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Hi Engin,<br>
<br>
these are the distances between non-hydrogen atoms (even if H atoms are
present in the model).<br>
<br>
The soft low limit cutoff allows to account for map imperfections due
to data and model quality. <br>
<br>
I did not systematically investigate this. If I recall correctly, I put
these numbers in based on 1) looking "what others do"; 2) PDB survey;
3) tests with a few models.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 2/28/09 6:38 PM, Engin Ozkan wrote:
<blockquote cite="mid:49A9F527.4030909@stanford.edu" type="cite">
<pre wrap="">While we are on the matter, I needed a clarification in default H-bond
distances in for water picking. The default parameters are:
h_bond_min_mac = 1.8
h_bond_min_sol = 1.8
h_bond_max = 3.2
These values do work well, actually.
Are these numbers the distance between the H-bond acceptor and the
hydrogen itself? More commonly, people speak of acceptor to donor
distances, but these values are too small for that (which are usually
~2.3-3.5 A)?
Engin
Engin Ozkan wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Thanks, Nigel. I had actually created the restraints manually with the
literature values (and that did match what I saw in density). I was
just testing this new tool, because it sure is bound to come handy. It
also gave me chance to point out the literature on this matter; this
work even suggests sigma values specifically for structure refinement.
Engin
Nigel W Moriarty wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Engin
Thanks for the posting. You have discovered a hole in the coverage of
the default bond lengths data. Thanks for the link. I'm sure it will
be incorporated in the near future.
In the meantime, I'm sure you are aware that you can change the value in
the "edits" file.
Nigel
On 2/28/09 9:44 AM, Engin Ozkan wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi, all,
Recently following the phenixbb, I was made aware of
phenix.metal_coordination. So I just gave it a try for a structure of
mine with sodium in it. Specifically, I decided to turn the
use-default-bondlengths option on. The result was surprising, because
the output file thinks that sodum to oxygen distances are supposed to be
1.9 Angstroms. Work done by Marjorie Harding and others have shown that
this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for
a summary of their numbers,
<a class="moz-txt-link-freetext" href="http://tanna.bch.ed.ac.uk/newtargs_06.html">http://tanna.bch.ed.ac.uk/newtargs_06.html</a>). I wonder why
phenix.metal_coordination chose 1.9 A as the default Na-O distance, or
is the default option a different type of bond distance, I am not sure.
Any clarification from the authors would be appreciated.
Below is part of the output, showing the distance:
refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = name NA and chain N and resname NA and resseq 1
atom_selection_2 = name O and chain A and resname PHE and resseq 76
distance_ideal = 1.920420
sigma = 0.01
}
}
Engin
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