[phenixbb] riding model and deposition
PAfonine at lbl.gov
Thu Feb 18 09:36:00 PST 2010
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?
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??
> *From:* Pavel Afonine <PAfonine at lbl.gov>
> *To:* PHENIX user mailing list <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
> > 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
> 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.
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> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
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