Re: [ccp4bb] REFMAC Riding Hydrogens

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

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Subject: Re: setting occupancy for disordered water
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2012-03-07

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Subject: Re: REFMAC Riding Hydrogens
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2012-03-07

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Dear Paul,

I doubt there is a foolproof way - if the authors did not describe the
refinement procedure properly in their publication and the PDB file
lacks this information in its header, I guess you cannot tell.

Tim

On 03/07/2012 04:00 PM, Paul Smith wrote:
> Hello CCP4bb,
>
> Firstly, thanks to all for your comments. However, I'm still unsure how to sort all of this riding hydrogen business out.
>
> Robbie's comments seem particularly apt:
>
> "Because there were some reporting errors in the past
> (http://proteincrystallography.org/ccp4bb/message18808.html) it is hard
> to tell from the PDB when refinement with hydrogens became hip."
>
> Is there any foolproof way to know if a recently deposited file was
> refined with riding hydrogens in REFMAC, especially since some such
> structures do not yet have publications associated with them? How about
> the value of NON-BONDED CONTACTS OTHERS? If that is other than NULL,
> does that mean riding hydrogens were present?
>
> Also, how about refmac version numbers? Is there a clear demarcation when riding hydrogens a) became available, b) became default, or c) became default in the CCP4i GUI?
>
> Thanks again,
>
> --Paul
>
>
>
> ________________________________
> From: Robbie Joosten
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Tuesday, March 6, 2012 4:26 AM
> Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
>
>
> Hi Everyone,
>
> Pavelâ€™s statement is likely a bit of an exaggeration, but he has a valid (yet hard to prove point). The default in CCP4i was (and is?) to use hydrogens only if present in the input file. This is IMO not a safe default.
> Because there were some reporting errors in the past (http://proteincrystallography.org/ccp4bb/message18808.html) it is hard to tell from the PDB when refinement with hydrogens became hip. Discussions on this BB show that at the use of riding hydrogens is still not fully accepted, especially at low resolution (where they actually help most).
>
> Cheers,
> Robbie
>
> From:CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel Afonine
> Sent: Monday, March 05, 2012 21:53
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
>
> Dear Tim,
>
> good catch, thanks; I could craft that phrase more carefully! Although often it may not be quite fair to take phrases out of context: this newsletter article was written in the context of macromolecular refinement. And yes, "recently" may be a broad term -:)
>
> All the best,
> Pavel
> On Mon, Mar 5, 2012 at 12:45 PM, Tim Gruene wrote:
> Dear Pavel,
>
> you may want to add to the structures mentioned in [1] one or two
> organic structures present in the Cambridge Database.
>
> "Until recently it was customary to ignore hydrogen atoms throughout the
> process of crystallographic X-Âray structure determination." [1]
>
> 'recently' as in 1997 [2]? Even though 1997 is probably a poor
> estimation of the corresponding year...
>
> Cheers,
> Tim
>
>
> [1] "On contribution of hydrogen atoms to X-ray scattering"
> http://www.phenix-online.org/newsletter/
> [2] http://shelx.uni-ac.gwdg.de/SHELX/shelx.pdf
>
> On 03/05/2012 09:14 PM, Pavel Afonine wrote:
>> Hi,
>
>> On Mon, Mar 5, 2012 at 11:52 AM, Matthew Franklin wrote:
>
>>> Adding the riding hydrogens generally gives you some improvement in R
>>> factors even with a good quality (i.e. stereochemically correct) model.
>>>
>
>> and here are the results of more or less systematic test that prove this:
>
>> see "On contribution of hydrogen atoms to X-ray scattering"
>> here:
>> http://www.phenix-online.org/newsletter/
>
>> Pavel
>

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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

Previous message:
Subject: Re: setting occupancy for disordered water
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2012-03-07

Next message:
Subject: Re: FW: endotoxin removal
From: lieh low liehyoon {- at -} GMAIL {- dot -} COM
Date: 2012-03-07