Uppsala Software News @ 2001-01-26
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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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       | The first USF News of the third millennium ! |
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* RAVE-4-LINUX !
****************
- Use C routines to do dynamic memory allocation in all versions
  and ported to Linux (at last !). The latest version numbers of
  the affected programs are:
  - AVE     Version 1.0
  - COMA            1.0
  - COMAP           3.0
  - COMDEM          3.0
  - DATAMAN         6.0
  - ESSENS          3.0
  - IMP             3.0
  - MAMA            6.0
  - MAPFIX          3.0
  - MAPMAN          7.0
  - MASKIT          1.0
  - MAVE            4.1
  - NCS6D           3.0
  - SOLEX           2.0
  - SPANCSI         1.0


* LSQMAN Version 7.7.1
********
- New command FAst_force, a quicker (but dirtier) variant of the
  BRute_force command for ab initio superpositioning of two
  structures (only using the first of the user-selected atom
  types, e.g. CA or C4*)
- Removed bug in APply command (using chain id '*' did not work
  as intended; thanks to Aaron Chandler for persevering ;-)
- Also in the APply command, the operators of the moved molecule
  are only reset if the entire molecule was moved (so you can
  apply the same operator to several chains and/or zones in
  turn without having to regenerate the operator every time)
- The PHipsi_plot, DIstance_plot, DDihe_plot and D1_D2_plot
  commands now all have the parameters: mol1 range1 mol2
  range2 plot_file [cut-off] [hist_bin] [hist_max]. The
  cut-off is used to print all residue pairs for which
  delta-phi or delta-psi etc. exceeds the cut-off value
  (so you can find out which residues show the largest
  differences; use a negative value for the cut-off to
  suppress printing). The hist_bin and hist_max parameters
  are used for the histograms of delta-phi etc. values
- New ALter REnumber command to renumber residues in a certain
  chain sequentially
- New DChi command to list large side-chain torsion angle
  differences between two similar models
- Better O macros produced by the OM commands


* O2D Version 5.2.1
*****
- Increased array dimensioning for 1D and 2D plots


* MOLEMAN2 Version 2.8.2
**********
- Minor changes


* MOLEMAN Version 7.3.1
*********
- In the WATEr_sort option, now always convert the user's water
  residue type to uppercase


* MAVE Version 4.1
******
- In the EZ-skewing option: if no mask is supplied, use all but
  a border cushion of 3 grid points thickness (to prevent unnecessary
  FRCSYM errors)


* ESSENS
********
We came across an ad of the "Essens Specialist". Right now
they sell strands for only 10 SEK (while stocks last, of course) !
Don't believe me ? See for yourself:
  http://xray.bmc.uu.se/cgi-bin/gerard/image_page.pl?image=dombo/pics/essens_strands.jpg


* OMAC
******
- New version of the hetero.pdb file, containing 2971 hetero
  compounds (up from 2640 in July 2000)


* ALL PROGRAMS
**************
- Linux version in synch with SGI and ALPHA versions again.


* FAME ?
********
In volume 5, issue 2 of Bioinform (15 January, 2001), one of
the headlines reads "USF Upgrades Protein Structure Software;
Web-Based Interface Boosts Functionality" :-) For the whole
story, see http://xray.bmc.uu.se/gerard/news.html


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


The Crystallographer Formerly Known As "CD"'s Words of the Month:

RHABDOPHOBIA: fear of being severely criticised ("r. kept him
  from publishing his amazing results")
RHOMBICOSIDODECAHEDRON: Archimedean solid with 62 faces ("the
  virus crystals consisted of beautiful r.")
RICTUS: very wide mouth ("the ligand enters the cavity through
  a r.")
RIPARIAL / RIPARIAN / RIPARIOUS / RIPICOLOUS: pertaining to or
  living near water ("arginines and lysines are usually r. residues")
RUBEDINOUS / RUFESCENT: reddish ("the r. North-American post-doc
  obtained r. crystals")
RUBIGINOUS: rust-coloured, rusty ("the r. professor grew r. crystals")
RUBINEOUS / RUBIOUS: ruby-red ("I have never been able to reproduce
  those beautiful r. crystals")
SATURNALIAN: unrestrained ("first, do some s. dynamics to get new
  NCS-operators")
SCANTLING: measurement, size ("what's the s. of your cavity ?")
SCOPOPHOBIA: fear of being seen ("my crystals tend to suffer from s.")
SCROBICULATE: with numerous shallow depressions ("your mask is a
  trifle too s.")
SCROTIFORM: pouch-shaped ("what a magnificent s. cavity you have
  there")
SEBACEOUS: pertaining to or composed of fat; fatty ("is this a
  s.-acid-binding protein ?")
SECULUM: a long time ("don't worry, a rotation function with XPLOR
  only takes a s.")
SEELY: blessed, happy, blissful, good, king, innocent, harmless,
  weak, feeble, poor, wretched, frail, simple, timid, foolish,
  silly ("you look absolutely s. today")
SEJUGATE: disconnect ("you'll have to s. some bones here")
SESQUIALTERAL: having a ratio of 1:1.5 ("we added s. amounts of
  protein and inhibitor")
SFUMATO: painted with hazy outlines ("have you tried the new s.
  option to contour your density ?")
SIDEREAL: pertaining to stars; astral, stellar ("why do most of
  our workstations have s. names ?")
SIDERODROMOPHOBIA: fear of train travel ("sorry, my s. is playing
  up - I have to fly")
SIGLA: abbreviations, symbols ("you forgot to include a list of s.")
SIGMATE: to add a sigma or S ("here in S., people tend to s. all
  plural verbs")
SIMOUS: concave ("the active site is a s. pocket")
SINISTRAL: left-handed; illegitimate ("but all your helices are
  s. !")
SISYPHEAN: unending ("writing a paper is a s. enterprise in this
  group")
SKIAGRAPHY: making X-rays ("the generator takes care of the s.")
SKYGODLIN: diagonally ("that line should have been drawn s.")