[phenixbb] riding model and deposition

Thu Feb 18 11:00:09 PST 2010

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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