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On 13/06/14 00:19, Ethan A Merritt wrote:
Earlier this year for the first time I got back a validation report
from the PDB for a deposited structure that included wwPDB validation
of a ligand. This is great stuff. I approve. I am happy.
Unfortunately the validation check reported problems with my ligand.
This is bad. I am unhappy.
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On Fri, 13 Jun 2014, Paul Emsley wrote:
In the mean-time you can use the Coot's Mogul plug-in to update the restraint
information from cprodrg. Or of course, Just Use Grade (as you imply :-).
Ethan,
As you and Paul mentioned the use of Grade, I thought it might be
useful to point out that as well as being included with
BUSTER (so free for Academics) the Grade Web Server:
http://grade.globalphasing.org/
This allows you to produce Grade dictionaries (for non-confidential
ligands) without having to install BUSTER or CSDS (for the Mogul program).
Grade generates geometrical restraints for novel small molecules. It does
so by querying the Cambridge Structural Database (CSD) as a main source of
restraint information (using Mogul), and then invoking quantum chemical
procedures to obtain whatever information the CSD is unable to supply.
Grade CIF restraint dictionaries can be used in Coot and REFMAC. In
addition Grade and the Grade Web Server can produce SHELX restraint files.
Mogul provides additional very useful validation measures for dihedrals
and rings that go beyond the bond and angle results included in the wwPDB
Structure Validation Report. These can be obtained using Mogul itself or
using CSDS Mercury but I tend to get a bit lost using these. So we have
added Mogul analysis to our buster-report tool and use colored 2D diagrams
to quickly show the information. For details see
http://www.globalphasing.com/buster/wiki/index.cgi?BusterReport
For an example where Mogul validation metrics help to diagnose a
ligand that has been mis-fit see:
http://grade.globalphasing.org/tut/erice_workshop/1pmq_tutorial/
For difficult ligands BUSTER provides the facility to use a weighted
Quantum Chemical or Force Field Energy in place of convential
restraint terms. A recent advance is support for the MMFF94 force field
using a helper program from OpenEye. This is particularly attractive
as it is the force field used by many computational chemists. For details
see
http://www.globalphasing.com/buster/wiki/index.cgi?AutobusterLigandQM
If you have concerns about Grade or other dictionaries then using MMFF94
instead provides a really good 2nd opinion.
Hope that ccp4bb will forgive this bit of promotion but Grade can be used
with CCP4 (and SHELX....).
Regards,
Oliver
| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK |
| http://www.globalphasing.com/people/osmart/ |
