[SA_scat] New ATSAS release

Dmitri Svergun svergun at embl-hamburg.de
Fri Aug 19 18:05:37 BST 2005


Dear ATSAS User,

-----------------------------------------------------------
This mail is being sent to you because you might be interested 
in the new release of the small-angle scattering analysis package ATSAS. 
As the mail will be sent via a listserver and a mailing list 
you may receive duplicate messages. Sorry for inconvenience. 
If you are NOT interested in receiving such announcements in 
future, please send a message to Svergun at embl-hamburg.de  
with "Remove ATSAS" in the subject or message body. Thank you.
-----------------------------------------------------------

This is to announce a new release of the small-angle
scattering analysis program package ATSAS version 2.1.

For those attending the IUCr meeting in Florence (August, 2005):
demonstrations of ATSAS 2.1 programs will be performed at the EMBL booth
(Pavilion A, Booth 6). Please come there if you are interested to learn
more.

The download page of ATSAS will now have a request to enter the E-mail
address.
This information is required for statistical purposes only and the address
will not be disclosed by us to any other party. 

ATSAS 2.1 team: M.Petoukhov, P.Konarev, A.Sokolova, V.Volkov, D.Svergun


===   Main new features of ATSAS 2.1  ====

 --- Ab initio programs ---

DAMMIN version 51
- can be run in a command-line mode (most important parameters specified in
the UNIX style when starting the program)
- KEEP mode introduced (program keeps the list of best solutions and
produces
 up to 15 different models fitting the data for subsequent analysis by
DAMAVER)
- symmetry groups P1-P19, P222-P122, icosahedral symmetry as well as cubic
types P23 and P432 are supported 

GASBOR version 22 (reciprocal and real space versions)
- can be run in a command-line mode (most important parameters specified in
the UNIX style when starting the program)
- symmetry groups P1-P19, P222-P122, icosahedral symmetry as well as cubic
types P23 and P432 are supported
- large size versions (up to 8000 residues) are compiled for PC Windows, DEC
Alpha,  Red Hat Linux,   platforms. For SGI IRIX 64 and MacOSX, subject to
the compiler limitations, the maximum number of residues is 4000 and 2000,
respectively.

DAMAVER package for averaging multiple ab initio solutions
- automated mode in DAMAVER (runs all other programs)
- a new program DAMSTART generates a file, which can be used to define the
search volume in DAMMIN

--- Rigid body analysis programs ---

SASREF
- a new program for global rigid body modelling of macromolecular complexes
- fits simultaneously multiple scattering data sets from subcomplexes
- accounts for the symmetry of the complex (groups P1, P2-P6, P22-P62)
- avoids models with steric clashes and disconnected ones
- information on distances between specific residues/nucleotides can be
included 

GLOBSYMM
- sorts the solutions in groups based on rms
- enables fast solution generation from the log file
- cross and contacts criteria are computed from the
  coordinates of Ca atoms (or P atoms for nucleic acids)
- enforces contacts between the given residues

MASSHA version 2.3
- permits 'Group' operations with selected bodies.
The center of rotation can be defined either as the geometrical center
of individual body in the active group or individual residue atom of these
bodies.
- menu 'Oligomer' allows interactive rigid body modelling
for the complexes with different types of symmetry
(P2,P3,P4,P5,P6,P32,P42,P52,P62,P222)
- menu 'Modeling' -> 'Multibody' allows interactive rigid body
modeling for multi domain macromolecular complexes without symmetry.


--- Addition of missing fragments to macromolecules --- 

BUNCH
- a new program for determination of three-dimensional domain structure
  of proteins based on multiple scattering data sets from deletion mutants
- utilizes all-atoms representation for known structures of domains
  and dummy residues chains for unknown linkers
- accounts for the symmetry (groups P1, P2-P6, P22-P62)
- provides native-like fold of the loops and linkers 

CREDO
- reads all atoms model and selects Ca atoms
- automatically shifts the model to the origin in User mode
- increases the radius of the search volume if the maximum size of
  the input model greater than diameter specified by the user

CHADD
- reads all atoms model and selects Ca atoms
- automatically shifts the model to the origin in User mode
- increases the radius of the search volume if the maximum size of
  the input model greater than diameter specified by the user

GLOOPY
- reads all atoms model and selects Ca atoms
- automatically shifts the model to the origin in User mode
- increases the radius of the search volume if the maximum size of
  the input model greater than diameter specified by the user
- reading sequence procedure improved
- output style of PDB file rehashed
- User choice where to add the loop

CHARGE
- reads all atoms model and selects Ca atoms
- reading sequence procedure improved
- output style of PDB file rehashed
- bug corrected (not sufficient memory for big models)

--- Computation of scattering from atomic models --- 

CRYSOL
- can be run in a command-line mode (most important parameters specified in
the UNIX style when starting the program)
- output file names not restricted to 8 characters
- uses PDB dictionary of heteroatoms for accurate calculation of HETATM
  scattering, a number of new atomic groups added
- able to account for portions of the structure represented by Ca atoms only
in a PDB file
- is able to account for explicit hydrogen atoms
- more accurate calculation of the excluded volume scattering for wide
angles (at resolution better than 0.5 nm) 

CRYSON
- can be run in a command-line mode (most important parameters specified in
the UNIX style when starting the program)
- deuteration introduced for each individual chain
- output file names not restricted to 8 characters
- uses PDB dictionary of heteroatoms for accurate calculation of HETATM
  scattering, a number of new atomic groups added
- is able to account for explicit deuterium and hydrogen atoms

 --- Rapid screening of proteins ---

A database DARA for a rapid search of structural neighbours of proteins
based on their X-ray small-angle scattering patterns is available at  
http://dacha.embl-hamburg.de/dara.php

--- Data processing ---

PRIMUS Version 2.3
- 'Sapoko' and 'Mar2D' modules added to reduce raw OTOKO and MAR
files in one step and convert the data into ASCII form.
- file manipulation options and connection to external modules (GNOM,
OLIGOMER, SVDPLOT etc) was improved. OLIGOMER program can be run for
multiple files in batch mode.



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