Ligand chirality error

From: Debajyoti Dutta
Date: 27 January 2012 07:25



Hi all,

How to check the presence of improper chirality of a fitted ligand. Is there any way to get rid of such error.

All suggestions are welcome. Thanks in advance.

sincerely
Debajyoti


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From: <Herman.Schreuder

Dear Debajyoti,

 

The way I check the chirality is to compare the fitted compound with the structural formula. In coot, I rotate the ligand such that it has the same orientation as in the formula and check that the "out of plane" group goes in the right direction. However, it happens quite often that the chirality of the bound compound is not the chirality the chemist thinks it has, or the chirality is not known. In that case, I refine both enantiomers and look which one fits best. Things to look for are distorted bond angles, poor fitting and small positive and negative blobs of difference density (green and red blobs in coot with default settings).

 

To change the chirality, you have to edit the cif dictionary which contains the description of your compound. In the dictionaries I use you have to change the  _chem_comp_chir.volume.sign from positiv to negativ or vice versa.

 

Good luck!

Herman

 

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From: Paul Emsley


With Coot,  Validate -> Incorrect Chiral Volumes Extensions -> Modelling -> Invert this Chiral Centre.


Paul.

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From: <Herman.Schreuder

Hi Paul,

Does this also update the cif dictionary, or stays the change inside
coot?

Best,
Herman

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From: Paul Emsley

It stays within Coot. It does not update the cif dictionary - IMHO, that would be a Bad Thing - maybe you are just experimenting.

It creates new set of restraints under a new name (comp-id) and renames the residue accordingly [1].

You can write out the new restraints:  Edit -> Restraints -> Save as mmCIF...

Paul.

[1] Incidentally, some of us developers would like wwPDB to reserve a set of comp-ids so that we can do this safely without bumping into comp-ids for which a dictionary already exists.

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From: Eleanor Dodson


Do remember you can assign chirality as both.. This can be useful as otherwise the refinement programs force the requested chirality and espec at low resolution it can be hard to see any indication of error..
..
Eleanor