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Hi Carsten,<br>
<br>
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.<br>
<br>
You can add hydrogens using phenix.reduce or phenix.ready_set. <br>
<br>
Pavel.<br>
<br>
<br>
On 2/18/10 11:00 AM, Schubert, Carsten [PRDUS] wrote:
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<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Hi
Pavel,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">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? <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">
Carsten<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div
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<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;">
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
[<a class="moz-txt-link-freetext" href="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</a>] <b>On Behalf Of </b>Pavel
Afonine<br>
<b>Sent:</b> Thursday, February 18, 2010 12:36 PM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] riding model and deposition<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Christina,<br>
<br>
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. <br>
<br>
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. <br>
<br>
Destroying is always easier than building: removing existing hydrogens
is a
matter of running one command :<br>
<br>
phenix.reduce -trim model.pdb > model_noH.pdb<br>
<br>
and takes 1 or 2 seconds. However, to build the H atoms back the
*exact* same
way they were before is not that straightforward. <br>
<br>
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? <br>
<br>
Pavel.<br>
<br>
<br>
On 2/18/10 6:55 AM, Christina Bourne wrote: <o:p></o:p></p>
<div>
<div>
<p class="MsoNormal">Alex, Pavel,<br>
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??<br>
-Christina<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div class="MsoNormal" style="text-align: center;" align="center"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">
<hr align="center" size="1" width="100%"></span></div>
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> Pavel
Afonine <a moz-do-not-send="true" href="mailto:PAfonine@lbl.gov"><PAfonine@lbl.gov></a><br>
<b>To:</b> PHENIX user mailing list <a moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a><br>
<b>Sent:</b> Wed, February 17, 2010 8:06:40 PM<br>
<b>Subject:</b> Re: [phenixbb] riding model and deposition<br>
</span><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"><br>
Hi Alex,<br>
<br>
> 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%), <br>
<br>
this is not surprising at all -- hydrogens do contribute to the
scattering.<br>
<br>
> although bond length and angle outliers did increase (anyone know
why that
would be?).<br>
> <br>
<br>
Different model - slightly different Xray/Restraints weights - slightly
different statistics.<br>
<br>
> I have decided to deposit the model obtained using the riding
model, but
am unsure whether to include the hydrogen coordinates in the deposition.<br>
> <br>
<br>
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.<br>
<br>
> 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:<br>
> <br>
<br>
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.<br>
<br>
> 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.<br>
> <br>
<br>
Which is, in my opinion, not good.<br>
<br>
> 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.<br>
> <br>
<br>
This most likely indicates a manipulation with a file contained refined
model,
which is, again, in my opinion, not good.<br>
<br>
> 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.<br>
> <br>
<br>
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.<br>
<br>
I believe that any manipulation on the refined structure is bad.<br>
<br>
Pavel.<br>
<br>
<br>
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