<div dir="ltr">It's possible that the code using using the CCP4 environmental variable to look for monomers. Phenix (cctbx really) does have a mechanism for looking into a user defined CCP4 library.</div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, Jan 10, 2018 at 3:59 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Which is not Phenix.. So that explains the difference.<br>
<br>
Question for Nigel is: why elbow.where_is_that_cif_file pulls cif
from CCP4 distribution?<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div><div class="h5"><br>
<br>
<div class="m_-1334522978634243506moz-cite-prefix">On 1/10/18 14:57, wtempel wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">$CCP4/lib<br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jan 10, 2018 at 5:53 PM,
Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
ideal O3'-C3' bond in *geo is 1.422, which interestingly
matches C3*-O3* in `modules/chem_data/geostd/t/da<wbr>ta_TD.cif`.<br>
</blockquote>
<br>
This is expected. I would be worried if they didn't match.
So, 1.422 is what actually used.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
`elbow.where_is_that_cif_file DT` pointed me to
`${CLIB}/data/monomers/d/DT.ci<wbr>f`, where O3'-C3' is
(now, but may be not at time of *geo generation) 1.431.<br>
</blockquote>
<br>
What is ${CLIB} ? I'm wondering because Phenix
distribution does not have "data/monomers" folders (if I
remember correctly).<span class="m_-1334522978634243506m_-5761680062829920146HOEnZb"><font color="#888888"><br>
<br>
Pavel<br>
<br>
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