Uppsala Software News @ 2001-09-28
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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 2.8.6
**********
- http://xray.bmc.uu.se/usf/xutil.html
- Implemented ONo CEll command. With this command you can generate
  an ODL file that will draw the unit cell (as read from the CRYST1
  card or entered with the PDb CRyst command) in O, either as a set
  of lines or a set of planes (solid mode). You can define the
  colour as well.
- Implemented DIstance LIst command (e.g., to find atoms that are
  too close to one another; for instance, try it out on 1BP8).
- Added some pictures to the manual page to illustrate some of
  the options that produce O2D plot files, ODL files, VRML files,
  or PostScript files.


* O2D Version 5.3.5
*****
- http://xray.bmc.uu.se/usf/xutil.html
- Implemented new 1D plot type SPike_plot. This looks a bit like
  a mass spectrum with every point represented as a line from
  (x,0) to (x,y)
- In BOx plots the average of each bin is now shown as a "+" sign
- In BOx plots, the correlation and least-squares fit of the
  averages (X and Y) of the boxes (those that contain at least
  10 data points) are now also listed


* OOPS2 Version 1.1.3
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- Option WIF (WhatIf) changed as follows: if you don't use nit-picking
  mode, you can now select a cut-off for inclusion of short contacts
  (bumps) [to avoid you having to look at contacts that are deemed
  to be 0.03 A too short]. Also, the format of the Bumps lines in the
  O macros that OOPS2 generates has been changed slightly


* DATAMAN Version 6.0.1
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- http://xray.bmc.uu.se/usf/rave.html
- Fixed bug in Wilson scaling that sometimes put all data in one bin.
- Added some pictures to the manual page to illustrate some of
  the options that produce O2D plot files, ODL files, or PostScript
  files.
 

* ODBMAN Version 2.2
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- http://xray.bmc.uu.se/usf/xutil.html
- New COmbine command to combine two datablocks using the +, -, *,
  /, MIN or MAX operator.
- Added a number of pictures to the manual to illustrate the results
  of some commands.


* XPLO2D Version 2.9
********
- http://xray.bmc.uu.se/usf/xutil.html
- In the dictionary-generation routine, there is now a better handling
  of FORMUL records. Also, the program will now bail out if any bond
  distance is less than 0.5 A or any bond angle is less than 60 degrees
  (yes, they *do* occur in the PDB ...)


* XPAND Version 1.4.1
*******
- http://xray.bmc.uu.se/usf/xutil.html
- Bug fix in C option (format was wrong and limited the number of
  nb_ncs_matrix_* to nine)


* HETZE Version 0.5
*******
- http://xray.bmc.uu.se/usf/xutil.html
- Better handling of FORMUL records
- Check for distances < 0.5 A and angles < 60 degrees


* RIGOR Version 2.4.2
*******
- http://xray.bmc.uu.se/usf/spasm.html
- Minor changes and bug fixes
- New version of the database is available (with 18,379 motifs)


* SPASM Version 3.7.1
*******
- http://xray.bmc.uu.se/usf/spasm.html
- Minor changes


* VOIDOO Version 3.2
********
- http://xray.bmc.uu.se/usf/voidoo.html
- Minor changes


* RAVE
******
- http://xray.bmc.uu.se/usf/rave.html
- Added some pictures to the MAPMAN and MAMA manual pages to illustrate
  some of the options that produce O2D plot files, ODL files, VRML files,
  or PostScript files.


* MANUALS
*********
- http://xray.bmc.uu.se/usf
- Updated the list of references in all manuals.
- Added a brief DEJAVU tutorial.


* PRACTICAL
***********
- As announced previously in another forum, I recently prepared a
  web-based practical about model validation for students in the EMBO
  Bioinformatics Course we had here in Uppsala. Although this practical
  was aimed at non-crystallographers, it may be useful for relative
  newcomers to the area as well. It can be found at:
  http://xray.bmc.uu.se/embo2001/modval


* OMAC
******
- http://xray.bmc.uu.se/usf/omac_index.html
- multi_probe - improved version that should even work with
                extremely variable (NMR) models (such as 1AP0)
- seq2comp.f  - now also generates an O sequence datablock from
                a file containing a sequence in one-letter code


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