Uppsala Software News @ 2001-03-16
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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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* FTP
*****
If you cannot locate a certain file on the ftp-server, have a look
at the following file: ftp://xray.bmc.uu.se/lspub - this is a daily
updated listing of the pub/alwyn and pub/gerard directory trees.


* RAVE
******
- Doubled the size of the level buffer in all programs (to enable
  reading of very large map sections)
- Sanjoy Ray (sray@genetics.com) has compiled a version of RAVE
  for Alpha Linux: "The executables are not compiled for any particular
  alpha (ev5, ev6 etc) and so ought to run without penalty on all
  types. Users will need to get hold of the Compaq compilers so that
  they have the necessary runtime libs though. I believe that they
  can be obtained at: http://www.support.compaq.com/alpha-tools/software/ "
  The gzip-ed tar-ed archive can be downloaded from:
     ftp://xray.bmc.uu.se/pub/gerard/rave/rave_linux_alpha.tar.gz


* ESSENS Version 3.0.3
********
- Changed the multi-processing directives (thanks to Pete Dunten
  and Kay Diederichs). But I no longer use them in my own compilations
  since I can't test them. A compiled parallellised SGI version
  (courtesy of Kay) can be downloaded from:
     ftp://xray.bmc.uu.se/pub/gerard/rave/rave_irix6/6d_parallel_essens


* MAPMAN Version 7.0.2
********
- Fixed mini-bug in peak picking (crashed on Alpha and Linux; didn't
  do any harm on SGI)


* NCS6D Version 3.1
*******
- To speed up the calculations, only use every Nth atom (value of N
  is user-defined; e.g. N=10 should give 10-fold speed-up)


* STRUPAT Version 1.1
*********
- Calculate probability for each generated PROSITE pattern to occur
  by chance (a la EMOTIF; CG Nevill-Manning, TD Wu, DL Brutlag, PNAS 95,
  5865-5871 (1998))
- Implemented EMOTIF's substitution-group mode and made it the default 


* LSQMAN Version 7.8
********
- Implemented LEsk_plot command; see:  JA Irving, JC Whisstock & AM
  Lesk, Proteins: Struct. Funct. Genet., 42, 378-382 (2001)


* MOLEMAN Version 7.3.2
*********
- Fixed reading of CRYST1 card (crashed Linux version if the value
  of ZMOL wasn't there)


* Side-chain torsions
*********************
Just as for the Ramachandran plots, I have put plots of the distributions
of chi-1 to chi-4, as well as of the joint distribution of chi-1
and chi-2 on the web. These may be useful for teaching, or to convince
colleagues that using rotamers in model building really isn't such
a bad idea. The data used were discussed in: GJ Kleywegt and TA Jones
(1998). Databases in protein crystallography. Acta Cryst D54, 1119-1131.
Throw your browser at http://xray.bmc.uu.se/gerard/supmat/ and click
on "Rotamers revisited".
  By the way - I hate to have to say this, but there's an error in
that paper ... In the rotamer table, we missed the omission of two
Ile-rotamers in the proofs stage. The complete set of rotamers is:

   Residue  Rotamer     Pop.%      Chi-1       Chi-2
   Ile      g+t         58         300         170
            g+g+        14         300         300
            g-t         13          70         170
            tt           7         190         170


* DOMBO
*******
Volume 10, issue number 2 (7 March, 2001), is now available
from a Dombo web site near you:
       http://xray.bmc.uu.se/dombo
Contributions for Dombo can be sent to:
       mailto:dumbo@xray.bmc.uu.se?subject=copy


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


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

TABEFY: to waste away gradually ("old consumers don't die, they t.")
TAUTOOOUSIOUS: being absolutely the same ("if you use NCS-constraints
  you'll get t. molecules")
TEUTOPHOBIA: fear and dislike of Germans or German things ("just
  because I suffer from t. doesn't mean that Germans are nice")
TODDICK: very small quantity ("don't forget to add a t. of
  beta-mercaptoethanol")
TORQUATED: formed like a twisted chain ("that beta-strand looks
  rather t.")
TRAGOMASCHALIA: smelly armpits ("I really hope that your research
  will help to find a cure against t.")
TRANSMOGRIFY: to change into a strange or absurd form ("oh no,
  X-PLOR has completely t. that loop !")
TRANSVASE: to pour out of one container into another ("could you t.
  that PEG-solution for me ?")
TREFOIL: a group of three closely related units ("the protein
  crystallises with a t. in the asymmetric unit")
TRICHOTILLOMANIA / TRICHOLOGIA / CARPHOLOGY: mania for pulling out
  one's hair ("t. isn't so bad when you need to do seeding experiments")
TRILLIBUB: a trifle ("I would add a t. more BOG if I were you")
TRIMENON: a three-month period ("the crystals grow during a t.")
TROCHILICS: the science of rotary motion ("before doing a rotation
  function, brush up your knowledge of t.")
TROGLODYTE: cave dweller ("he calls the ligand in his protein's
  cavity a t.")
TURDEFY: to turn into a turd ("at first the new post-doc seemed
  nice, but he soon t.")
UBIETY: placement ("go back to the display and re-do the u. of the
  C-alphas")
UNICITY: uniqueness ("are you sure about the u. of this fold ?")
UVID: moist or wet ("keep your crystal u. in the capillary")