Uppsala Software News @ 961228
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* ESSENS - The Next Generation - Version 2.0
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ESSENS has been completely rewritten. Some of the major changes:
- the program uses dynamic memory allocation
- the only scoring function available is the K-minimum sum function
- the good news: you get "Morten's method" essentially for free
(once I realised I could do this a posteriori)
- a new program SOLEX (see below) has been written to extract the
best solution(s), and it even makes an attempt at auto-tracing
your strands and helices (very experimental bit of code, though !)
Note that the input has changed slightly, so your old ESSENS scripts
will have to be changed. See the manual for more details:
http://alpha2.bmc.uu.se/~gerard/manuals/essens_man.html
Note that both ESSENS and SOLEX are part of the RAVE package (i.e.,
look in pub/gerard/rave on the Uppsala ftp-server).
* SOLEX Version 1.0
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In the original version of ESSENS, the program could save the best-
fitting orientation of a search fragment or molecule to a PDB
file, but extracting the second-best solution etc. was tedious
to say the least. In addition, in feature extraction mode, all
you got was a map showing where helices or strands might fit,
but the information regarding their best orientation was lost.
From version 2.0 onwards, ESSENS saves two maps (a "score map" and
a "display map"), as well as a "rotation file" which contains the
Euler or polar angles which gave the best fit of the template
to your electron density at every point in the grid.
This new program SOLEX (SOLution EXtractor) uses these files to
extract the best solution(s). For alpha-helices and beta-strands
it can even attempt to auto-trace (but this is still an experimental
piece of code !!!). It also produces an SSE file for DEJAVU, so you
can try to find out if your protein looks like something that has
already been solved (and, if so, "steal" some coordinates). All this
works beautifully for the averaged P2 myelin map ;-) I would be
interested to learn of any particularly positive or negative
results you might obtain with SOLEX in auto-trace mode !
See the SOLEX manual for more details:
http://alpha2.bmc.uu.se/~gerard/manuals/solex_man.html
==> PS: does anybody have a GIF picture for me of a *real* Solex ?
* VOIDOO
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I made a new library file of atomic radii. The values are derived from the
atomic volumes listed by Pontius et al., J Mol Biol 264, 121-136 (1996), for
the PROVE program. The new file is "prove_cavity.lib" and can be found in
/nfs/public/lib (Uppsala), and in voidoo_etc.dirtar.Z (directory
pub/gerard/voidoo on rose).
* DEJAVU
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I made a new database (pub/gerard/dejavu/dejavu.de96.Z), containing ~1300
protein entries with no more than 95% sequence homology.
* HETERO
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I made a new version of the "hetero.pdb" file, a collection of > 1100 HETERO
entities extracted from PDB files. The new files is in the OMAC directory
(pub/gerard/omac on the ftp-server).
I also made a new collection of O dictionary files for the new set of
hetero-compounds; check out URL:
http://alpha2.bmc.uu.se/~gerard/hetero/hetero.html
Did the same for the X-PLOR topology and parameter file collection:
http://xplor.csb.yale.edu/hetero/
* WWW Services
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For those of you who missed it, the following WWW services are now available
from Uppsala:
- ODICT -> generation of O dictionaries for hetero-entities:
http://alpha2.bmc.uu.se/~gerard/servers/odict.html
- XDICT -> generation of X-PLOR topology and parameter files:
http://alpha2.bmc.uu.se/~gerard/servers/xdict.html
- RAMA -> Tom Taylor's generation of Ramachandran plots:
http://alpha2.bmc.uu.se/~tom/pdb_rama.html
Note that all services, manuals, pre-prints etc. are available via URL:
http://alpha2.bmc.uu.se/~gerard/manuals/gerard_manuals.html
This page now also contains a form with which you can register this URL with
URL-Minder, a free service which will notify you by E-mail whenever the page
changes.
* SPASM
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A second application of SPASM has been published (Heikinheimo et al., Structure
4, 1491-1508 (1996)). SPASM can be used to find out if a small structural
motif (say, two or three active site residues, or a strange loop) occurs in any
other PDB structure (i.e., a bit like DEJAVU but on the level of residues
rather than secondary-structure elements). SPASM is not yet available outside
Uppsala (I want to write it up first), but if you have a particularly pressing
or interesting case I might be talked into running the program for you.
(The first application was described in: Harel et al., Structure 3, 1355-1366
(1995).)
For more details about the program, see:
http://alpha2.bmc.uu.se/~gerard/manuals/spasm_man.html
Uppsala only: I made new databases for SPASM and RIGOR (in /nfs/public/lib).
* MOLEMAN Version 7.2.5
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Minor bug fix (Ramachandran plot sometimes crashed on Alphas).
--cd
CD's Word of the Month: Oligophrenia
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