SoftwareMogulRelease2013Issue

This page is no longer valid as the 2013 CSDS Release has expired and will no longer run.

Issue with Mogul from Cambridge Structural Database System 2013 Release v5.34

• There is a problem using grade, grade_PDB_ligand or buster-report with the mogul from the initial 2013 release of Cambridge Structural Database System. CSD System 5.34 Update 1 provides a fix for the problem, see How to fix section below.

Contents

• Identification of the problem release
• The problem
• How to fix
• grade and buster-report changes
• Further help on this issue

Identification of the problem release

• Run mogul interactively and select "Help", "About Mogul". This should fire up an information window like:
• 
• The problem release is "Mogul 1.5 Build (RC5)"

The problem

• The issue is that mogul reading from a PDB file now does not automatically identify the bond orders and instead sets all bonds to single.
• To illustrate this the buster-report schematic for an ATP changes so the nucleic acid part and phosphates cease to find matching bonds in the CSD.

results with 2012 release mogul	results with 2013 release mogul

• grade will also be badly affected. To show this we will produce a dictionary for benzene

grade 'c1ccccc1' -f
head grade-XXX.cif

• Running grade With the 2012 mogul release this produces a dictionary where all the non-hydrogen bond lengths and bonds angles are set from mogul CSD values. This is recorded at the top of the output dictionary.

head grade-XXX.cif
#  Bonds defined by QM have a sigma of 0.030
#  Angles defined by QM have a sigma of 3.0
# Number of restraints found:
# Bond lengths
#     lengths/sigmas set by mogul                 6
#     bonds to hydrogen set to neutron values     6
#     bonds lengths set by partial QM             0
# Bond Angles
#     angles/sigmas set by mogul                  6
#     non-H angles set by partial QM              0

• But with the 2013 mogul release no bond lengths or angles are set from mogul value

#  Bonds defined by QM have a sigma of 0.030
#  Angles defined by QM have a sigma of 3.0
# Number of restraints found:
# Bond lengths
#     lengths/sigmas set by mogul                 0
#     bonds to hydrogen set to neutron values     6
#     bonds lengths set by partial QM             6
# Bond Angles
#     angles/sigmas set by mogul                  0
#     non-H angles set by partial QM              6

How to fix

• Do not use grade, grade_PDB_ligand or buster-report with "Mogul 1.5 Build (RC5)".
• The problem has been fixed CSD System 5.34 Update 1 for instructions on how to install this update see: http://www.ccdc.cam.ac.uk/products/csd_system/updates
• To check that the update has correctly installed run mogul interactively and select option "Help", "About Mogul". This should report "Mogul 1.5 Build (RC6)".

grade and buster-report changes

• We are now working on updates to both grade and buster-report so that they will refuse to run with the problematic version of mogul. These will be released via the "Snapshot build" mechanism when they are ready (and this page will be updated).

For further help on this issue

• Please email:
• buster-develop@globalphasing.com
• support@ccdc.cam.ac.uk

Page original version 14th March 2013, Updated 26th March 2013. Address problems, corrections and clarifications to buster-develop@globalphasing.com