 60 degrees)
- AUTO: make sure that the number of bonds found is not less than the
  number of atoms minus one


* RAVE
******
- http://xray.bmc.uu.se/usf/rave.html
- Linked all RAVE programs on all platforms with the CCP4 4.1.1
  library (libccp4.a) since the versions I used previously were
  getting on in age (2-5 years)


* DATAMAN Version 6.1
*********
- http://xray.bmc.uu.se/usf/rave.html
- Changed default for max nr of reflections to 200,000 (but note
  that this can be overridden in three different ways; see the manual:
  http://xray.bmc.uu.se/usf/dataman_man.html#H5 )
- More importantly, DATAMAN will now *fail* when there are more than
  the max nr of reflections in a file (previously, it would print an
  error message and simply skip the remaining reflections, but this
  has lead to at least one case in which a colleague "lost" ~10% of
  his reflections and didn't notice it until it was time to deposit
  the data in the PDB ...). Now, the program will refuse to read
  the offending dataset and tell you to allocate more memory using
  the ZP_restart command


* DEJAVU Version 5.8
********
- http://xray.bmc.uu.se/usf/dejavu.html
- Changes to the LSQMAN input files created by DEJAVU (echo commands;
  only keep the first NMR model of ensembles; generate a global
  structure-based sequence alignment)
- MAXHITS now applies to the number of database entries that are
  found as hits rather than the total number of hits


* MAPMAN Version 7.2.4
********
- http://xray.bmc.uu.se/usf/rave.html
- Changed default atom name for picked peaks to " O  " (instead of
  " O1 "; note that the defaults can be changed with the PIck PDb
  command)
- Minor changes


* ESSENS Version 3.0.4
********
- http://xray.bmc.uu.se/usf/rave.html
- Give more output when checking if the probe can be rotated inside
  the map


* O2D Version 5.5
*****
- http://xray.bmc.uu.se/usf/xutil.html
- New 1D plot type CD_plot (grey-scale mapping of Y-values; see Jones,
  T.A. and Kleywegt, G.J. (1999). CASP3 comparative modelling evaluation.
  Proteins: Struct. Funct. Genet. Suppl. 3, 30-46)
- The buffer size for 2D plots can now be passed through the environment
  variable or command-line argument GKBUFFER (run o2d gkbuffer 1000000);
  otherwise, the default is 500000 points


* HETZE Version 0.6
*******
- http://xray.bmc.uu.se/usf/xutil.html
- Check the correspondence of the FORMUL formula and the one
  derived from the file contents
- Make sure that the number of bonds found is not less than the
  number of atoms minus one


* MKSPAZ Version 2.2.3
********
- http://xray.bmc.uu.se/usf/spasm.html
- Fixed bug which made it crash on Alphas


* OOPS2 Version 1.1.4
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- http://xray.bmc.uu.se/usf/xutil.html
- Minor changes


* MAMA Version 6.0.2
******
- http://xray.bmc.uu.se/usf/rave.html
- Minor changes


* USF MIRRORING
***************
- http://xray.bmc.uu.se/usf/mirrors.html
- Mirroring the USF manuals site has been made a tad simpler. For
  detailed instructions, see: http://xray.bmc.uu.se/usf/mirrors.html


* OMAC
******
- http://xray.bmc.uu.se/usf/omac_index.html
- plt2pov.c - Morten's C-program to convert O plot files to PovRay
- auto_amore.com - changed the TABFUN CRYSTAL line since that has
    changed in a recent version and now chokes on the 'CELL' keyword
- gen_o_symm.f - slightly changed to print more spacegroup info
    in the O datablock files
- localise_usf_mirror.csh - jiffy script to change links in mirror
    copies of the USF manuals site so they don't point to the
    Uppsala site any longer
- As announced earlier on O-info: I fixed a serious bug in the program
  that generates the "hetero.pdb" file (available in the OMAC directory).
  If you obtained a copy of this file after 4 September of this year,
  please get the current version from:
     ftp://xray.bmc.uu.se/pub/gerard/omac/hetero.pdb


* SYMM
******
- ftp://xray.bmc.uu.se/pub/gerard/extras/symm
- Updated the set of O datablocks with spacegroup symmetry operators
  using the most recent version of CCP4's symop.lib. The previous
  set dated back to October 1995 and some corrections have been
  made since then. You can pick up individual files or a gzip-ed
  tar-ed directory containing all 230 files (and including soft
  links so you can refer to the files by the spacegroup number).


* OPLOT
*******
- ftp://xray.bmc.uu.se/pub/gerard/extras/oplot/oplot.tar.gz
- As announced on O-info previously, I couldn't find the source of
  Morten's program oplot v. 1.15 anywhere on our ftp server in Uppsala,
  so I put it there. It contains ready-to-run executables for SGI, ALPHA,
  and LINUX, as well as source code if you want to play with it yourself.
  I had to make two small changes to get the program to compile under
  LINUX, which are documented in the README file.


* HIC-Up
********
- http://xray.bmc.uu.se/hicup
- As announced earlier on O-info: a company asked if they could set up
  the HIC-Up database locally, so I have made a gzip-ed tar file
  of the entire HIC-Up www directory tree available for ftp-ing. For
  details, see: http://xray.bmc.uu.se/hicup/mirror.html
  I'm not sure how well a local version will work, since there are
  several hard-wired references to the HIC-Up site at xray.bmc.uu.se
  (e.g., the hicup server, search, and quickxs results). On the other
  hand: it's free ;-)
- There will be a new release of HIC-Up soon. Amongst other things
  it will have links to the Uppsala Electron Density Server,
  improved O torsion datablocks, better error-checking, more LIGPLOTs,
  and it will also be easier to mirror.


* DOMBO
*******
- http://xray.bmc.uu.se/dombo
- Volume 10, issue number 5 (20 November, 2001), is now available.
- If you're a carrier of exoterran DNA, you might want to check out
  the link provided in the November 19 entry of the Dombo guestbook !


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


P.S.: Look what I found in an old file on my Mac:

      "It's is not, it isn't ain't, and it's it's, not its, if you
       mean it is.   If you don't, it's its.  Then too, it's hers.
       It isn't her's.  It isn't our's either.  It's ours, and
       likewise yours and theirs."

      Oxford University Press, Edpress News