Re: [ccp4bb] Molprobity Clashscore

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: JLigand distorts molecules
From: Garib N Murshudov garib {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2012-01-13

Next message:
Subject: Re: JLigand distorts molecules
From: Wolfgang Skala Wolfgang {- dot -} Skala {- at -} SBG {- dot -} AC {- dot -} AT
Date: 2012-01-13

Subject: Re: Molprobity Clashscore
From: Antony Oliver Antony {- dot -} Oliver {- at -} SUSSEX {- dot -} AC {- dot -} UK
Date: 2012-01-13

Ok, I'm completed baffled... and have obviously started something
unintentionally...

NB: it was a joke!

I was amused that Molprobity, after 'adding' hydrogens to my model, had
'improved' the clashscore of my model by an obviously unnecessary number
of decimal places...!
[0.0099999999999998 point apparently].

Just me apparently.

Off to put my head in a cardboard box.

T.

---
Dr Antony W Oliver

Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ

email: antony.oliver@sussex.ac.uk
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512

On 1/12/12 11:14 PM, "Tim Fenn" wrote:

>On Thu, Jan 12, 2012 at 8:11 AM, Pavel Afonine wrote:
>>
>>> Who needs hydrogens?
>>
>>
>> may be you need to read this (for example):
>>
>> http://www.phenix-online.org/papers/dz5209_reprint.pdf
>>
>
>While this reference is useful, it neglects the role of prior chemical
>forces (vdW and electrostatics, for example) in positioning hydrogen
>atoms. The X-ray/neutron data is often not sufficient to uniquely
>define an atomic position (hydrogen or otherwise), which can be
>especially problematic for atoms with several degrees of freedom, like
>water or a hydroxyl hydrogen. Force fields have come a long way in
>defining these forces with reasonable chemical accuracy in the past 10
>years, and there is work to show this does benefit X-ray/neutron
>refinement (e.g. http://dx.doi.org/10.1016/j.str.2011.01.015) -
>suggesting its worthwhile to include this information in X-ray target
>functions. At the very least, it should not be left out of the
>discussion, especially when hydrogen atoms are concerned!!!
>
>Regards,
>Tim

CCP4bb navigation

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

Previous message:
Subject: Re: JLigand distorts molecules
From: Garib N Murshudov garib {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2012-01-13

Next message:
Subject: Re: JLigand distorts molecules
From: Wolfgang Skala Wolfgang {- dot -} Skala {- at -} SBG {- dot -} AC {- dot -} AT
Date: 2012-01-13