[phenixbb] [ccp4bb] Adding H in refinement

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Wed Jan 13 10:55:55 PST 2010

Hi Pavel,

sorry I hijacked the thread a bit... A question about the riding Hydrogens and their B-factors. I noticed that at least with earlier versions of PHENIX the B-factor of the Hydrogens was not fixed to the B-factor of the bonded atoms. If I would generate the Hydrogens in reduce they would inherit the appropriate B-factors, but during the course of the refinement and rebuilding they would start to diverge, sometimes drastically. Are you saying the current implementation restrains the B-factors to the bonded atoms and forces them to be equal or are they just inherited and are allowed to float afterwards? 



> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB at JISCMAIL.AC.UK] On Behalf Of
> Pavel Afonine
> Sent: Tuesday, January 12, 2010 12:24 PM
> Subject: Re: [ccp4bb] Adding H in refinement
> Hi Sara,
> - what you observe should not happen since phenix.refine uses riding
> model for H atoms. The hydrogen's B-factors are automatically inherited
> from the atoms these hydrogens are bonded to. For example, in X-H bond
> the B-factor of X should be equal to B-factor of H.
> - make sure you are using the latest version of PHENIX:
> http://www.phenix-online.org/download/
> - if this does not help, please contact me directly, and send the data
> and model so I can tell you what exactly is not right (all the files
> will be handled confidentially).
> - there is PHENIX bulletin board:
> http://www.phenix-online.org/mailman/listinfo/phenixbb
> Pavel.
> > I did refinement with phenix of my 1.9-2.0 Angstroem structures and
> included the hydrogens (riding). However, when I checked on the
> statistics (refinement close to the end), the average B-factor was
> extremely high (in phenix.polygon it was higher than with any other
> structure in similar resolution range). It makes sense though that this
> happens, if you have a residue which has a high B-factor and carries a
> lot of hydrogens the average B-factor will raise quite a lot (since the
> B-factor of hydrogens is calculated  1-1.5x of B-factor from the atom
> it sits on), right?
> > (When I removed the hydrogens again, the average B-factor was
> fine...)
> >
> > My question is now did I do something wrong in my refinement (-> do I
> have to change something that this does not happen), or is this
> something everybody sees?
> >
> > If this is common, what would happen (during evaluation) if you want
> to publish a structure and the statistics show such a high average B-
> factor? Is it better to have hydrogens on, but a bad average B, or no
> hydrogens on and a good average B... Obviously, I never published a
> structure ;)
> >

More information about the phenixbb mailing list