Uppsala Software News @ 2002-08-02
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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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* Harry Plotter - Quo Vadis ?
*****************************
For those of you who want to experiment with the raw data we collected
for the Quo Vadis paper, we now have a little Java applet called "Harry
Plotter" with which you can produce plots, e.g. of Rfree versus
resolution, zoom in on outliers, and then click on them to find
out their PDB identifiers. Click again, and a new browser window
will take you straight to the corresponding page at the RCSB-PDB !
To try it out, throw your browser at:
  http://xray.bmc.uu.se/gerard/supmat/rfree2000/plotter.html


* MOLEMAN2 Version 3.0.2
**********
- http://xray.bmc.uu.se/usf/xutil.html
- New DIstance CHains command to quickly find contacts between two
  different chains (e.g., two monomers in a dimer, or protein vs.
  DNA, or protein vs. ligand)
- New XYz AXis_rotate command to rotate around the X, Y or Z axis
  by a user-specified amount
- New ONo MOlray command to generate a trace pseudo-molecule if you
  want to "fly" along a protein chain in a MolRay movie
- New OCcupancy PLot command
- Optional 'how' parameter for the ONo DIsulfide command (default = S,
  draw as sticks; alternative L, draw as lines, i.e. like normal bonds).
  Option suggested by Marko Hyvonen. Also optional ODL object name (in
  case you want more than one SS-bond object)


* DEJAVU Version 5.8.7
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- http://xray.bmc.uu.se/usf/dejavu.html
- Minor bug fix


* LSQMAN Version 9.2.6
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- http://xray.bmc.uu.se/usf/dejavu.html
- Minor bug fix


* MAMA Version 6.0.4
******
- http://xray.bmc.uu.se/usf/rave.html
- Maximum number of (bones) atoms to generate masks around
  increased from 100000 to 500000


* MAPMAN Version 7.4.4
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- http://xray.bmc.uu.se/usf/rave.html
- Made the RS_fit command more robust against and informative about
  errors
- Minor changes


* MKSPAZ Version 2.3.2
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- http://xray.bmc.uu.se/usf/spasm.html
- Handle alternative conformations (keep only the one called 'A').
  Thanks to Elaine Meng for pointing out the problem and testing
  the fixed version
- Minor bug fix when using the -all command-line flag (thanks to
  Elaine again)


* HETZE Version 1.0
*******
- http://xray.bmc.uu.se/usf/xutil.html
- Check for bad bonded distances < 0.8 A
- Skip hydrogen atoms unless they are *all* in the PDB file
- Changed definition of a bad angle to be one that is < 80 degrees,
  does not occcur inside a three-membered ring, and the central atom
  is one of C, N, O, Si, P, or S


* XPLO2D Version 3.0
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- http://xray.bmc.uu.se/usf/xutil.html
- AUTO: recognises optional command-line argument "-noh" which will
  force the program to ignore any and all hydrogen atoms that may
  be present in the input PDB file
- AUTO: changed cut-off for suspicious bond angles to 80 degrees
  (remember to use the "-force" command-line argument to force the
  program not to bail out when it encounteres unusual bond lengths
  or angles)


* SOD Version 0.8
*****
- http://xray.bmc.uu.se/usf/xutil.html
- Minor change so that the macro created by MULT will also work with
  the Linux version of O ... Thanks to Anna Larsson for pointing out
  the problem


* OMAC
******
- http://xray.bmc.uu.se/usf/omac_index.html
- seq2comp.f - changed format for output of O sequence datablock
  so O can actually read it ... Thanks to Anna Larsson for pointing
  out the problem
- hetero.pdb - new version of this file, now containing 3,666
  hetero-compounds taken from PDB entries
- stat2o.f - Fortran jiffy to convert the log file that can be obtained
  from MAPMAN's real-space fit calculations into an ODB file that can be
  used to analyse the real-space fit etc. of your molecule


* USF Website
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- Added a tutorial on how to guestimate the dimensions and volume
  of your molecules with USF programs (and on the wide range of
  answers you may get depending on how you do the calculations ...).
  See: http://xray.bmc.uu.se/usf/tutorials.html


* SPASM Databases
*****************
- http://xray.bmc.uu.se/usf/libs.html
- There are two new SPASM databases, generated on 12 July 2002:
  - 25%   culled PDB list - 2284 PDB entries -   ~500,000 residues
  - 99.9% culled PDB list - 8255 PDB entries - ~2,000,000 residues


* DEJAVU Databases
******************
- http://xray.bmc.uu.se/usf/libs.html
- There are two new DEJAVU databases, generated on 12 July 2002:
  - 25%   culled PDB list - 2274 PDB entries -  ~42,000 SSEs
  - 99.9% culled PDB list - 8237 PDB entries - ~172,000 SSEs


* HIC-Up-date
*************
As announced earlier, version 6.1 of HIC-Up has been released. HIC-Up
now contains information on 3,666 hetero-entities that have been taken
from the PDB. In addition, a number of changes and improvements have
been made to the individual compound pages. For details, see the
release notes on the HIC-Up web-site at:
  http://xray.bmc.uu.se/hicup


* DOMBO
*******
- http://xray.bmc.uu.se/dombo
- Volume 11, issue number 1 (4 July, 2002), is now available
  (in PDF and PostScript format, nowadays).


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