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? Cheers, Carsten
-----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Pavel Afonine Sent: Tuesday, January 12, 2010 12:24 PM To: [email protected] 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 ;)