Uppsala Software News @ 19990301
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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
*****
Quite a few people have been experiencing trouble when trying
to ftp software etc. directly from within Netscape.  I have
no idea what causes this, but it seems that ftp-ing from
the command line always works.  So if Netscape barfs, try
ye olde terminal window for a manual download.  Which brings
to mind yet another incarnation of ye olde sketch ...

             THE FOUR YORK CRYSTALLOGRAPHERS
             -------------------------------

  (Starring: Eleanor Cleese, Keith Atkinson, Guy Palin, and one
   more whose name I have forgotten)

* York crystallographer #1: "Here we sit, ftp-ing files from
  all over the world, at the click of a button in our browser.
  Who would have thought that twenty years ago, eh ?"
* York crystallographer #2: "Yeah, when we was young ... we didn't
  have any browsers to ftp with ... we had to type the ftp commands
  ourselves !"
* York crystallographer #3: "Luxury ! When we were young, if the
  professor wanted a file, we had to write a letter and ask for a
  tape !"
* York crystallographer #4: "Oh, we would have given our right arm
  for a tape drive ... we had to get the Fortran listing through
  the mail, and then type in every line of code ourselves !"
* York crystallographer #1: "Sheer luxury ! We first had to write
  our own Fortran compiler in assembler ..."
* York crystallographer #2: "Oh, we would have loved to have an
  assembler ... we had to program in machine code, you see."
* York crystallographer #3: "You had machine code ? Lucky bastards !
  We had to to program every individual bit using switches !"
* York crystallographer #4: "Aye, you try and tell that to the
  young crystallographers of today, and they won't believe you !"
* All four York crystallographers: "Aye !"


* XPLO2D Version 2.8.4
********
- Fixed a ***VERY*** nasty bug in the AUTO-dictionary generation
  option.  Dihedral restraint targets used to be rounded to the
  nearest multiple of 10 degrees.  This will have lead to "silly"
  restraints targets, for bonds that should be flat, of 10 or
  170 degrees.  They will now be rounded to the nearest multiple
  of 30 degrees instead.  If you have generated dictionaries
  with XPLO2D, and there are DIHEdral target values of +/-10 or
  +/-170 degrees, please re-do them with the new version (or change
  "10" to "0" and "170" to "180" in your dictionaries).  Also, please
  check any dictionaries retrieved from the HIC-Up site (these have
  been corrected on 11 January, 1999).
  NOTE: all X-PLOR/CNS parameter files and O Refi dictionaries will be
        affected by this bug !!!  (TNT dictionaries should be okay,
        as far as I can see.)
  (I hate to think of all the "flat" bonds with 10 and 170 degree
  torsions that are going to end up in the PDB "thanks" to my bug ...)


* LSQMAN Version 7.1.3
********
- Minor changes to the CAsp command.
- Added extra optional parameter to the BRute_force command to speed up
  the calculations if the two molecules are different models of the
  same protein (i.e., same residue numbering).
- Echo some PDB header lines when reading a PDB file.


* COMA Version 0.7
******
- FRCSYM and interpolation errors are no longer listed (only their
  total number if any occured).


* MAMA Version 5.6
******
- The SMooth, CUt, EXpand and COntract commands now have as an extra
  (optional; default = 1) parameter the number of times the operation
  should be carried out.  So instead of issuing the "expand m1" command
  five times, you can use "expa m1 5".
- Sped up the ISland_erase command (typically, by a factor of 5-10).


* MASKIT Version 0.4
********
- FRCSYM and interpolation errors are no longer listed (only their
  total number if any occured).


* ESSENS Version 2.0.1
********
- Added check to see if allocated maximum mask size is sufficient for
  (internally used) mask.


* SOLEX Version 1.0.1
*******
- If the rotation file is too big, tell the user how much memory
  should be allocated to it (using MASKSIZE).


* MAPMAN Version 5.6.1
********
- BOnes commands will print more information when allocated storage
  space is exceeded.


* ACONIO Version 1.0.1
********
- Fixed small bug in reading X-PLOR/CNS files (if only one residue
  had an alt. conf., the program refused to help you). Ftp to
  xray.bmc.uu.se, then cd to pub/gerard/extras/freebies/aconio
  to pick up the corrected version.


* O2D Version 4.6.1
*****
- DASH and NODASH keywords for 1D, scatter, pie, and histogram plots
  to force or suppress dashing of lines.


* MOLEMAN2 Version 2.2.2
**********
- Doubled max nr of atoms and residues (on request).
- Removed "on_off" commands from O macros generated by MOLEMAN2.
- Echo some PDB header lines when reading a PDB file.


* SPASM Version 3.2
*******
- Separate distance cut-offs for CA/CA and sidechain/SC mismatches.
- The SPASM paper has now been published as: Kleywegt, G.J. (1999).
  Recognition of spatial motifs in protein structures. J Mol Biol
  285, 1887-1897.
- A nice application of SPASM is described in: Brodersen, Nyborg &
  Kjeldgaard, Biochemistry 38(6), pp. 1695-1704 (1999).


* RAVE
******
Pat Fleming (Yale) has compiled a 64-bit R10000 SGI version of RAVE.
Ftp to xray.bmc.uu.se, cd to pub/gerard/rave, and get the file
rave_r10k.tar.gz .


* Tunnels
*********
As announced earlier, I added a little tutorial to the USF web site
that shows how to use VOIDOO, MAMA, etc. to visualise tunnels (and
other cavities that are connected to the outside world).  The tutorial
includes some pictures, and can be re-worked using PDB entry 1CEL in
the comfort of your own lab.


--cd


CD's Words of the Month:

DIANOETIC: pertaining to logical reasoning ("their theory sounds very
  d., but it's a load of old cobblers")
DIASKEUASIS: editorial revision ("some journals manage to screw up
  your papers in the process of d.")
DICACITY: oral playfulness ("it was hard to tell whether d. or capacity
  had landed her the job with Blow")
DIFFUGIENT: scattering ("this crystal isn't very d.")
DIGONEUTIC: reproducing twice a year ("speaking of slow photocopiers,
  ours seems to be d.")
DILDO: a West Indian cactus with pink flower ("the protein was isolated
  from five thousand pink d.")
DIMIDIATE: to halve ("a referee told us we had to d. the R-factor
  before the manuscript could be accepted")
DIPTYCH: anything folded in two ("the protein is an almost perfect d.")
DITOKOUS: producing twins ("the mother liquor turned out to be d.")
DOLICHOPROSOPIC: having a disproportionately long face ("as the unit
  cell constants show, the crystals are rather d.")
DYSANIA: having a hard time waking up in the morning ("the new post-doc
  suffered from severe d.")