Re: [ccp4bb] Refmac unrestrained refinement on ligands only

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Andreas_Förster docandreas {- at -} GMAIL {- dot -} COM
Date: 2008-07-04

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Subject: build/refine individual methyl/metylene groups in membrane protein structures
From: "Van Den Berg, Bert" Lambertus {- dot -} VandenBerg {- at -} UMASSMED {- dot -} EDU
Date: 2008-07-05

Subject: Re: Refmac unrestrained refinement on ligands only
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-07-04

> -----Original Message-----
> From: owner-ccp4bb@jiscmail.ac.uk
> [mailto:owner-ccp4bb@jiscmail.ac.uk] On Behalf Of George M. Sheldrick
> Sent: 04 July 2008 13:42
> To: Matthew BOWLER
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Refmac unrestrained refinement on ligands only

> Perhaps what we
> really need are B-value dependent distance and other
> restraints, so they
> are tighter if the B-values are higher and vice versa.

I'm not so sure about that. The geometry SU's are supposed to reflect
possible variations which are in the main due to differences in the
chemical environment: for the original CSD structures from which the
restraints were derived the experimental errors (< 0.01) are typically
less than the RMSD's (> 0.01). The protein B factors clearly have very
little to do with differences due to chemical environment, or even with
the experimental errors in the CSD structures.

If anything, bonds involving atoms with large B, particularly where the
atoms are not part of a large rigid group such as an aromatic ring (e.g.
in an aliphatic side-chain), are more likely to suffer from libration
effects, and if this cannot be corrected by adjusting the target bond
lengths, the only alternative should be to *increase* the SU's in order
to allow the expected greater deviations from the 'ideal' mean value.
Note that the goal of refinement is to construct the model that
maximises the likelihood of making the observations, which is not the
same thing as making a geometrically correct model (since the model that
best fits the observations will be time & lattice-averaged and so will
not necessarily have chemically valid geometry). In practice this is
all academic: it's practically impossible to estimate the required
corrections with sufficient accuracy, unless you have ultra-high
resolution data, in which case restraints become irrelevant anyway.

-- Ian

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: more on thermofluor
From: Andreas_Förster docandreas {- at -} GMAIL {- dot -} COM
Date: 2008-07-04