Uppsala Software News @ 970115
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* DEJAVU Version 5.0
********
A lot of changes have been made to make the program package easier
to use:
(1) Changed the program such that the suggested default values for
    "Bones searches" (e.g., after ESSENS/SOLEX) are better.
(2) The program now sorts any hits it finds before listing
    them on the screen (hits are sorted by the number of matched
    SSEs, then by RMSD, and finally by Score).  This makes it much
    easier to assess how good or bad the hits are, and which ones
    are most promising.
(3) The amount of output the program produces for every hit has been
    greatly reduced.
(4) The PDB identifiers of hits are now included in the PRINT statements
    in the output O macro which enables easy "grep"-ing of results for
    a particular PDB entry, for instance:
            grep ^print lsq.omac | grep -i 1ack
(5) Changed the "make_sse" script to generate an SSE file
    from coordinates to work with O 6.x (since O can handle input
    redirection again).  This script is available from the OMAC
    directory on the server (pub/gerard/omac).
(6) Added a Quick Start Guide to the DEJAVU manual, both for
    searches with coordinates and for "Bones searches".
(7) Wrote a new jiffy called DEJANA.  This program takes the O
    macro produced by DEJAVU itself, or by LSQMAN (strongly
    recommended if you have atomic coordinates), sorts the hits,
    allows you to specify cut-offs (minimum number of matched
    SSEs or residues, maximum RMSD), and writes the surviving
    hits to a new O macro.  This means that you can use more liberal
    criteria in DEJAVU, producing perhaps 50 or 100 hits, then run
    these through LSQMAN (optional), and then select only the best
    hits for viewing in O.


* SPASM
*******
In the previous mailing I missed another published application
of SPASM: A. Matte et al., J Mol Biol 256, 126-143 (1996).


--cd

CD's Word of the Month: Hippopotomonstrosesquipedalian

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Current version numbers of all programs:

RAVE

'IMP' '961122/2.0'
'AVE' '961122/4.0'
'COMAP' '961122/2.0'
'COMDEM' '961122/2.0'
'CRAVE' '960415/0.03'
'MAPFIX' '961122/2.0'
'ESSENS' '961228/2.0'
'SOLEX' '961228/1.0'
'MAVE' '961122/3.0'
'NCS6D' '961122/2.0'

VOIDOO

'VOIDOO' '960415/3.1.1'
'FLOOD' '960415/1.0.2'
'MAPROP' '950118/0.5'

DEJAVU

'DEJAVU' '970102/5.0'
'DEJANA' '970115/1.0'
'PRO1' '930713/1.0'
'PRO2' '930713/1.0'
'POST' '930923/0.1'
'LSQMAN' '960821/4.7.3'

OOPS

'OOPS' '960801/4.5.1'

XUTIL

'D-CUP' '921217/0.4'
'AVEPDB' '960415/0.6'
'CELLO' '961121/0.9.4'
'MOLEMAN' '961218/7.2.5'
'O2D' '960415/4.4.1'
'ODBM' '940415/1.3'
'ODBMAN' '960517/1.4'
'XPAND' '951127/1.1'
'OST' '921020/0.02'
'SOD' '950204/0.5'
'PACMAN' '961121/0.6'
'RMSPDB' '940415/1.2'
'MOLEMAN2' '961101/1.1.1'
'SEAMAN' '961121/1.2'
'ODLedit' '950116/0.7'
'XPLO2D' '961213/2.2.1'