I would like to use this to check an existing ligand. I have the PDB
refined according to a cif file, and that cif file used for input to REFMAC
and phenix.
I dont want to lose the atom names assigned there so is it possible to
start GRADE with one of those inputs or do I have to convert it to a MOL2
file (I guess thsat is a SYBIL file?)
Eleanor
On Mar 19 2012, Gerard Bricogne wrote:
Dear all,
The generation of reliable restraints for novel small-molecule
ligands in macromolecular complexes is of great importance for both ligand
placement into density maps and subsequent refinement. This has led us to
develop Grade, a ligand restraint generator whose main source of restraint
information is the Cambridge Structural Database (CSD) of small-molecule
crystal structures, queried using the MOGUL program developed by the CCDC.
Where small-molecule information is lacking, Grade uses quantum chemical
procedures to obtain the restraint values.
Grade was released to academic users as part of the BUSTER package
in July 2011 and has proved popular. However, a problem for numerous
academic users has been that, in order to get the best restraints from
Grade, a CSD system licence is necessary to make use of MOGUL. Although
many institutions already have CSD site licences, and otherwise licences
are available at a reasonable cost, this has prevented the use of Grade
by small groups and occasional users.
To provide easy access to Grade, the CCDC has kindly agreed that we
can provide a public Web server that includes the use of MOGUL in its
invocation of Grade. The first version of the server is now available, free
of charge, at
http://grade.globalphasing.org
We hope this server will prove useful to academic users. We will
be very grateful for any feedback you might be able to provide about this
server, so that we can keep improving it to meet the needs of the
community. Please send us your feedback and comments at
[email protected]
rather than write to a specific developer.
With best wishes,
The Global Phasing developers: Gerard Bricogne, Claus Flensburg,
Peter Keller, Wlodek Paciorek, Andrew Sharff, Oliver Smart,
Clemens Vonrhein and Thomas Womack.
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
