From: Gerard Bricogne
Date: 19 March 2012 17:22
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
buster-develop@globalphasing.com
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.
----------
From: George Sheldrick
Dear Gerard,
That will be an extremely useful facility. Is a 'regrading' of the monomer library planned, at least for common cofactors and crystallization additives?
Best wishes, George
--
----------
From: <Herman.Schreuder
I would call it 'upgrading'.
Best wishes,
Herman
----------
From: Eleanor Dodson
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
--
Date: 19 March 2012 17:22
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
buster-develop@globalphasing.com
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.
----------
From: George Sheldrick
Dear Gerard,
That will be an extremely useful facility. Is a 'regrading' of the monomer library planned, at least for common cofactors and crystallization additives?
Best wishes, George
----------
From: <Herman.Schreuder
I would call it 'upgrading'.
Best wishes,
Herman
----------
From: Eleanor Dodson
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
----------
From: Thomas Womack
On 20 Mar 2012, at 12:34, Eleanor Dodson wrote:
> 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?)
You will have to convert it to a mol2 file; we have had very acceptable results doing this using openbabel, simply> 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?)
obabel ligand.pdb -Oligand.mol2
at least in the case where the ligand has all its hydrogen atoms present and named. If the ligand doesn't have hydrogen atoms, you will have to use
obabel ligand_noH.pdb -h -Oligand_H.mol2
then edit ligand_H.mol2 so that all the hydrogen atoms have different names (I appreciate this is tedious, it will be automatic in the next version), then use that as input.
Ton
----------
From: Oliver Smart
On Tue, 20 Mar 2012, George Sheldrick wrote:
George,Dear Gerard,
That will be an extremely useful facility. Is a 'regrading' of the monomer library planned, at least for common cofactors and crystallization additives?
Best wishes, George
Gerard asked me to reply. Yes providing pre-calculated grade results for all existing PDB chemical components is something we need to do.
The Grade Web Server is "work in progress": there are a number of limitations that need to be tackled:
http://www.globalphasing.com/buster/wiki/index.cgi?GradeWebServer#restrictions
But we hope that people find grade restraint dictionary useful.
Many thanks
Oliver
----------
From: dusan turk
Dear Gerard,
This is a marvelous political achievement. For years I have been trying to convince CCDC to allow us to
provide PURY restraint database "http://pury.ijs.si/", which is a compilation of CSDB, to unrestrained use to public via a web server interface. Now you have achieved this with GRADE.
Do I understand correctly that the CSD license restrain has been removed for anyone providing such a service or is the use of MOGUL the only way how one can provide CSDB derived parameters to public?
best wishes,
dusan
On Mar 21, 2012, at 1:01 AM, CCP4BB automatic digest system wrote:
Date: Tue, 20 Mar 2012 08:56:46 +0100
From: George Sheldrick
Subject: Re: Announcing a Web Server for the Grade ligand restraints generator.
Dear Gerard,
That will be an extremely useful facility. Is a 'regrading' of the
monomer library planned, at least for common cofactors and
crystallization additives?
Best wishes, George
Dr. Dusan Turk, Prof.
----------
From: dusan turk
Dear Gerard,
This is a marvelous political achievement. For years I have been trying to convince CCDC to allow us to
provide PURY restraint database "http://pury.ijs.si/", which is a compilation of CSDB, to unrestrained use to public via a web server interface. Now you have achieved this with GRADE.
Do I understand correctly that the CSD license restrain has been removed for anyone providing such a service or is the use of MOGUL the only way how one can provide CSDB derived parameters to public?
best wishes,
dusan
Dr. Dusan Turk, Prof.
----------
From: Sheriff, Steven
All:
I would like to second Herman Schreuder's witty repartee (and Steve Soisson's and Ian Tickle's comments referred to in a post by Oliver Smart) that using GRADE will be an upgrade to the standard CIF dictionaries.
Steven
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