-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 <robbie_joos...@hotmail.com> > To: CCP4BB@JISCMAIL.AC.UK > 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). > > 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 <t...@shelx.uni-ac.gwdg.de> 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-ray 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 <mfrank...@nysbc.org>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 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPV3q+UxlJ7aRr7hoRAs0ZAKCpft2FTDzTcsL4F9SZtUlTIAsIpQCg+d3m YFx6Pp3f0sFGIccyGnZ+ywM= =zini -----END PGP SIGNATURE-----
