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Joe<br>
<br>
I guess you are correct. I'll have a closer look.<br>
<br>
Nigel<br>
<br>
On 9/28/09 4:18 PM, Joe Krahn wrote:
<blockquote cite="mid:4AC14432.3060902@niehs.nih.gov" type="cite">
<pre wrap="">GeoStd seems not to have an files. Is it only available via SVN for now?
The GeoStd parameters still need some work. The equivalent hydroxyls are
not symmetric. One of the dihedrals has a base angle of -175.0 instead
of 180 (or +/-60). One has an esd of 30.0, and the others have an esd of
20.0. The hydrogen ESDs also seem a bit too tight, and probably should
have a periodicity of 3.
They are an improvement, but I don't think automated parameterization
will ever be perfect.
Joe
Nigel W Moriarty wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Joe
It is in the nightly builds if you are inclined. You are also free to
download the restraints from the GeoStd open source project.
Nigel
On 9/28/09 1:43 PM, Joe Krahn wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Nigel,
I am using PHENIX 1.4-6, which is newer that the most recent version on
the PHENIX web site, other than "nightly build" versions.
Nigel W Moriarty wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Joe
I think you may need to upgrade your version of PHENIX. In the current
version, the periodicity is 3. I have recently been using eLBOW, the
Chemical Components library and the Monomer Library to improve any
residue restraints that have short comings. These are freely available
at Source Forge from a project called GeoStd at
<a class="moz-txt-link-freetext" href="http://sourceforge.net/projects/geostd">http://sourceforge.net/projects/geostd</a>
Its included in more recent PHENIX versions in $PHENIX/chem_data/geostd
Nigel
On 9/28/09 11:45 AM, Joe Krahn wrote:
</pre>
<blockquote type="cite">
<pre wrap="">I found that residue TRS has different dihedral target angles for the
three hydroxyl oxygens, which are actually all equivalent. They have a
periodicity of 1, but should have a periodicity of 3. What is the best
way to handle such discrepancies?
Most ligand parameters are probably auto-generated based on a reference
structure, and there is probably a lot of conformation bias. In this
case, it seems that parameterization should have been able to detect
symmetry. It would be nice if parameters could include information about
whether a human has done any validation. Actually, a ligand Wiki might
be nice, where people can easily put comments, even if they are not sure
about how to improve the parameters.
Joe Krahn
</pre>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Web : CCI.LBL.gov</pre>
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