Uppsala Software News @ 2007-01-19
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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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* RECENT PAPERS
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- A paper about refinement of ligand complexes (dictionaries,
starting coordinates, etc.) has been published in the (2006) CCP4
proceedings in Acta D. Citation: GJ Kleywegt, "Crystallographic
refinement of ligand complexes", Acta Crystallographica, D63,
94-100 (2007). You can request a PDF reprint here:
http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=82
- A step-by-step guide to validation with O, OOPS2 and WHATCHECK
has appeared as: GJ Kleywegt, "Quality control and validation",
Methods in Molecular Biology, 364, 255-272 (2006). Sorry - no
electronic reprints are available, so you will have to beg, steal
or borrow the book.
- A discussion about the precision of calculated accessible-surface
areas has been published in Acta D. Citation: Novotny, M Siebert &
GJ Kleywegt, "On the precision of calculated solvent-accessible
surface areas", Acta Crystallographica, D63, 270-274 (2007). You
can request a PDF reprint here:
http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=84
* EDS
*****
- http://eds.bmc.uu.se/
- If you're a beginner w.r.t. O, you may want to have a look at
the tutorial "EDS and O - A quick guide" at this address:
http://xray.bmc.uu.se/gerard/embo2001/modval/edso/
It teaches you how to use O with the O files you can download
from EDS to very quickly get an overview of a structure and its
electron density.
- EDS entries now have much improved O files (download "All files"
to get these). For instance, symmetry objects are now generated
automatically. For more details, see the quick guide mentioned
above.
* HIC-Up
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- http://xray.bmc.uu.se/hicup
- HIC-Up version 11.1 has been released (11 January, 2007). It
contains 7078 entries. For all but 219 of these, ideal coordinates
(taken from MSDchem) are available. EDS statistics are available
for 4729 entries (of which 1598 have EDS stats for more than one
resolution range).
* SPASM
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- http://xray.bmc.uu.se/usf/spasm.html
- New libraries:
- 25% seq. ID - 4946 PDB entries - 1,116,849 residues
- 100% seq. ID - 19094 PDB entries - 4,775,498 residues
- download from ftp://xray.bmc.uu.se/pub/gerard/spasm/
- The databases of the SPASM server have of course been updated too:
http://portray.bmc.uu.se/spasm
* DEJAVU
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- http://xray.bmc.uu.se/usf/dejavu.html
- New libraries:
- 25% seq. ID - ~5200 chains in ~4950 PDB entries - ~93,000 SSEs
- 100% seq. ID - ~20900 chains in ~19100 PDB entries - ~407,000 SSEs
- download from ftp://xray.bmc.uu.se/pub/gerard/dejavu/
- The databases of the DEJAVU server have of course been updated too:
http://portray.bmc.uu.se/dejavu
* MAPMAN server
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- http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl
- Somewhat surprisingly, this server is still used a couple of
times every day. It has been modified so that it also produces
output maps in CNS and CCP4 format.
* DATAMAN Version 6.4.2
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- http://xray.bmc.uu.se/usf/rave.html
- The program can now write reflection files in OHKL format for O.
You will still need to edit some of the header lines, though.
See the manual for details.
* LIGCOM Version 0.4
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- http://xray.bmc.uu.se/usf/xutil.html
- Various changes (see the manual)
* O2D Version 5.6.2
*****
- http://xray.bmc.uu.se/usf/xutil.html
- Fixed CRICketgraph option (the one you use when you want to convert
a USF .plt file to ASCII tab-delimited data format) which was broken
(thanks to Mark Mayer at NIH for pointing me to the problem).
* MOLEMAN2 Version 3.3.8
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- http://xray.bmc.uu.se/usf/xutil.html
- Implemented a SElect POint command to allow selection of atoms in
a distance shell from a given point in space.
* MAPMAN Version 7.8.2
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- http://xray.bmc.uu.se/usf/rave.html
- Fixed a bug in writing ASCII CNS maps: the last line should
contain 0.0 and 1.0 instead of the actual average and st. dev. of
the density, since the maps are not scaled. The bug meant that
writing a CNS map and reading it in again would give a map that
was different from the original one (unless it happened to have
average density zero and st. dev. one to begin with) ...
Fortunately, most programs seem to ignore that last line so I hope
that no serious damage has been caused by this bug.
* OMAC
******
- http://xray.bmc.uu.se/usf/omac_index.html
- hetero.pdb - a new version is available containing more than
7000 hetero compounds
--DVD (The Crystallographer Formerly Known As "CD")
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