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Re: [ccp4bb] REFMAC Riding Hydrogens

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CCP4bb <-- 2012 <-- March 2012 <-- 07 March 2012
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From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
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From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2012-03-07

Subject: Re: REFMAC Riding Hydrogens
From: Paul Smith paul {- at -} PALADINSCIENTIFIC {- dot -} COM
Date: 2012-03-07

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,


From: Robbie Joosten
Sent: Tuesday, March 6, 2012 4:26 AM
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens

Hi Everyone,
Pavel’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).
From:CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel Afonine
Sent: Monday, March 05, 2012 21:53
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,
On Mon, Mar 5, 2012 at 12:45 PM, Tim Gruene wrote:
Hash: SHA1

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-­‐ray structure determination." [1]

'recently' as in 1997 [2]? Even though 1997 is probably a poor
estimation of the corresponding year...


[1] "On contribution of hydrogen atoms to X-ray scattering"
[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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