[phenixbb] riding model and deposition

Thu Feb 18 11:05:16 PST 2010

Hi Carsten,

phenix.refine does not add hydrogens. If you want to use H atoms in 
refinement then you need to add them first, before going into refinement.

You can add hydrogens using phenix.reduce or phenix.ready_set.

Pavel.

On 2/18/10 11:00 AM, Schubert, Carsten [PRDUS] wrote:
>
> Hi Pavel,
>
>  
>
> if I understand Christina's question correctly, she was stating that 
> when phenix.refine runs with riding hydrogens enabled using a pdb 
> file, which does not contain hydrogens, the final hydrogens are not 
> written out. I presume this is the case, since a phenix.reduce run is 
> required to add hydrogens prior to refinement, phenix.refine does not 
> add hydrogens, correct?
>
>  
>
> Cheers,
>
>  
>
>                 Carsten
>
>  
>
>  
>
> *From:* phenixbb-bounces at phenix-online.org 
> [mailto:phenixbb-bounces at phenix-online.org] *On Behalf Of *Pavel Afonine
> *Sent:* Thursday, February 18, 2010 12:36 PM
> *To:* PHENIX user mailing list
> *Subject:* Re: [phenixbb] riding model and deposition
>
>  
>
> Hi Christina,
>
> if H atoms were used in refinement then they should not be removed 
> from the model you are going to PDB deposit. Post-refinement model 
> manipulation is bad. This makes the reported statistics 
> irreproducible. The R-factor computed for a model with and without H 
> atoms is different.
>
> Different programs use different libraries of ideal X-H parameters 
> (some put them at longer "neutron" X-H distances, and some place at 
> the position where the electron cloud is expected - shorter X-H 
> distance). The B-factors of H atoms can be inherited from atoms they 
> are bonded to or can be multiplied by a scale from 1 to 1.5. There is 
> a class of X-H geometries where this position of H atoms is not 
> unique: for example, C-O-H group in Tyrosine residue, where H can 
> rotate around C-O axis. Some programs optimize the position of H atom 
> to accommodate potential hydrogen bond and some doesn't.
>
> Destroying is always easier than building: removing existing hydrogens 
> is a matter of running one command :
>
> phenix.reduce -trim model.pdb > model_noH.pdb
>
> and takes 1 or 2 seconds. However, to build the H atoms back the 
> *exact* same way they were before is not that straightforward.
>
> It's just counterintuitive why you need to manipulate the refined 
> model for which you have obtained all the statistics numbers? If you 
> remove hydrogen atoms then you need to update the statistics. By 
> stripping off H atoms you will get somewhat smaller file, but does the 
> file size matter these days?  
>
> Pavel.
>
>
> On 2/18/10 6:55 AM, Christina Bourne wrote:
>
> Alex, Pavel,
> In my experience when using a riding hydrogen model they are not 
> included in the output pdb file.  It is only when they are added 
> explicitly that they are given output coordinates, which should of 
> course be kept unchanged.  Can you please verify this??
> -Christina
>
>  
>
> ------------------------------------------------------------------------
>
> *From:* Pavel Afonine <PAfonine at lbl.gov> <mailto:PAfonine at lbl.gov>
> *To:* PHENIX user mailing list <phenixbb at phenix-online.org> 
> <mailto:phenixbb at phenix-online.org>
> *Sent:* Wed, February 17, 2010 8:06:40 PM
> *Subject:* Re: [phenixbb] riding model and deposition
>
> Hi Alex,
>
> > I have refined a 1.3A structure using individual anisotropic 
> B-factors (Rfactor, 15.5%; Rfree, 17.7%). Additional use of the riding 
> model during refinement has improvement the R values (Rf, 14.5%; 
> Rfree, 16.6%),
>
> this is not surprising at all -- hydrogens do contribute to the 
> scattering.
>
> > although bond length and angle outliers did increase (anyone know why 
> that would be?).
> > 
>
> Different model - slightly different Xray/Restraints weights - 
> slightly different statistics.
>
> > I have decided to deposit the model obtained using the riding model, 
> but am unsure whether to include the hydrogen coordinates in the 
> deposition.
> > 
>
> If H atoms were used in refinement and final statistics calculation 
> (such as R-factors, etc), then the H atoms have to be included into 
> depositing model. Otherwise your statistics will not be reproducible.
>
> > The Phenix.refine documentation advises that they are left in, as 
> they are needed to reproduce the  refinement statistics. However, 
> reviewing the high resolution structures in the PDB I found that:
> > 
>
> Reviewing statistics in the PDB you can find many interesting things, 
> such as Fobs labeled as Iobs (and Iobs labeled as Fobs), atoms with 
> unknown scattering types labeled X (which makes R-factor impossible to 
> compute), O-H distances in water longer than 10A, etc. one can go on 
> for a long list.
>
> > 1. In the case of structures refined using REFMAC or SHELX, the 
> riding model does not seem to be included, although its use during 
> refinement is mentioned in the pdb header.
> > 
>
> Which is, in my opinion, not good.
>
> > 2. In the case of structures refined using PHENIX, use of the riding 
> model is sometimes indicated in the header, but hydrogen coordinates 
> only appear to be included in the pdb in the case of structures 
> refined to a resolution better than 1.3A.
> > 
>
> This most likely indicates a manipulation with a file contained 
> refined model, which is, again, in my opinion, not good.
>
> > As far as I can understand the purpose of the riding model is to 
> provide additional restraints for refinement, so as long as its use is 
> made evident in the pdb header (and maybe the methods section of the 
> publication) that should be enough. Inclusion of hydrogens in the 
> model, when you can't see them seems inappropriate.
> > 
>
> Different programs use different libraries of ideal X-H parameters. 
> Depending on the program, the B-factors of H atoms can be inherited 
> from atoms they are bonded to or can be multiplied by a scale from 1 
> to 1.5. These all makes adding H program-dependent, and therefore 
> statistics from such models may vary.
>
> I believe that any manipulation on the refined structure is bad.
>
> Pavel.
>
>
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