CDS News - Cambridge Mogul Package   [updated 25 Mar 2014]

This section gives the latest information on the CDS implementation of the Mogul Knowledge Base of Molecular Geometry which is part of the Cambridge Structural Database System (CSDS). There is also a related CSD Knowledge Base called IsoStar which covers Intermolecular Interactions.

Mogul 1.6.1 is available

See details below:

Item added 25/03/14

The latest Mogul upgrade has been installed

Mogul verion 1.6.1. has been installed. The speed of Mogul searches has been improved.

Item added 11/03/14

The Mogul knowledge base has been updated

In line with recent changes to the handling of libraries by Mogul its knowledge base has been updated in parallel with the main CSD Feb14 update.

Item added 31/01/14

The Mogul 1.6 Release Notes list the following improvements

Item added 02/04/13

Mogul 1.5.1 is now available

A patch has been applied which brings Mogul to version 1.5.1.

Item added 27/03/13

Mogul 1.5 is now available

A new version of Mogul was made available with the CSD software release 5.34.

Item added 21/12/11

Mogul 1.4 is now available

A new version of Mogul was made available with the CSD software release 5.33. There are more details available. Click on the "Links..." menu bar at the head of this Newsfile for fuller information.

Item added 21/01/11

Mogul 1.3 is now available with the latest Cambridge Release

Mogul 2.4 has been made available with the new Cambridge Release (v5.32). This includes the latest version of the knowledge base. There do not appear to be any major new features with this version.

Details of new features of all CSD components are available. Click on the "Links..." menu bar at the head of this Newsfile for fuller information.

Item added 17/03/10

Fuller details of Mogul 1.2 are now available

The following section has been extacted from the latest Cambridge Release Notes relating to Mogul.

There is improved validation of ring conformations.

Mogul now contains a library of ring conformations, allowing you to assess how the geometry of a ring in a query structure compares with that of similar rings in the CSD. A single figure measure of geometrical similarity is calculated and a histogram containing matching CSD rings displayed. This makes it easy to identify if the query ring has an unusual geometry.

The addition of the ring library significantly strengthens Mogul's capabilities for the geometric evaluation of models created either during the refinement of a crystal structure, or from a computational technique such as molecular docking, or molecular mechanics simulation.

Item added 20/11/09

Mogul 1.2 was installed with the latest major Release of the Cambridge software installed on the CDS server.

Item added 12/12/08

Mogul 1.1.3 has been installed. See the "Cambridge Release Notes" link
for details of modifications and bug fixes.

Item added 11/12/06

Cambridge have provided us with a software modification. Mogul 1.1.1
is now available on the Service.

We have added better links to the Cambridge User Guide & Tutorial
material (including that for Mogul). These are now available under the
heading "Manual & Training Material" in the top pulldown menu on the
CDS Homepage

   http://cds.dl.ac.uk

Item added 08/12/06

Mogul 1.1.1 was included with the lastest major Release of the Cambridge
system (CSD 5.28) and is based on the latest data. Unfortunately a
problem was encountered when using the Mogul Sketch module with CDS
implemementation. We are, therefore, retaining Mogul 1.1 in the interim.

Item added 29/11/05

Mogul 1.1 was included with the lastest major Release of the Cambridge
system. 

Results will now be generated for fragments involving metals
(currently for bonds only). Metal bond fragments are characterised in
the same way as organic fragments.

It includes improved facilities for batch processing of
multiple entry input files. There are also further output file
options. 

There are also addition filters available. It is now possible to
filter results basis on including or excluding of:

   Heaviest Element present
   Solvents or Non-solvents
   Organics or Organometallics

For for details see the Mogul User Guide (link to Support
Documentation given above)

Item added 12/01/05

Mogul 1.0.1 was included with the latest major Release of the
Cambridge system. It includes improvements to the generalised settings
window, available from the main Mogul interface. A problem with
relevance calculations has been fixed.

Item added 03/08/04

Mogul is a Library of Molecular Geometry information derived from the
Cambridge Structure Database involving bonded contacts. The first full
production version of Mogul has recently been released by Cambridge,
and we now include it as part of the CDS. To use Mogul you need access
to a system with X-Windows graphics and a reasonably good network
connection to the CDS server. If you have set up your system to access
to ConQuest you should be able to use Mogul (logon to the CDS server
and type "mogul" at the prompt), but if you encounter any problems
contact cdsbb@stfc.ac.uk. 

Cambridge have provided the following information on Mogul with
suggestions for its potential use and benefits.

 MOGUL v 1.0

 CSD System Molecular Geometry Library

 Potential Applications:

    * Validation of newly determined crystal structures (and
      identification of unusual geometrical features)

    * In protein-ligand docking, filtering out ligands that have been
      docked with unlikely torsion angles

    * The setting up of ligand dictionaries for protein crystal structure
      refinement

    * Facilitating the solution of structures from powder diffraction data

 Features:

    * Rapid access to bond lengths, valence angles and acyclic torsions in
      the CSD

    * Generation and optional assignment of bond type information and
      hydrogen atoms if missing from the input structure

    * An intuitive sketcher for generation of user-defined molecules in 2D

    * A graphical interface allowing inspection of bond-length, angle and
      torsion histograms, with selection/deselection of histogram bars and
      viewing of crystal structures contributing to the histogram

    * The ability to load files in a number of formats (e.g. MOL2, CIF,
      RES, MOL/SD, PDB) into the Mogul graphical interface
  
  * A command-line interface which can be used to initiate Mogul
    searches for all bond lengths, angles and torsions in a molecule, with
    results (mean values, standard deviations, etc.) being written to an
    output file to facilitate integration with other applications

  * Filtering on experimental precision
 
  * The ability to find structurally related entries if insufficient
    hits are retrieved 
    
For further details follow links to the Cambridge documentation at the
head of the page.