Uppsala Software News @ 19991119
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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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* Ramachandran
**************
A few new items have been added to the "Ramachandran revisited" site
at: http://xray.bmc.uu.se/gerard/rama/


* CASP3
*******
Supplementary material to:
  Jones, T.A. and Kleywegt, G.J. (1999).
  CASP3 comparative modelling evaluation.
  Proteins: Struct. Funct. Genet. Suppl. 3, 30-46
can be found at: http://xray.bmc.uu.se/casp3/


* LDC
*****
A tutorial describing how to calculate Local-Density Correlation
maps and how to use them to assess differences between (NCS-)
related molecules is available from the USF tutorials page
( http://xray.bmc.uu.se/usf/tutorials.html ). A paper describing
this method has been published as:
  Kleywegt, G.J. (1999).
  Experimental assessment of differences between related protein
  crystal structures.
  Acta Cryst. D55, 1878-1884.


* HIC-Up
********
HIC-Up, the Hetero-compound Information Centre - Uppsala, has been
updated and now contains information on 2,290 hetero entities that
have been taken from the PDB (up from 1,981 in April, and from ~1,100
at the start in September 1997). In addition to a larger set of
compounds, many small changes have been made "under the hood".
  The URL for HIC-Up is:  http://xray.bmc.uu.se/hicup


* HIC-Up server
***************
I have written a little "HIC-Up server" script that replaces all
the previous servers on the HIC-Up site (e.g., for X-PLOR/CNS, TNT
and O dictionaries). Try it out at the HIC-Up site:
               http://xray.bmc.uu.se/hicup


* OMAC
******
- New version of the "hetero.pdb" file, now containing 2290 hetero
  entities.


* MOLEMAN2 Version 2.4.2
**********
- Fixed bug in XYZ PErturb command (shift for B and Q used to be equal
  to the shift for Z, no matter what ...) - thanks to Pete Dunten for
  pointing this out.


* DATAMAN Version 5.8.2
*********
- New RFree MUlti command to generate multiple-value test sets (i.e.,
  sets in which the TEST flag can be 1, 2, 3, ...).


* DEJAVU Version 5.4
********
- The initial two lines in a database file, declaring the existence
  of helices and strands, are now no longer needed (and will be
  ignored if they are present).
- New database (May 1999 Hobohm list) containing 2919 proteins (95%
  sequence identity or less).


* SPASM Version 3.3.5
*******
- Print warning if encountering HETATM or hydrogen in user's motif
  PDB file.
- New database (May 1999 Hobohm list) containing 2897 proteins (95%
  sequence identity or less), up from 2591 in December 1998. The
  database now also contains amino acids that are flagged as hetero
  compounds (such as MSE = SeMet, PCA = pyroglutamate, etc.).


* SAVANT Version 1.1
********
- SAVANT now does the least-squares superpositioning of the hits itself
  before it writes the small PDB files.


* LSQMAN Version 7.2
********
- Improvements to the MOrph command such that internal coordinate
  morphing is now also possible for hetero-entities. See the tutorial
  for more information. Example (trans/cis retinoic acid):
  http://xray.bmc.uu.se/cgi-bin/gerard/image_page.pl?image=usf/pics/rea_morph.gif
- The MOrph command now also generates an O macro that, when executed,
  will create one big O plot file (for later rendering). Example (RBP):
  http://xray.bmc.uu.se/cgi-bin/gerard/image_page.pl?image=usf/pics/rbp_molray.gif


* XPLO2D Version 2.8.5
********
- AUTO: uniquefying the 4-character atom-type names for X-PLOR/CNS
  dictionaries should now actually work ...


* OOPS2 Version 1.0.3
*******
- Minor bug fix.


* RIGOR
*******
* New database ("rigor.lib"; May 1999 Hobohm list).


* VOIDOO
********
- New version of the "cavity.lib" file.


* MAPMAN
********
- Added a brief explanation of the "PROD/PLUS problem" with DSN6
  format map files (and how to fix it) to the manual.


* DOMBO
*******
Volume 8, issue number 8, is now available from the (completely
revamped !!!) Dombo web site at: http://xray.bmc.uu.se/dombo


--cd


CD's Words of the Month:

IATROGENIC: illness caused by doctors ("if you got the virus from
  Dr. Sz. it means your flu is i.")
IATROMISIA: dislike of doctors ("even a glut of affable post-docs
  couldn't cure her i.")
IDIOLALIA: mental state characterised by use of invented language
  ("I can't help but suspect that theoreticians suffer from i.")
IDONEOUS: apt; suitable ("no crystals were i. for mounting")
ILLATION: inference, conclusion ("it may be shocking, but it's not
  an illicit i.")
ILLUMINATI: people who claim exceptional spiritual or intellectual
  insight ("did you know that there are no fewer than sixteen i. in
  all of Finland ?")
IMBIBITION: absorption ("what's the i. coefficient at 450 nm ?")
INCONDITE: crude, unfinished ("this slide shows the i. model before
  refinement")
INCUNABULA: the early stages of anything ("you don't worry too much
  about the R-factors in the i. of your refinement")
INFAUST: unlucky ("one i. movement of the hand and the crystal was
  gone")
INFUNDIBULAR: funnel-shaped ("the substrate binds in an i. crevice
  on the protein surface")
INNASCIBLE: without a beginning ("the first draft of the paper
  was i.")
INNUBILOUS: cloudless; clear ("after some stirring we obtained an
  i. solution")
INTERSILIENT: suddenly emerging in the midst of something ("when you
  see i. holes in your tyrosine rings you know you're getting close")
JACINTHE: (n.) a brilliant reddish-yellow ("they called their clever
  sunburnt Japanese student j.")
JARGOGLE: to mess up ("if you j. your structure, press control-C")
JERQUE: to search for smuggled goods ("when travelling alone, that
  post-doc invariably gets j. by Swedish customs officials")
KOPOPHOBIA: fear of physical or mental exhaustion ("everybody in
  their lab seems to suffer from k.")
KYLIE: the Australian boomerang ("only Jason Donovan would nickname
  his k. "Minogue" ...")