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
>
> [log in to unmask]
>
>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
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