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Joe<br>
<br>
It is in the nightly builds if you are inclined. You are also free to
download the restraints from the GeoStd open source project.<br>
<br>
Nigel<br>
<br>
On 9/28/09 1:43 PM, Joe Krahn wrote:
<blockquote cite="mid:4AC11FF5.7040605@niehs.nih.gov" 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
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</blockquote>
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<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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