Uppsala Software News @ 2000-03-22
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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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* DEJAVU Server
***************
Dennis Madsen (http://xray.bmc.uu.se/dennis) has written a DEJAVU
server. If you are in Uppsala, you can use the full-blown version
on the intranet server (http://intray.bmc.uu.se/cgi-bin/dennis/dejavu.pl).
Otherwise, you can use a demo version (slow and only with a small
database) at http://xray.bmc.uu.se/cgi-bin/dennis/dejavu.pl . If
you want to install a DEJAVU server locally, contact Dennis
(mailto:dennis@xray.bmc.uu.se) for a copy of his Perl script.


* SPASM Server
***************
Dennis has also written a SPASM server. If you are in Uppsala, you
can use the full-blown version on the intranet server
(http://intray.bmc.uu.se/cgi-bin/dennis/spasm.pl). Otherwise, you can
use a demo version (slow and only with a small database) at
http://xray.bmc.uu.se/cgi-bin/dennis/spasm.pl . If you want to install
a SPASM server locally, contact Dennis (mailto:dennis@xray.bmc.uu.se)
for a copy of his Perl script.


* VALIDATION REVIEW
*******************
The topical review "Validation of protein crystal structures"
(Acta Cryst. D56, pp. 249-265) is now available from the IUCr
web site in HTML format:
   http://journals.iucr.org/d/issues/2000/03/00/gr0949/
and as a PDF file:
   http://journals.iucr.org/d/issues/2000/03/00/gr0949/gr0949.pdf


* LINUX
*******
- While I am working on the Linux port of RAVE, those of you who
  just want to mappage maps may be interested in a RedHat 6.1
  version of xdlMAPMAN contributed by Guoguang Lu
  (Guoguang.Lu@mbfys.lu.se), available from:
    fttp://xray.bmc.uu.se/pub/gerard/junk/LX_XDLMAPMAN.gz


* MAPMAN Version 5.9
********
- New OPerate command. Given two maps M1 and M2, this command will
  replace M1 by: M1 (operator) M2, where (operator) can be "+", "-",
  or "*". Using the "*" operator to multiply a map and a mask will
  keep all density within the mask and set all density outside the
  mask to zero.
- For a Linux version of xdlMAPMAN, see the previous item !


* VOIDOO Version 3.1.8
********
- Removed hideous bug from PDB-reading code ;-)
- Allow column 6 of an ATOM record to be non-blank (for very large
  structures with consecutively numbered atoms).
- Increased maximum number of cavities from 500 to 10000.


* XPLO2D Version 2.8.7
********
- Skip atoms with duplicate names in the dictionary-generation option.
- Minor changes.


* MOLEMAN2 Version 2.6.2
**********
- Minor bug fix for CHain AUto command (used to coredump on Alphas)
- Minor bug fix in REad command (Linux version choked on some CRYST1
  cards)


* DATAMAN Version 5.8.3
*********
- New parameter to the WRite command to control writing of only
  Centrics, only Acentrics, or Both


* OMAC
******
- add_waters.odb - this is a set of macros and datablocks that enable
    you to "spink" waters out of the blue. It was broken but should
    work properly now (thanks to Frank von Delft for pointing out
    the fact that there was a problem).


* DOMBO
*******
Volume 9, issue number 1, is now available from the Dombo web site at:
       http://xray.bmc.uu.se/dombo
Note: the Dombo web site has now become a genuine digital companion
to the printed journal, containing lots of material that cannot
easily be included in the journal (links, photos, newspaper clippings,
etc.). Check out the site's Berries, DirtyPix, PermaLinks, etc. !
And if you're interested in the story of O, read this:
       http://xray.bmc.uu.se/dombo/pics/story_of_o.gif
Contributions for Dombo can be sent to:
       mailto:dumbo@xray.bmc.uu.se?subject=copy


* CD2DVD
********
As announced earlier, with the advent of the third millennium (as
of the first of January, 2001), I was thinking of upgrading my
monicker from "CD" to "DVD". For those of you who always wondered,
the meaning of "CD" was ... "Charm and Diplomacy" - apparently the
two qualities least likely to be associated with me. The whole
thing was a slanderous invention of a certain T.A. Jones of Dalby,
Sweden. But now the question arises as to what "DVD" should stand
for ... Divine Virile Dutchman ? Danger - Venereally Diseased ?
Debauched Valetudinarian Dotage ? Diligent Vicissitudinous Diehard ?
Disgruntled Vociferous Dickhead ? Delectable Voluptuous Dude ?
Dyspeptic Voluptuary Drone ? Dismal Vitriolic Dud ? If you have
any better suggestions, please E-mail them directly to:
       mailto:dumbo@xray.bmc.uu.se?subject=dvd
(*not* to the mailing list, please !).


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


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

MAMMOCK: a shapeless piece ("you dare call that m. a crystal ?")
MATAEOTECHNY: an unprofitable science ("nope, academic protein
  crystallography is definitely a m.")
MEABLE: easily penetrated ("the invagination appears to be rather m.")
MERKIN: false pubic hair ("in the original publication they used m.
  for seeding")
METAGNOSTIC: unknowable ("why do phases have to be m. ?")
MISOSCOPIST: hater of beauty ("the m. microscopist was unimpressed
  by his 2D crystals")
MOIETY: a half (!) ("it's a bit of an understatement to call the
  carboxylate group a m. !")
MORPHOUS: having a definite form ("I keep getting m. precipitates")
MULTIVERSANT: infinitely variable ("if dihedrals weren't m., we
  could solve the protein-folding problem")
NEXUS: connection, link ("residues 78 to 85 form the n. between the
  two domains")
NOESIS: conceptual knowledge ("the PhD-candidate in NMR spectroscopy
  was found lacking in n.")
NOLL-ME-TANGERETARIAN: rigid, unbending ("use CNS to do fifty cycles
  of n. corpus refinement")
NULLIBIQUITOUS: non-existent ("you mean you wasted two days of beam
  time on a n. crystal ?")
NYCHTHEMERON: a 24-hour period ("the crystals grow to full size in a n.")