Uppsala Software News @ 19990315
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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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* OOPS Version 5.3.1
******
- Implemented facility that enables you to keep track of your
  subjective judgement of every (flagged) residue (see the
  manual, section entitled SUBJECTIVITY, for details !).  This
  can be very useful, e.g. for students who want to ask their
  supervisor just to have a (quick) look at the most problematic
  residues.
- Changed default answers to many questions (mostly from YES to NO).
- When an OOPS macro is executed, the current residue name and
  number will be shown on the message line.
- In case of HETATM residues, the macros will not be called
  oops/$300 etc since this confuses O and makes them more difficult to
  remove - instead, the dollar sign will be replaced by an _underscore_
- When reading a PDB file, don't ask for the maximum CA-CA distance
  (fixed at 4.5 A).
- NOTE: for bold OOPSers a version of "OOPS - The Next Generation" is
  available from ftp://xray.bmc.uu.se/pub/gerard/junk . This version
  can now also "learn" from your previous subjective judgment of
  the density.  In other words: residues which you have flagged as
  having rock-solid density (despite their being an outlier for one
  or more criteria) can be skipped in the next cycle of rebuilding.
  Conversely, residues which you have flagged as having poor or
  no density (or a poor fit to otherwise good density) can be included,
  even if they don't violate any criterion at all.  In addition, the
  interface has been changed drastically, and the number of questions
  you have to answer in a typical OOPS run has been halved.  Please,
  give it a go and send any comments to me directly, not to the
  O-info list (mailto:gerard@xray.bmc.uu.se).


* ODBMAN Version 1.9.2
********
- Minor fix in SImilarity and ALl_correlations options.  The last
  (optional) parameter for these commands is now actually used
  (it may be Table of List and determines the output format).


* USF Tutorials
***************
After the tunnel visualisation tutorial announced earlier, a new
tutorial has been added that shows how to visualise least-squares
planes (using MOLEMAN2 and O). The example in this tutorial (using
PDB entry 8CEL) shows how a cellulose chain twists and turns through
the tunnel in cellobiohydrolase I. Go to the USF web site and click
on "Tutorials".


* OMAC directory
****************
- all_on_off.odb - a datablock containing two one-line macros that
  switch all objects on or off without using the menus ! This means
  that this mechanism can be used inside macros. Submitted by
  doug@zinc.uoregon.edu and suggested by his local Unix operator.
- ncssgs.txt - a file containing a Fortran/C program and instructions
  that creates an artifical space group that is the combination of
  crystallographic SG operators and NCS operators. Read in your protomer,
  during "sym_setup" tell O to use the artificial space group, and
  "sym_object" (or "sym_sphere") does all the rest: Any changes to
  the protomer show up in the symmetry objects, too. Submitted by
  Jim Clifton.
- alt_sc_tors.odb - a different approach to tor_residue.  The sidechain
  torsions CHI1 and CHI2 occur twice for each residue that has more
  two CHIs.  This means that all sidechain torsions can be modified
  at the same time, but you can still modify PHI and PSI if you want
  to.  It is an alternative to Phil Evans' sidechain_tors.odb (also
  in the OMAC directory).  The new idea is from Thierry Fischmann.
- zone_one_type.omac - O macro to draw an object containing all copies
  of a certain residue type (that you input). This enables you to
  inspect all cysteines, or all tryptophans, or all waters, etc. in
  your structure without too much clutter.
- zone_each_type.odb - an O datablock containing several macros. This
  is an extension of the idea behind the previous macro. It will draw
  an object for each of the twenty types of amino acid. Handy if you
  want to check if there are interesting clusters in your structure,
  e.g. of charged residues, or of aromatic residues, etc.
- plane.momac - a MOLEMAN2 macro that generates an ODL file with a
  least-squares plane for a glucose residue (GLC; can be changed by
  editing the file, of course).  This macro is used in the plane
  visualisation tutorial mentioned above.


* DOMBO Vol. 8, Nr. 1
*******
Those of you who know what DOMBO is (and those of you who don't
but are curious), may want to download the latest issue of this
illustrious journal. This month's issue features an interesting
Randomchandran plot, as well as a 3D centrefold of Miss Phi-Phi
Philipsson !
You can find DOMBO (individual issues all the way back to its
inception in 1992 are available as compressed PostScript files)
at: http://xray.bmc.uu.se/dombo


--cd


CD's Words of the Month:

EAN: to give birth ("the mother liquor e. a shower of needles")
ECDEMIC: of foreign origin ("we have lots of e. academics in our lab")
ECHOPRAXIA: habit of mimicking people ("e. leads to me-too science")
ECLAIRCISSEMENT: clarification ("we haven't received any e. regarding
  the budget cuts yet")
ECOPHOBIA: fear of home ("some people spend so much time in the lab
  you begin to wonder whether they suffer from e.")
EDULCORATE: to purify ("maybe the protein should have been further e.")
EESOME: pleasing to the eye ("my new crystals are enormously e.")
EGEST: to excrete ("this protein is e. by healthy cells")
EGLOMERATE: to unwind ("at room temperature the protein e. rapidly")
EGOTHEISM: self-deification ("the professor suffered from e. but,
  unfortunately for him, all his students were atheists")
EIDETIC: pertaining to the ability of visualising anything previously
  seen ("when it comes to protein folds, Brändén is the most e. person
  I know")
EISTEDDFOD: annual assembly of Welsh poets and musicians ("no,
  professor Jones isn't here; he's off to the e. conference in
  Cwmbrmwrddllogogogoch")
ELLIPSIS: deletion of words from a sentence ("PhD-student first draft
  manuscript always suffer e.")
EMBULALIA: insertion of nonsense into speech ("e. is an old trick to
  check if your audience is still paying attention")
EMPRESSEMENT: extreme politeness ("whatever happened to that good old
  Swedish e. ?")